Ursgal Parameters¶

A Dash script has been built in order to make it easier to explore uparams. It allows for searching for specific uparams, filtering by UNodes (i.e. engines), and filtering by utags. To install Dash, follow the instructions on

https://dash.plot.ly/

Afterwards, just go to the docs folder and execute the script:

user@localhost:~/ursgal/docs$ python uparams_to_dash.py

A local server will be created and you can view the interactive page:

http://127.0.0.1:8050/

Besides this, all uparams are still listed here as part of the documentation.

Note

This sphinx source file was auto-generated using ursgal/docs/source/conf.py, which parses ursgal/ursgal/uparams.py Please do not modify this file directly, but commit changes to ursgal.uparams.

-xmx¶

Set maximum Java heap size (used RAM)

Default value:	13312m
type:	str
triggers rerun:	False

Available in unodes¶

msgfplus2csv_v2016_09_16
msgfplus2csv_v2017_01_27
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
mzidentml_lib_1_6_10
mzidentml_lib_1_6_11
mzidentml_lib_1_7
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
ptmshepherd_0_3_5

Ursgal key translations for -xmx¶

Style Translation

msfragger_style_1 -Xmx

msfragger_style_2 -Xmx

msfragger_style_3 -Xmx

msgfplus_style_1 -Xmx

mzidentml_style_1 -Xmx

pipi_style_1 -Xmx

ptmshepherd_style_1 -Xmx

aa_exception_dict¶

Unusual aminoacids that are not accepted (e.g. by unify_csv_1_0_0), but reported by some engines. Given as a dictionary mapping on he original_aa as well as the unimod modification name. U is now accepted as regular amino acid (2017/03/30).In Tag Graph this can be used to define amino acids other thanthe standard 20 to be included in the search.For those, chemical composition, monoisotopic mass and avg massas well as name and 3-letter code need to be given.

Default value:	[‘J’, ‘O’]
type:	dict
triggers rerun:	True

Available in unodes¶

unify_csv_1_0_0
upeptide_mapper_1_0_0
compomics_utilities_4_11_5
tag_graph_1_8_0

Ursgal key translations for aa_exception_dict¶

Style Translation

compomics_utilities_style_1 aa_exception_dict

tag_graph_style_1 Amino Acids

unify_csv_style_1 aa_exception_dict

upeptide_mapper_style_1 aa_exception_dict

accept_conflicting_psms¶

If True, multiple PSMs for one spectrum can be reported if their score difference is below the threshold. If False, all PSMs for one spectrum are removed if the score difference between the best and secondbest PSM is not above the threshold, i.e. if there are conflicting PSMs with similar scores.

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

sanitize_csv_1_0_0

Ursgal key translations for accept_conflicting_psms¶

Style Translation

sanitize_csv_style_1 accept_conflicting_psms

add_contaminants¶

Contaminants are added automatically to the database by the search engine. PIPI uses the same contaminants database as MaxQuant

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

pipi_1_4_5
pipi_1_4_6

Ursgal key translations for add_contaminants¶

Style Translation

pipi_style_1 add_contaminant

Ursgal value translations¶

Ursgal Value Translated Value

. pipi_style_1

0 0

1 1

allow_multiple_variable_mods_on_residue¶

Static mods are not considered

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for allow_multiple_variable_mods_on_residue¶

Style Translation

msfragger_style_1 allow_multiple_variable_mods_on_residue

msfragger_style_2 allow_multiple_variable_mods_on_residue

msfragger_style_3 allow_multiple_variable_mods_on_residue

Ursgal value translations¶

Ursgal Value Translated Value

. msfragger_style_1 msfragger_style_2 msfragger_style_3

0 0 0 0

1 1 1 1

base_mz¶

m/z value that is used as basis for the conversion from ppm to Da

Default value:	1000
type:	int
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62
novor_1_05
omssa_2_1_9
pepnovo_3_1
pipi_1_4_5
pipi_1_4_6
pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
deepnovo_0_0_1
deepnovo_pointnovo
tag_graph_1_8_0
glycopeptide_fragmentor_1_0_0
ptmshepherd_0_3_5

Ursgal key translations for base_mz¶

Style Translation

deepnovo_style_1 base_mz

glycopeptide_fragmentor_style_1 base_mz

moda_style_1 base_mz

novor_style_1 base_mz

omssa_style_1 base_mz

pepnovo_style_1 base_mz

pipi_style_1 base_mz

ptmshepherd_style_1 base_mz

pyqms_style_1 REL_MZ_RANGE

sugarpy_plot_style_1 REL_MZ_RANGE

sugarpy_run_style_1 REL_MZ_RANGE

tag_graph_style_1 base_mz

batch_size¶

Sets the number of sequences loaded in as a batch from the database file

Default value:	100000
type:	int
triggers rerun:	False

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665

Ursgal key translations for batch_size¶

Style Translation

msamanda_style_1 LoadedProteinsAtOnce

myrimatch_style_1 NumBatches

xtandem_style_1 spectrum, sequence batch size

batch_size_spectra¶

sets the number of spectra loaded into memory as a batch

Default value:	2000
type:	int
triggers rerun:	False

Available in unodes¶

msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
deepnovo_0_0_1

Ursgal key translations for batch_size_spectra¶

Style Translation

deepnovo_style_1 buffer_size

msamanda_style_1 LoadedSpectraAtOnce

bayesian_fold_change¶

Perform Bayesian protein fold change analysis

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for bayesian_fold_change¶

Style Translation

flash_lfq_style_1 –bay

bayesian_fold_change_control_condition¶

Control condition for bayesian fold change analysis

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for bayesian_fold_change_control_condition¶

Style Translation

flash_lfq_style_1 –ctr

bigger_scores_better¶

Defines if bigger scores are better (or the other way round), for scores that should be validated (see validation_score_field) e.g. by percolator, qvality

Default value:	None
type:	select
triggers rerun:	True

Available in unodes¶

add_estimated_fdr_1_0_0
percolator_2_08
percolator_3_2_1
percolator_3_4_0
qvality_2_02
sanitize_csv_1_0_0
svm_1_0_0
ptminer_1_0

Ursgal key translations for bigger_scores_better¶

Style Translation

add_estimated_fdr_style_1 bigger_scores_better

percolator_style_1 bigger_scores_better

ptminer_style_1 bigger_scores_better

qvality_style_1 -r

sanitize_csv_style_1 bigger_scores_better

svm_style_1 bigger_scores_better

Ursgal value translations¶

Ursgal Value Translated Value

. add_estimated_fdr_style_1 percolator_style_1 qvality_style_1 sanitize_csv_style_1 svm_style_1

None None None None None None

deepnovo_0_0_1 1 1 1 1 1

deepnovo_pointnovo 1 1 1 1 1

mascot_x_x_x 1 1 1 1 1

moda_v1_51 1 1 1 1 1

moda_v1_61 1 1 1 1 1

moda_v1_62 1 1 1 1 1

msamanda_1_0_0_5242 1 1 1 1 1

msamanda_1_0_0_5243 1 1 1 1 1

msamanda_1_0_0_6299 1 1 1 1 1

msamanda_1_0_0_6300 1 1 1 1 1

msamanda_1_0_0_7503 1 1 1 1 1

msamanda_1_0_0_7504 1 1 1 1 1

msamanda_2_0_0_10695 1 1 1 1 1

msamanda_2_0_0_11219 1 1 1 1 1

msamanda_2_0_0_13723 1 1 1 1 1

msamanda_2_0_0_14665 1 1 1 1 1

msamanda_2_0_0_9695 1 1 1 1 1

msamanda_2_0_0_9706 1 1 1 1 1

msfragger_20170103 1 1 1 1 1

msfragger_20171106 1 1 1 1 1

msfragger_20190222 1 1 1 1 1

msfragger_20190628 1 1 1 1 1

msfragger_2_3 1 1 1 1 1

msfragger_3_0 1 1 1 1 1

msgfplus_v2016_09_16 0 0 0 0 0

msgfplus_v2017_01_27 0 0 0 0 0

msgfplus_v2018_01_30 0 0 0 0 0

msgfplus_v2018_06_28 0 0 0 0 0

msgfplus_v2018_09_12 0 0 0 0 0

msgfplus_v2019_01_22 0 0 0 0 0

msgfplus_v2019_04_18 0 0 0 0 0

msgfplus_v2019_07_03 0 0 0 0 0

msgfplus_v9979 0 0 0 0 0

myrimatch_2_1_138 1 1 1 1 1

myrimatch_2_2_140 1 1 1 1 1

omssa_2_1_9 0 0 0 0 0

pglyco_db_2_2_0 1 1 1 1 1

pglyco_db_2_2_2 1 1 1 1 n/t

pipi_1_4_5 1 1 1 1 1

pipi_1_4_6 1 1 1 1 1

pnovo_3_1_3 1 1 1 1 n/t

tag_graph_1_8_0 1 1 1 1 1

xtandem_alanine 1 1 1 1 1

xtandem_cyclone_2010 1 1 1 1 1

xtandem_jackhammer 1 1 1 1 1

xtandem_piledriver 1 1 1 1 1

xtandem_sledgehammer 1 1 1 1 1

xtandem_vengeance 1 1 1 1 1

build_pyqms_result_index¶

Build index for faster access

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for build_pyqms_result_index¶

Style Translation

pyqms_style_1 BUILD_RESULT_INDEX

sugarpy_plot_style_1 BUILD_RESULT_INDEX

sugarpy_run_style_1 BUILD_RESULT_INDEX

calibrate_mass¶

Perform mass calibration

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for calibrate_mass¶

Style Translation

msfragger_style_2 calibrate_mass

msfragger_style_3 calibrate_mass

Ursgal value translations¶

Ursgal Value Translated Value

. msfragger_style_2 msfragger_style_3

0 0 0

1 1 1

cleavage_cterm_mass_change¶

The mass added to the peptide C-terminus by protein cleavage

Default value:	17.00305
type:	float
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for cleavage_cterm_mass_change¶

Style Translation

xtandem_style_1 protein, cleavage C-terminal mass change

cleavage_nterm_mass_change¶

The mass added to the peptide N-terminus by protein cleavage

Default value:	1.00794
type:	float
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for cleavage_nterm_mass_change¶

Style Translation

xtandem_style_1 protein, cleavage N-terminal mass change

clip_nterm_m¶

Specifies the trimming of a protein N-terminal methionine as a variable modification

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for clip_nterm_m¶

Style Translation

msfragger_style_1 clip_nTerm_M

msfragger_style_2 clip_nTerm_M

msfragger_style_3 clip_nTerm_M

Ursgal value translations¶

Ursgal Value Translated Value

. msfragger_style_1 msfragger_style_2 msfragger_style_3

0 0 0 0

1 1 1 1

compensate_small_fasta¶

Compensate for very small database files.

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for compensate_small_fasta¶

Style Translation

xtandem_style_1 scoring, cyclic permutation

Ursgal value translations¶

Ursgal Value Translated Value

. xtandem_style_1

0 no

1 yes

compomics_utility_name¶

Default value accesses the PeptideMapper tool, other tools are not implemented/covered yet

Default value:	com.compomics.util.experiment.identification.protein_inference.executable.PeptideMapping
type:	str
triggers rerun:	True

Available in unodes¶

compomics_utilities_4_11_5

Ursgal key translations for compomics_utility_name¶

Style Translation

compomics_utilities_style_1 compomics_utility_name

compomics_version¶

Defines the compomics version to use

Default value:	compomics_utilities_4_11_5
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for compomics_version¶

Style Translation

ucontroller_style_1 compomics_version

compress_raw_search_results_if_possible¶

Compress raw search result to .gz: True or False

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for compress_raw_search_results_if_possible¶

Style Translation

ucontroller_style_1 compress_raw_search_results_if_possible

Ursgal value translations¶

Ursgal Value Translated Value

. ucontroller_style_1

crux_2_1 0

deepnovo_0_0_1 0

deepnovo_pointnovo 0

kojak_1_5_3 0

mascot_x_x_x 1

moda_v1_51 0

moda_v1_61 0

moda_v1_62 0

msamanda_1_0_0_5242 0

msamanda_1_0_0_5243 0

msamanda_1_0_0_6299 0

msamanda_1_0_0_6300 0

msamanda_1_0_0_7503 0

msamanda_1_0_0_7504 0

msamanda_2_0_0_10695 0

msamanda_2_0_0_11219 0

msamanda_2_0_0_13723 0

msamanda_2_0_0_14665 0

msamanda_2_0_0_9695 0

msamanda_2_0_0_9706 0

msfragger_20170103 0

msfragger_20171106 0

msfragger_20190222 0

msfragger_20190628 0

msfragger_2_3 0

msfragger_3_0 0

msgfplus_v2016_09_16 1

msgfplus_v2017_01_27 1

msgfplus_v2018_01_30 1

msgfplus_v2018_06_28 1

msgfplus_v2018_09_12 1

msgfplus_v2019_01_22 1

msgfplus_v2019_04_18 1

msgfplus_v2019_07_03 1

msgfplus_v9979 1

myrimatch_2_1_138 1

myrimatch_2_2_140 1

novor_1_05 0

novor_1_1beta 0

omssa_2_1_9 0

pepnovo_3_1 0

pglyco_db_2_2_0 0

pglyco_db_2_2_2 0

pipi_1_4_5 0

pipi_1_4_6 0

xtandem_alanine 1

xtandem_cyclone_2010 1

xtandem_jackhammer 1

xtandem_piledriver 1

xtandem_sledgehammer 1

xtandem_vengeance 1

compute_xcorr¶

Compute xcorr

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140

Ursgal key translations for compute_xcorr¶

Style Translation

myrimatch_style_1 ComputeXCorr

Ursgal value translations¶

Ursgal Value Translated Value

. myrimatch_style_1

0 0

1 1

consecutive_ion_prob¶

Probability of consecutive ion (used in correlation correction)

Default value:	0.5
type:	float
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for consecutive_ion_prob¶

Style Translation

omssa_style_1 -scorp

convert_aa_in_motif¶

Convert a single aminoacid in a sequence motif into another characeter using a string “new_aa,motif,position_to_be_replaced” where new_aa is the new character, motif is the regular expression that identifies the sequenc motif and position_to_be_replaced is the position in the motif that should be replaced (e.g. use “J,N[^P][ST],0” to convert N-X-S/T into J-X-S/T

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

generate_target_decoy_1_0_0

Ursgal key translations for convert_aa_in_motif¶

Style Translation

generate_target_decoy_style_1 convert_aa_in_motif

convert_to_sfinx¶

If True, the header of the identifier column is “rownames”. If False, the joined identifier header name will be used

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

csv2counted_results_1_0_0

Ursgal key translations for convert_to_sfinx¶

Style Translation

csv2counted_results_style_1 convert2sfinx

count_by_file¶

the number of unique hits for each identifier is given in separate columns for each raw file (file name as defiened in Spectrum Title)

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

csv2counted_results_1_0_0

Ursgal key translations for count_by_file¶

Style Translation

csv2counted_results_style_1 count_by_file

count_column_names¶

List of column headers which are used for counting. The combination of these headers creates the unique countable element.

Default value:	[‘Sequence’, ‘Modifications’]
type:	list
triggers rerun:	True

Available in unodes¶

csv2counted_results_1_0_0

Ursgal key translations for count_column_names¶

Style Translation

csv2counted_results_style_1 count_column_names

cpus¶

Number of used cpus/threads

-1 : ‘max - 1’ >0 : cpu num

Default value:	-1
type:	int _uevaluation_req
triggers rerun:	False

Available in unodes¶

kojak_1_5_3
moda_v1_61
moda_v1_62
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
ucontroller
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
moda_v1_62
moda_v1_61
pglyco_db_2_2_0
pglyco_db_2_2_2
pnovo_3_1_3
flash_lfq_1_1_1
ptmshepherd_0_3_5

Ursgal key translations for cpus¶

Style Translation

flash_lfq_style_1 –thr

kojak_style_1 cpus

moda_style_1 -@

msfragger_style_1 num_threads

msfragger_style_2 num_threads

msfragger_style_3 num_threads

msgfplus_style_1 -thread

myrimatch_style_1 -cpus

omssa_style_1 -nt

pglyco_db_style_1 process

pipi_style_1 thread_num

pnovo_style_1 thread

ptmshepherd_style_1 threads

ucontroller_style_1 cpus

xtandem_style_1 spectrum, threads

Ursgal value translations¶

Ursgal Value Translated Value

. kojak_style_1 moda_style_1 msfragger_style_1 msfragger_style_2 msfragger_style_3 msgfplus_style_1 myrimatch_style_1 omssa_style_1 pglyco_db_style_1 pipi_style_1 pnovo_style_1 ucontroller_style_1 xtandem_style_1

-1 max - 1 max - 1 max - 1 max - 1 max - 1 max - 1 max - 1 max - 1 max - 1 max - 1 max - 1 max - 1 max - 1

cross_link_definition¶

Cross-link and mono-link masses allowed. May have more than one of each parameter. Format for cross_link is:

[amino acids] [amino acids] [mass mod] [identifier]

One or more amino acids (uppercase only!!) can be specified for each linkage moiety. Use lowercase ‘n’ or ‘c’ to indicate protein N-terminus or C-terminus

Default value:	nK nK 138.0680742 BS3
type:	str
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for cross_link_definition¶

Style Translation

kojak_style_1 cross_link_definition

csv_filter_rules¶

Rules are defined as list of lists with three elements:

the column name/csv fieldname,
the rule,
the value which should be compared

e.g.: [‘Is decoy’, ‘equals’, ‘false’]

Default value:	None
type:	list
triggers rerun:	True

Available in unodes¶

filter_csv_1_0_0

Ursgal key translations for csv_filter_rules¶

Style Translation

filter_csv_style_1 filter_rules

Ursgal value translations¶

Ursgal Value Translated Value

. filter_csv_style_1

database¶

Path to database file containing protein sequences in fasta format.

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
unify_csv_1_0_0
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
upeptide_mapper_1_0_0
compomics_utilities_4_11_5
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
pglyco_db_2_2_0
pglyco_db_2_2_2
deepnovo_0_0_1
tag_graph_1_8_0
ptminer_1_0

Ursgal key translations for database¶

Style Translation

compomics_utilities_style_1 database

deepnovo_style_1 db_fasta_file

kojak_style_1 database

moda_style_1 Fasta

msamanda_style_1 database

msfragger_style_1 database_name

msfragger_style_2 database_name

msfragger_style_3 database_name

msgfplus_style_1 -d

myrimatch_style_1 ProteinDatabase

omssa_style_1 -d

pglyco_db_style_1 fasta

pipi_style_1 db

ptminer_style_1 protein_database

tag_graph_style_1 fmindex

unify_csv_style_1 database

upeptide_mapper_style_1 database

xtandem_style_1 file URL

database_taxonomy¶

If a taxonomy ID is specified, only the corresponding protein sequences from the fasta database are included in the search.

Default value:	all
type:	str
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for database_taxonomy¶

Style Translation

xtandem_style_1 taxon label

Ursgal value translations¶

Ursgal Value Translated Value

. omssa_style_1

all 0

de_novo_results¶

Path to the unified de novo results used as input for TagGraph

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for de_novo_results¶

Style Translation

tag_graph_style_1 de_novo

decoy_generation_mode¶

Decoy database: creates a target decoy database based on shuffling of peptides (shuffle_peptide) or complete reversing the protein sequence (reverse_protein).

Default value:	shuffle_peptide
type:	select
triggers rerun:	True

Available in unodes¶

generate_target_decoy_1_0_0

Ursgal key translations for decoy_generation_mode¶

Style Translation

generate_target_decoy_style_1 mode

decoy_tag¶

decoy-specific tag to differentiate between targets and decoys

Default value:	decoy_
type:	str
triggers rerun:	True

Available in unodes¶

generate_target_decoy_1_0_0
kojak_1_5_3
myrimatch_2_1_138
myrimatch_2_2_140
mzidentml_lib_1_6_10
mzidentml_lib_1_6_11
mzidentml_lib_1_7
unify_csv_1_0_0
xtandem2csv_1_0_0
upeptide_mapper_1_0_0
percolator_3_2_1
ptminer_1_0
percolator_3_4_0
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for decoy_tag¶

Style Translation

generate_target_decoy_style_1 decoy_tag

kojak_style_1 decoy_tag

msfragger_style_2 decoy_prefix

msfragger_style_3 decoy_prefix

myrimatch_style_1 DecoyPrefix

mzidentml_style_1 -decoyRegex

percolator_style_1 -P

ptminer_style_1 decoy_tag

unify_csv_style_1 decoy_tag

upeptide_mapper_style_1 decoy_tag

xtandem2csv_style_1 decoy_tag

deepnovo_beam_search¶

DeepNovo builds beam search

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

deepnovo_0_0_1

Ursgal key translations for deepnovo_beam_search¶

Style Translation

deepnovo_style_1 beam_search

deepnovo_beam_size¶

Number of optimal paths to search during decoding

Default value:	5
type:	int
triggers rerun:	True

Available in unodes¶

deepnovo_0_0_1
deepnovo_pointnovo

Ursgal key translations for deepnovo_beam_size¶

Style Translation

deepnovo_style_1 beam_size

deepnovo_build_knapsack¶

DeepNovo builds the knapsack matrix

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

deepnovo_0_0_1

Ursgal key translations for deepnovo_build_knapsack¶

Style Translation

deepnovo_style_1 knapsack_build

deepnovo_direction¶

Defines the direction for DeepNovo

Default value:	bi_directional
type:	select
triggers rerun:	True

Available in unodes¶

deepnovo_0_0_1

Ursgal key translations for deepnovo_direction¶

Style Translation

deepnovo_style_1 direction

Ursgal value translations¶

Ursgal Value Translated Value

. deepnovo_style_1

bi_directional 2

forward 0

reverse 1

deepnovo_knapsack_file¶

Path to the knapsack matrix for DeepNovo. Use “default” for the default file location in the resources

Default value:	default
type:	str
triggers rerun:	True

Available in unodes¶

deepnovo_0_0_1
deepnovo_pointnovo

Ursgal key translations for deepnovo_knapsack_file¶

Style Translation

deepnovo_style_1 knapsack_file

deepnovo_mode¶

Defines the search mode for DeepNovo

Default value:	search_denovo
type:	select
triggers rerun:	True

Available in unodes¶

deepnovo_0_0_1
deepnovo_pointnovo

Ursgal key translations for deepnovo_mode¶

Style Translation

deepnovo_style_1 (‘search_denovo’, ‘search_hybrid’, ‘search_db’, ‘decode’)

deepnovo_shared_weights¶

DeepNovo uses shared weights

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

deepnovo_0_0_1

Ursgal key translations for deepnovo_shared_weights¶

Style Translation

deepnovo_style_1 shared

deepnovo_use_intensity¶

DeepNovo uses intensity

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

deepnovo_0_0_1

Ursgal key translations for deepnovo_use_intensity¶

Style Translation

deepnovo_style_1 use_intensity

deepnovo_use_lstm¶

DeepNovo uses lstm

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

deepnovo_0_0_1
deepnovo_pointnovo

Ursgal key translations for deepnovo_use_lstm¶

Style Translation

deepnovo_style_1 use_lstm

deisotope_spec¶

Perform Deisotoping for MS2 spectra. Options are: “none”, “deisotope_with_singleton_charge_one”, “perform_deisotoping”

Default value:	deisotope_with_singleton_charge_one
type:	select
triggers rerun:	True

Available in unodes¶

msamanda_2_0_0_9695
msamanda_2_0_0_9706
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msfragger_3_0

Ursgal key translations for deisotope_spec¶

Style Translation

msamanda_style_1 PerformDeisotoping

msfragger_style_3 deisotope

Ursgal value translations¶

Ursgal Value Translated Value

. msamanda_style_1 msfragger_style_3

deisotope_with_singleton_charge_one n/t 1

none false 0

perform_deisotoping true 2

del_from_params_before_json_dump¶

List of parameters that are deleted before .json is dumped (to not overload the .json with unimportant informations)

Default value:	[‘grouped_psms’]
type:	list
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for del_from_params_before_json_dump¶

Style Translation

ucontroller_style_1 del_from_params_before_json_dump

delta_mass_exclude_range¶

The given mass range is excluded from searching for shifted ions.

Default value:	[0.0, 0.0]
type:	list
triggers rerun:	True

Available in unodes¶

msfragger_3_0

Ursgal key translations for delta_mass_exclude_range¶

Style Translation

msfragger_style_3 delta_mass_exclude_ranges

deltamass_allowed_residues¶

Only used in MSFragger labile mode, specifies which amino acids are allowed to contain a labile modification

Default value:
type:	str
triggers rerun:	True

Available in unodes¶

msfragger_3_0

Ursgal key translations for deltamass_allowed_residues¶

Style Translation

msfragger_style_3 deltamass_allowed_residues

Ursgal value translations¶

Ursgal Value Translated Value

. msfragger_style_3

denovo_model¶

PepNovo model used for de novo sequencing. Based on the enzyme and fragmentation type. Currently only CID_IT_TRYP available.

Default value:	cid_trypsin
type:	select
triggers rerun:	True

Available in unodes¶

pepnovo_3_1

Ursgal key translations for denovo_model¶

Style Translation

pepnovo_style_1 -model

Ursgal value translations¶

Ursgal Value Translated Value

. pepnovo_style_1

cid_trypsin CID_IT_TRYP

denovo_model_dir¶

Directory containing the model files de novo sequencing. Use “default” for the default folder of the engine (DeepNovo: <deepnovo_resources>/train.example; PepNovo: resources/<platform>/<architecture>/pepnovo_3_1)

Default value:	default
type:	str
triggers rerun:	True

Available in unodes¶

pepnovo_3_1
deepnovo_0_0_1
deepnovo_pointnovo

Ursgal key translations for denovo_model_dir¶

Style Translation

deepnovo_style_1 train_dir

pepnovo_style_1 -model_dir

Ursgal value translations¶

Ursgal Value Translated Value

. pepnovo_style_1

default None

determine_localization¶

specifying whether positions for mass shifts should be determined or not

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

ptminer_1_0

Ursgal key translations for determine_localization¶

Style Translation

ptminer_style_1 is_localized

Ursgal value translations¶

Ursgal Value Translated Value

. ptminer_style_1

0 0

1 1

determine_unimod_annotation¶

specifying whether mass shifts should be annotated or not

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

ptminer_1_0

Ursgal key translations for determine_unimod_annotation¶

Style Translation

ptminer_style_1 is_annotated

Ursgal value translations¶

Ursgal Value Translated Value

. ptminer_style_1

0 0

1 1

diagnostic_fragments¶

Specify molecules (or masses) that will be used as diagnostic fragments in the search. Assuming a charge of 1, the mass of a proton is added to all molecules (and masses). Specify as a dictionary with the keys “chemical_formulas”, “unimods”, “glycans”, “masses”, and lists with the corresponding molecules as values.

Default value:	[‘chemical_formulas’, ‘glycans’, ‘masses’, ‘unimods’]
type:	dict
triggers rerun:	True

Available in unodes¶

msfragger_3_0

Ursgal key translations for diagnostic_fragments¶

Style Translation

msfragger_style_3 diagnostic_fragments

engine_internal_decoy_generation¶

Engine creates an own decoy database. Not recommended, because a target decoy database should be generated independently from the search engine, e.g. by using the uNode generate_target_decoy_1_0_0

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
pipi_1_4_5
pipi_1_4_6

Ursgal key translations for engine_internal_decoy_generation¶

Style Translation

msamanda_style_1 generate_decoy

msgfplus_style_1 -tda

pipi_style_1 add_decoy

xtandem_style_1 scoring, include reverse

Ursgal value translations¶

Ursgal Value Translated Value

. msamanda_style_1 msgfplus_style_1 pipi_style_1 xtandem_style_1

0 false 0 0 no

1 true 1 1 yes

engines_create_folders¶

Create folders for the output of engines that allow this option in their META_INFO (‘create_own_folder’ : True). True or False

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for engines_create_folders¶

Style Translation

ucontroller_style_1 engines_create_folders

enzyme¶

Enzyme: Rule of protein cleavagePossible cleavages are :: argc -> [R]|{P} aspn -> [X]|[D] aspn_gluc chymotrypsin -> [FMWY]|{P} chymotrypsin_p -> [FMWY]|[X] cnbr -> [M]|{P} elastase -> [AGILV]|{P} formic_acid -> [D]|{P} gluc lysc lysc_p lysn no_cleavage nonspecific pepsina semi_chymotrypsin semi_gluc semi_tryptic thermolysin_p top_down trypsin trypsin_chymotrypsin trypsin_cnbr trypsin_p lysc_gluc

Default value:	trypsin
type:	select
triggers rerun:	True

Available in unodes¶

generate_target_decoy_1_0_0
kojak_1_5_3
moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
novor_1_1beta
novor_1_05
omssa_2_1_9
pepnovo_3_1
percolator_2_08
percolator_3_2_1
percolator_3_4_0
unify_csv_1_0_0
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
pglyco_db_2_2_0
pglyco_db_2_2_2
deepnovo_0_0_1
deepnovo_pointnovo
pnovo_3_1_3
tag_graph_1_8_0

Ursgal key translations for enzyme¶

Style Translation

deepnovo_style_1 cleavage_rule

generate_target_decoy_style_1 enzyme

kojak_style_1 enzyme

moda_style_1 Enzyme

msamanda_style_1 enzyme specificity

msfragger_style_1 enzyme

msfragger_style_2 enzyme

msfragger_style_3 enzyme

msgfplus_style_1 -e

myrimatch_style_1 CleavageRules

novor_style_1 enzyme

omssa_style_1 -e

pepnovo_style_1 -digest

percolator_style_1 enz

pglyco_db_style_1 enzyme

pipi_style_1 enzyme

pnovo_style_1 enzyme

tag_graph_style_1 Enzyme

unify_csv_style_1 enzyme

xtandem_style_1 protein, cleavage site

Ursgal value translations¶

Ursgal Value Translated Value

. deepnovo_style_1 generate_target_decoy_style_1 kojak_style_1 moda_style_1 msamanda_style_1 msfragger_style_1 msfragger_style_2 msfragger_style_3 msgfplus_style_1 myrimatch_style_1 novor_style_1 omssa_style_1 pepnovo_style_1 percolator_style_1 pglyco_db_style_1 pipi_style_1 pnovo_style_1 tag_graph_style_1 unify_csv_style_1 xtandem_style_1

alpha_lp n/t n/t n/t n/t n/t n/t n/t n/t 8 n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

argc arg-c R;C;P n/t argc, R/C R;after;P R;C;P R;C;P R;C;P 6 n/t n/t 1 n/t R;C;P n/t n/t Arg-C R P C R;[^P].* R;C;P [R]|{P}

aspn asp-n D;N; n/t aspn, D/N; D;before; D;N; D;N; D;N; 7 Asp-N n/t 12 n/t D;N; n/t AspN;0;D;- Asp-N D _ N .*;D D;N; [X]|[D]

aspn_gluc n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t 14 n/t n/t n/t n/t n/t n/t n/t n/t

chymotrypsin n/t FMWY;C;P n/t chymotrypsin, FMWY/C FMWY;after;P FMWY;C;P FMWY;C;P FMWY;C;P 2 Chymotrypsin n/t 3 n/t FMWY;C;P Chymotrypsin_FYWL-P-C Chymotrypsin;1;FMWY;P Chymotrypsin_P FYWML P C n/t FMWY;C;P [FMWY]|{P}

chymotrypsin_p n/t FMWY;C; n/t chymotrypsin, FMWY/C FMWY;after; FMWY;C; FMWY;C; FMWY;C; n/t n/t n/t 18 n/t FMWY;C; n/t n/t n/t n/t FMWY;C; [FMWY]|[X]

clostripain clostripain R;C; n/t clostripain, R/C R;after; R;C; R;C; R;C; 10 n/t n/t n/t n/t R;C; n/t n/t n/t n/t R;C; [R]|[X]

cnbr cnbr M;C;P n/t cnbr, M/C M;after;P M;C;P M;C;P M;C;P 11 CNBr n/t 2 n/t M;C;P n/t n/t n/t n/t M;C;P [M]|{P}

elastase n/t AGILV;C;P n/t elastase, AGILV/C AGILV;after;P AGILV;C;P AGILV;C;P AGILV;C;P 12 n/t n/t n/t n/t AGILV;C;P n/t n/t n/t n/t AGILV;C;P [AGILV]|{P}

formic_acid formic acid D;C;P n/t formic_acid, D/C D;after;P D;C;P D;C;P D;C;P 13 Formic_acid n/t 4 n/t D;C;P n/t n/t n/t D;[^P].* D;C;P [D]|{P}

formic_acid_p n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t FormicAcid_D-C n/t FormicAcid D _ C n/t n/t n/t

gluc n/t DE;C;P [DE]|{P} gluc, DE/C DE;after;P DE;C;P DE;C;P DE;C;P 5 n/t n/t 13 n/t DE;C;P GluC_DE-P-C GluC;1;DE;P GluC_P DE P C D|E;[^P].* DE;C;P [DE]|{P}

gluc_bicarb n/t E;C;P n/t gluc_bicarb, E/C E;after;P E;C;P E;C;P E;C;P 14 n/t n/t n/t n/t E;C;P n/t n/t n/t n/t E;C;P [E]|{P}

iodosobenzoate n/t W;C; n/t iodosobenzoate, W/C W;after; W;C; W;C; W;C; 15 n/t n/t n/t n/t W;C; n/t n/t n/t n/t W;C; [W]|[X]

lysc lysc K;C;P n/t lysc, K/C K;after;P K;C;P K;C;P K;C;P 3 Lys-C n/t 5 n/t K;C;P Lys_K-P-C n/t Lys-K_P K P C K;[^P].* K;C;P [K]|{P}

lysc_gluc n/t DEK;C;P [DEK]|{P} n/t DEK;after;P DEK;C;P DEK;C;P DEK;C;P n/t n/t n/t n/t n/t DEK;C;P n/t n/t n/t n/t DEK;C;P [DEK]|[X]|{P}

lysc_p n/t K;C; n/t lysc_p, K/C K;after; K;C; K;C; K;C; n/t Lys-C/P n/t 6 n/t K;C; Lys_K-C LysC;1;K;- Lys-K K _ C n/t K;C; [K]|[X]

lysn n/t K;N; |[K] lysn, K/N K;before; K;N; K;N; K;N; 4 n/t n/t 21 n/t K;N; n/t LysN;0;K;- n/t n/t K;N; [X]|[K]

lysn_promisc n/t AKRS;N; n/t lysn_promisc, AKRS/N AKRS;before; AKRS;N; AKRS;N; AKRS;N; n/t n/t n/t n/t n/t AKRS;N; n/t n/t n/t n/t AKRS;N; [X]|[AKRS]

no_cleavage n/t n/t n/t NONE n/t n/t n/t n/t 9 n/t n/t 11 n/t n/t n/t n/t n/t n/t n/t n/t

nonspecific n/t n/t n/t n/t ;; ACDEFGHIKLMNPQRSTVWY;C; ACDEFGHIKLMNPQRSTVWY;C; ACDEFGHIKLMNPQRSTVWY;C; 0 n/t n/t 17 NON_SPECIFIC ACDEFGHIKLMNPQRSTVWY;C; n/t n/t n/t n/t ACDEFGHIKLMNPQRSTVWY;C; [X]|[X]

pepsina n/t FL;C; n/t pepsina, FL/C FL;after; FL;C; FL;C; FL;C; 16 PepsinA n/t 7 n/t FL;C; PepsinA_FL-C n/t PepsinA-FL FL _ C n/t FL;C; [FL]|[X]

protein_endopeptidase n/t P;C; n/t protein_endopeptidase, P/C P;after; P;C; P;C; P;C; 17 n/t n/t n/t n/t P;C; n/t n/t n/t n/t P;C; [P]|[X]

staph_protease n/t E;C; n/t staph_protease, E/C E;after; E;C; E;C; E;C; n/t n/t n/t n/t n/t E;C; n/t n/t n/t n/t E;C; [E]|[X]

tca n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t [FMWY]|{P},[KR]|{P},[X]|[D]

thermolysin_p n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t 22 n/t n/t n/t n/t n/t n/t n/t n/t

top_down n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t 15 n/t n/t n/t n/t n/t n/t n/t n/t

trypsin trypsin KR;C;P [KR]|{P} trypsin, KR/C KR;after;P KR;C;P KR;C;P KR;C;P 1 Trypsin Trypsin 0 TRYPSIN KR;C;P Trypsin_KR-P-C Trypsin;1;KR;P Trypsin_P KR P C K|R;[^P].* KR;C;P [KR]|{P}

trypsin_chymotrypsin n/t n/t n/t n/t n/t n/t n/t n/t n/t TrypChymo n/t 9 n/t n/t n/t n/t n/t n/t n/t n/t

trypsin_cnbr n/t KRM;C;P n/t trypsin_cnbr, KRM/C KRM;after;P KRM;C;P KRM;C;P KRM;C;P n/t n/t n/t 8 n/t KRM;C;P n/t n/t n/t n/t KRM;C;P [KR]|{P},[M]|{P}

trypsin_gluc n/t DEKR;C;P n/t trypsin_gluc, DEKR/C DEKR;after;P DEKR;C;P DEKR;C;P DEKR;C;P n/t n/t n/t n/t n/t DEKR;C;P n/t n/t n/t n/t DEKR;C;P [DEKR]|{P}

trypsin_p n/t KR;C; [RK]| trypsin_p, KR/C KR;after; KR;C; KR;C; KR;C; 1 Trypsin/P n/t 10 n/t KR;C; Trypsin_KR-C n/t Trypsin KR _ C K|R;.* KR;C; [RK]|[X]

evidence_score_field¶

Field which is used for scoring in pyqms_1_0_0

Default value:	PEP
type:	str
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0

Ursgal key translations for evidence_score_field¶

Style Translation

pyqms_style_1 evidence_score_field

experiment_setup¶

Default value:	[]
type:	list
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for experiment_setup¶

flash_lfq_style_1 experiment_setup

Format: {“1”: {“FileName”: <filename as in identfile>, “Condition”:<str>, “Biorep”: <int>, “Fraction”: <int>, “Techrep”: <int>}, “2”: …. }

extract_venndiagram_file¶

The user can retrieve a csv file containing results from the venn diagram

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

venndiagram_1_0_0
venndiagram_1_1_0

Ursgal key translations for extract_venndiagram_file¶

Style Translation

venndiagram_style_1 extract_venndiagram_file

fdr_cutoff¶

Target PSMs with a lower FDR than this threshold will be used as a positive training set for SVM post-processing

Default value:	0.01
type:	float
triggers rerun:	True

Available in unodes¶

svm_1_0_0

Ursgal key translations for fdr_cutoff¶

Style Translation

svm_style_1 fdr_cutoff

fdr_method¶

specifying the fdr method to use

Default value:	transferred
type:	str
triggers rerun:	True

Available in unodes¶

ptminer_1_0

Ursgal key translations for fdr_method¶

Style Translation

ptminer_style_1 fdr_method

Ursgal value translations¶

Ursgal Value Translated Value

. ptminer_style_1

global 1

separate 2

transferred 3

fixed_label_isotope_enrichment_levels¶

Enrichment of labeled elements in labeled chemical used

Default value:	[‘13C’, ‘15N’, ‘2H’]
type:	dict
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for fixed_label_isotope_enrichment_levels¶

Style Translation

pyqms_style_1 FIXED_LABEL_ISOTOPE_ENRICHMENT_LEVELS

sugarpy_plot_style_1 FIXED_LABEL_ISOTOPE_ENRICHMENT_LEVELS

sugarpy_run_style_1 FIXED_LABEL_ISOTOPE_ENRICHMENT_LEVELS

fold_change_cutoff¶

fold-change cutoff for Bayesian protein fold-change analysis

Default value:	0.1
type:	float
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for fold_change_cutoff¶

Style Translation

flash_lfq_style_1 –fcc

forbidden_cterm_mods¶

List of modifications (unimod name) that are not allowed to occur at the C-terminus of a peptide, e.g. [‘GG’]

Default value:	[]
type:	list
triggers rerun:	True

Available in unodes¶

xtandem_vengeance
xtandem_alanine

Ursgal key translations for forbidden_cterm_mods¶

Style Translation

xtandem_style_1 residue, potential modification mass

forbidden_residues¶

Aminoacids that are not allowed during/taken into account during denovo searches. Given as a string of comma seperated aminoacids (single letter code)

Default value:	I,U
type:	str
triggers rerun:	True

Available in unodes¶

novor_1_1beta
novor_1_05

Ursgal key translations for forbidden_residues¶

Style Translation

novor_style_1 forbiddenResidues

force¶

If set ‘True’, engines are forced to re-run although no node-related parameters have changed

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for force¶

Style Translation

ucontroller_style_1 force

frag_clear_mz_range¶

Removes peaks in this m/z range prior to matching. Given as list [min_clear_mz, max_clear_mz]. Useful for iTRAQ/TMT experiments, i.e. [0.0, 150.0].

Default value:	[0.0, 0.0]
type:	list
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6

Ursgal key translations for frag_clear_mz_range¶

Style Translation

msfragger_style_1 clear_mz_range

msfragger_style_2 clear_mz_range

msfragger_style_3 clear_mz_range

pipi_style_1 frag_clear_mz_range

frag_mass_tolerance¶

Mass tolerance of measured and calculated fragment ions

Default value:	20
type:	int
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
myrimatch_2_1_138
myrimatch_2_2_140
novor_1_1beta
novor_1_05
omssa_2_1_9
pepnovo_3_1
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
pglyco_db_2_2_0
ptminer_1_0
pglyco_db_2_2_2
pnovo_3_1_3
tag_graph_1_8_0
deepnovo_pointnovo
glycopeptide_fragmentor_1_0_0
ptmshepherd_0_3_5

Ursgal key translations for frag_mass_tolerance¶

Style Translation

deepnovo_style_1 AA_MATCH_PRECISION

glycopeptide_fragmentor_style_1 frag_mass_tolerance

moda_style_1 FragTolerance

msamanda_style_1 ms2_tol

msfragger_style_1 fragment_mass_tolerance

msfragger_style_2 fragment_mass_tolerance

msfragger_style_3 fragment_mass_tolerance

myrimatch_style_1 FragmentMzTolerance

novor_style_1 fragmentIonErrorTol

omssa_style_1 -to

pepnovo_style_1 -fragment_tolerance

pglyco_db_style_1 search_fragment_tolerance

pipi_style_1 ms2_tolerance

pnovo_style_1 frag_tol

ptminer_style_1 fragment_tol

ptmshepherd_style_1 spectra_ppmtol

pyqms_style_1 REL_MZ_RANGE

sugarpy_plot_style_1 REL_MZ_RANGE

sugarpy_run_style_1 REL_MZ_RANGE

tag_graph_style_1 ppmstd

xtandem_style_1 spectrum, fragment monoisotopic mass error

frag_mass_tolerance_unit¶

Fragment mass tolerance unit: available in ppm (parts-per-millon), da (Dalton) or mmu (Milli mass unit)

Default value:	ppm
type:	select
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
myrimatch_2_1_138
myrimatch_2_2_140
novor_1_1beta
novor_1_05
omssa_2_1_9
pepnovo_3_1
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
pglyco_db_2_2_0
ptminer_1_0
pglyco_db_2_2_2
pnovo_3_1_3
tag_graph_1_8_0
deepnovo_pointnovo
glycopeptide_fragmentor_1_0_0
ptmshepherd_0_3_5

Ursgal key translations for frag_mass_tolerance_unit¶

Style Translation

deepnovo_style_1 AA_MATCH_PRECISION

glycopeptide_fragmentor_style_1 frag_mass_tolerance_unit

moda_style_1 FragTolerance

msamanda_style_1 ms2_tol unit

msfragger_style_1 fragment_mass_units

msfragger_style_2 fragment_mass_units

msfragger_style_3 fragment_mass_units

myrimatch_style_1 FragmentMzTolerance

novor_style_1 fragmentIonErrorTol

omssa_style_1 frag_mass_tolerance_unit

pepnovo_style_1 frag_mass_tolerance_unit

pglyco_db_style_1 search_fragment_tolerance_type

pipi_style_1 frag_mass_tolerance_unit

pnovo_style_1 frag_tol_type_ppm

ptminer_style_1 fragment_tol_type

ptmshepherd_style_1 spectra_ppmtol

pyqms_style_1 REL_MZ_RANGE

sugarpy_plot_style_1 REL_MZ_RANGE

sugarpy_run_style_1 REL_MZ_RANGE

tag_graph_style_1 frag_mass_tolerance_unit

xtandem_style_1 spectrum, fragment monoisotopic mass error units

Ursgal value translations¶

Ursgal Value Translated Value

. msamanda_style_1 msfragger_style_1 msfragger_style_2 msfragger_style_3 myrimatch_style_1 novor_style_1 omssa_style_1 pglyco_db_style_1 pnovo_style_1 ptminer_style_1 xtandem_style_1

da Da 0 0 0 Da Da Da Da 0 0 Daltons

ppm n/t 1 1 1 n/t n/t n/t n/t 1 1 n/t

frag_mass_type¶

Fragment mass type: monoisotopic or average

Default value:	monoisotopic
type:	select
triggers rerun:	True

Available in unodes¶

omssa_2_1_9
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for frag_mass_type¶

Style Translation

omssa_style_1 -tom

xtandem_style_1 spectrum, fragment mass type

Ursgal value translations¶

Ursgal Value Translated Value

. omssa_style_1

average 1

monoisotopic 0

frag_max_charge¶

Maximum fragment ion charge to search.

Default value:	4
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for frag_max_charge¶

Style Translation

msfragger_style_1 max_fragment_charge

msfragger_style_2 max_fragment_charge

msfragger_style_3 max_fragment_charge

omssa_style_1 -zoh

frag_method¶

Used fragmentation method, e.g. collision-induced dissociation (cid), electron-capture dissociation (ecd), electron-transfer dissociation (etd), Higher-energy C-trap dissociation (hcd)

Default value:	hcd
type:	select
triggers rerun:	True

Available in unodes¶

msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
novor_1_1beta
novor_1_05
pnovo_3_1_3

Ursgal key translations for frag_method¶

Style Translation

msgfplus_style_1 -m

novor_style_1 fragmentation

pnovo_style_1 activation_type

Ursgal value translations¶

Ursgal Value Translated Value

. msgfplus_style_1 novor_style_1 pnovo_style_1

cid 1 CID CID

etd 2 n/t ETD

hcd 3 HCD HCD

frag_min_mz¶

Minimal considered fragment ion m/z

Default value:	150
type:	int
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for frag_min_mz¶

Style Translation

xtandem_style_1 spectrum, minimum fragment mz

ftp_blocksize¶

Blocksize for ftp download

Default value:	1024
type:	int
triggers rerun:	True

Available in unodes¶

get_ftp_files_1_0_0

Ursgal key translations for ftp_blocksize¶

Style Translation

get_ftp_style_1 ftp_blocksize

ftp_folder¶

ftp folder that should be downloaded

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

get_ftp_files_1_0_0

Ursgal key translations for ftp_folder¶

Style Translation

get_ftp_style_1 ftp_folder

ftp_include_ext¶

Only files with the defined file extension are downloaded with ftp download

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

get_ftp_files_1_0_0

Ursgal key translations for ftp_include_ext¶

Style Translation

get_ftp_style_1 ftp_include_ext

ftp_login¶

Login name/user for the ftp server e.g. “PASS00269” in peptideatlas.orgftp download: ‘’ : None

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

get_ftp_files_1_0_0

ftp_max_number_of_files¶

Maximum number of files that will be downloaded: 0 : No Limitation

Default value:	None
type:	int
triggers rerun:	True

Available in unodes¶

get_ftp_files_1_0_0

Ursgal key translations for ftp_max_number_of_files¶

Style Translation

get_ftp_style_1 ftp_max_number_of_files

ftp_output_folder¶

Default ftp download path: ‘’ : None

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

get_ftp_files_1_0_0

Ursgal key translations for ftp_output_folder¶

Style Translation

get_ftp_style_1 ftp_output_folder

ftp_password¶

ftp download password: ‘’ : None

Default value:	None
type:	str_password
triggers rerun:	True

Available in unodes¶

get_ftp_files_1_0_0

Ursgal key translations for ftp_password¶

Style Translation

get_ftp_style_1 ftp_password

ftp_url¶

ftp download URL, will fail if it is not set by the user: ‘’ : None

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

get_ftp_files_1_0_0

Ursgal key translations for ftp_url¶

Style Translation

get_ftp_style_1 ftp_url

glycans_incl_as_mods¶

List of Unimod PSI-MS names corresponding to glycans that were included in the database search as modification (will be removed from the peptidoform by SugarPy).

Default value:	[‘HexNAc’, ‘HexNAc(2)’]
type:	list
triggers rerun:	True

Available in unodes¶

sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for glycans_incl_as_mods¶

Style Translation

sugarpy_plot_style_1 unimod_glycans_incl_in_search

sugarpy_run_style_1 unimod_glycans_incl_in_search

header_translations¶

Translate output headers into Ursgal unify_csv style headers: ‘None’ : None

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

kojak_percolator_2_08
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus2csv_v2016_09_16
msgfplus2csv_v2017_01_27
novor_1_1beta
novor_1_05
omssa_2_1_9
pepnovo_3_1
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
msgfplus2csv_v2017_07_04
msgfplus2csv_v1_2_0
msgfplus2csv_v1_2_1
pipi_1_4_5
pipi_1_4_6
pglyco_db_2_2_0
pglyco_db_2_2_2
pglyco_fdr_2_2_0
pglyco_fdr_2_2_2
deepnovo_0_0_1
deepnovo_pointnovo
tag_graph_1_8_0
flash_lfq_1_1_1

Ursgal key translations for header_translations¶

Style Translation

deepnovo_style_1 header_translations

flash_lfq_style_1 header_translations

kojak_percolator_style_1 header_translations

msamanda_style_1 header_translations

msfragger_style_1 header_translations

msfragger_style_2 header_translations

msfragger_style_3 header_translations

msgfplus_style_1 header_translations

novor_style_1 header_translations

omssa_style_1 header_translations

pepnovo_style_1 header_translations

pglyco_db_style_1 header_translations

pglyco_fdr_style_1 header_translations

pipi_style_1 header_translations

tag_graph_style_1 header_translations

Ursgal value translations¶

Ursgal Value Translated Value

. deepnovo_style_1 flash_lfq_style_1 kojak_percolator_style_1 msamanda_style_1 msfragger_style_1 msfragger_style_2 msfragger_style_3 msgfplus_style_1 novor_style_1 omssa_style_1 pepnovo_style_1 pglyco_db_style_1 pglyco_fdr_style_1 pipi_style_1 tag_graph_style_1

Accession n/t n/t n/t n/t n/t n/t n/t n/t n/t Accession n/t n/t n/t n/t n/t

Charge n/t n/t n/t n/t n/t n/t n/t n/t n/t Charge n/t n/t n/t n/t n/t

Defline n/t n/t n/t n/t n/t n/t n/t n/t n/t proteinacc_start_stop_pre_post_; n/t n/t n/t n/t n/t

E-value n/t n/t n/t n/t n/t n/t n/t n/t n/t OMSSA:evalue n/t n/t n/t n/t n/t

Filename/id n/t n/t n/t n/t n/t n/t n/t n/t n/t Spectrum Title n/t n/t n/t n/t n/t

Mass n/t n/t n/t n/t n/t n/t n/t n/t n/t Exp m/z n/t n/t n/t n/t n/t

Mods n/t n/t n/t n/t n/t n/t n/t n/t n/t Modifications n/t n/t n/t n/t n/t

NIST score n/t n/t n/t n/t n/t n/t n/t n/t n/t NIST score n/t n/t n/t n/t n/t

P-value n/t n/t n/t n/t n/t n/t n/t n/t n/t OMSSA:pvalue n/t n/t n/t n/t n/t

Peptide n/t n/t n/t n/t n/t n/t n/t n/t n/t Sequence n/t n/t n/t n/t n/t

RT n/t n/t n/t n/t n/t n/t n/t n/t Retention Time (s) n/t n/t n/t n/t n/t n/t

Start n/t n/t n/t n/t n/t n/t n/t n/t n/t Start n/t n/t n/t n/t n/t

Stop n/t n/t n/t n/t n/t n/t n/t n/t n/t Stop n/t n/t n/t n/t n/t

Theo Mass n/t n/t n/t n/t n/t n/t n/t n/t n/t Calc m/z n/t n/t n/t n/t n/t

aaScore n/t n/t n/t n/t n/t n/t n/t n/t Novor:aaScore n/t n/t n/t n/t n/t n/t

err(data-denovo) n/t n/t n/t n/t n/t n/t n/t n/t Error (exp-calc) n/t n/t n/t n/t n/t n/t

gi n/t n/t n/t n/t n/t n/t n/t n/t n/t gi n/t n/t n/t n/t n/t

mz(data) n/t n/t n/t n/t n/t n/t n/t n/t Exp m/z n/t n/t n/t n/t n/t n/t

pepMass(denovo) n/t n/t n/t n/t n/t n/t n/t n/t Calc mass n/t n/t n/t n/t n/t n/t

peptide n/t n/t n/t n/t n/t n/t n/t n/t Sequence n/t n/t n/t n/t n/t n/t

ppm(1e6*err/(mz*z)) n/t n/t n/t n/t n/t n/t n/t n/t Error (ppm) n/t n/t n/t n/t n/t n/t

scanNum n/t n/t n/t n/t n/t n/t n/t n/t Spectrum ID n/t n/t n/t n/t n/t n/t

score n/t n/t n/t n/t n/t n/t n/t n/t Novor:score n/t n/t n/t n/t n/t n/t

z n/t n/t n/t n/t n/t n/t n/t n/t Charge n/t n/t n/t n/t n/t n/t

# id n/t n/t n/t n/t n/t n/t n/t n/t Novor:id n/t n/t n/t n/t n/t n/t

#Index n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Pepnovo:id n/t n/t n/t n/t

#SpecFile n/t n/t n/t n/t n/t n/t n/t Raw data location n/t n/t n/t n/t n/t n/t n/t

1-lg10 EM n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t TagGraph: 1-log10 EM

A_score n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t A-Score n/t

Alignment Score n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t TagGraph:Alignment Score

Amanda Score n/t n/t n/t Amanda:Score n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Base Sequence n/t Sequence n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Base Sequences Mapped n/t FlashLFQ:Base Sequences Mapped n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

C-Gap n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Pepnovo:C-Gap n/t n/t n/t n/t

Charge n/t n/t n/t Charge n/t n/t n/t Charge n/t n/t n/t Charge Charge n/t Charge

Composite Score n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t TagGraph:Composite Score

Context n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Sequence

Context Mod Variants n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Context Mod Variants

CoreFuc n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t CoreFuc CoreFuc n/t n/t

CoreMatched n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t CoreMatched CoreMatched n/t n/t

CumProb n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Pepnovo:CumProb n/t n/t n/t n/t

De Novo Peptide n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t De Novo Peptide

De Novo Score n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t De Novo Score

DeNovoScore n/t n/t n/t n/t n/t n/t n/t MS-GF:DeNovoScore n/t n/t n/t n/t n/t n/t n/t

Downstream Amino Acid n/t n/t n/t n/t Sequence Post AA n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

EM Probability n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t TagGraph:EM Probability

EValue n/t n/t n/t n/t n/t n/t n/t MS-GF:EValue n/t n/t n/t n/t n/t n/t n/t

File Name n/t Raw Filename n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Filename n/t n/t n/t Filename n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Full Sequence n/t FlashLFQ:Full Sequence n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Full Sequences Mapped n/t FlashLFQ:Full Sequences Mapped n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

GlyDecoy n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t GlyDecoy GlyDecoy n/t n/t

GlyFrag n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Glycan Fragments Glycan Fragments n/t n/t

GlyID n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Glycan ID Glycan ID n/t n/t

GlyIonRatio n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t GlyIonRatio GlyIonRatio n/t n/t

GlyMass n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Glycan Mass Glycan Mass n/t n/t

GlyScore n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t pGlyco:GlyScore pGlyco:GlyScore n/t n/t

GlySite n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Glycosite Glycosite n/t n/t

GlySpec n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Spectrum Title Spectrum Title n/t n/t

Glycan(H,N,A,G,F) n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Glycan Glycan n/t n/t

GlycanFDR n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Glycan FDR n/t n/t

Hit rank n/t n/t n/t n/t Rank n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Hyperscore n/t n/t n/t n/t MSFragger:Hyperscore n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Intercept of expectation model (expectation in log space) n/t n/t n/t n/t MSFragger:Intercept of expectation model (expectation in log space) n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

MBR Score n/t FlashLFQ:MBR Score n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

MGF_title n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Spectrum Title n/t

MS1_pearson_correlation_coefficient n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t PIPI:MS1_pearson_correlation_coefficient n/t

MS2 Retention Time n/t FlashLFQ:MS2 Retention Time n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

MSGFScore n/t n/t n/t n/t n/t n/t n/t MS-GF:RawScore n/t n/t n/t n/t n/t n/t n/t

Mass difference n/t n/t n/t n/t Mass Difference n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

MassDeviation n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Mass Difference Mass Difference n/t n/t

Matched fragment ions n/t n/t n/t n/t MSFragger:Matched fragment ions n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Matching Tag Length n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Matching Tag Length

Mod n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Modifications Modifications n/t n/t

Mod Ambig Edges n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t TagGraph:Mod Ambig Edges

Mod Ranges n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t TagGraph:Mod Ranges

Modifications n/t n/t n/t Modifications n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Mods n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Modifications

N-Gap n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Pepnovo:N-Gap n/t n/t n/t n/t

Neutral mass of peptide n/t n/t n/t n/t MSFragger:Neutral mass of peptide n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Next score n/t n/t n/t n/t MSFragger:Next score n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Num Charge States Observed n/t FlashLFQ:Num Charge States Observed n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Num Matches n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Num DB Matches

Num Mod Occurrences n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Num Mod Occurrences

Number of missed cleavages n/t n/t n/t n/t MSFragger:Number of missed cleavages n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Number of tryptic termini n/t n/t n/t n/t MSFragger:Number of tryptic termini n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Obs M+H n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Exp Mass

PPM n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Accuracy (ppm) Accuracy (ppm) n/t Accuracy (ppm)

PSMId n/t n/t PSMId n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

PSMs Mapped n/t FlashLFQ:PSMs Mapped n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Peak Apex Mass Error (ppm) n/t Accuracy (ppm) n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Peak Charge n/t FlashLFQ:Peak Charge n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Peak Detection Type n/t FlashLFQ:Peak Detection Type n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Peak MZ n/t FlashLFQ:Peak MZ n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Peak RT Apex n/t FlashLFQ:Peak RT Apex n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Peak RT End n/t FlashLFQ:Peak RT End n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Peak RT Start n/t FlashLFQ:Peak RT Start n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Peak Split Valley RT n/t FlashLFQ:Peak Split Valley RT n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Peak intensity n/t FlashLFQ:Peak intensity n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

PepDecoy n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t PepDecoy PepDecoy n/t n/t

PepIonRatio n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t PepIonRatio PepIonRatio n/t n/t

PepScore n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t pGlyco:PepScore pGlyco:PepScore n/t n/t

PepSpec n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Spectrum Title Spectrum Title n/t n/t

Peptide n/t n/t n/t n/t n/t n/t n/t Sequence n/t n/t n/t Sequence Sequence n/t n/t

Peptide Monoisotopic Mass n/t Calc mass n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Peptide Sequence n/t n/t n/t n/t Sequence n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

PeptideFDR n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Peptide FDR n/t n/t

PeptideMH n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Calc Mass Calc Mass n/t n/t

PlausibleStruct n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Plausible Glycan Structure Plausible Glycan Structure n/t n/t

PnvScr n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Pepnovo:PnvScr n/t n/t n/t n/t

Precursor n/t n/t n/t n/t n/t n/t n/t Exp m/z n/t n/t n/t n/t n/t n/t n/t

Precursor Charge n/t Charge n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Precursor charge n/t n/t n/t n/t Charge n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Precursor neutral mass (Da) n/t n/t n/t n/t MSFragger:Precursor neutral mass (Da) n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

PrecursorMH n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Exp Mass Exp Mass n/t n/t

PrecursorMZ n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Exp m/z Exp m/z n/t n/t

Protein n/t n/t n/t n/t Protein ID n/t n/t proteinacc_start_stop_pre_post_; n/t n/t n/t n/t n/t n/t n/t

Protein Accessions n/t n/t n/t proteinacc_start_stop_pre_post_; n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Protein Group n/t Protein ID n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Proteins n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Protein ID

RT n/t n/t n/t Retention Time (s) n/t n/t n/t n/t n/t n/t n/t Retention Time (s) Retention Time (s) n/t n/t

Rank n/t n/t n/t Rank n/t n/t n/t n/t n/t n/t n/t Rank Rank n/t n/t

RawName n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Raw Filename Raw Filename n/t n/t

Retention Time n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Retention Time (s)

Retention time (minutes) n/t n/t n/t n/t Retention Time (s) n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

RnkScr n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Pepnovo:RnkScr n/t n/t n/t n/t

Scan n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Spectrum ID Spectrum ID n/t n/t

Scan Number n/t n/t n/t Spectrum ID n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

ScanF n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Spectrum ID

ScanID n/t n/t n/t n/t Spectrum ID n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

ScanNum n/t n/t n/t n/t n/t n/t n/t Spectrum ID n/t n/t n/t n/t n/t n/t n/t

Sequence n/t n/t n/t Sequence n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Slope of expectation model (expectation in log space) n/t n/t n/t n/t MSFragger:Slope of expectation model (expectation in log space) n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

SpecEValue n/t n/t n/t n/t n/t n/t n/t MS-GF:SpecEValue n/t n/t n/t n/t n/t n/t n/t

SpecFile n/t n/t n/t n/t n/t n/t n/t Raw data location n/t n/t n/t n/t n/t n/t n/t

Spectrum Score n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t TagGraph:Spectrum Score

Spectrum number n/t n/t n/t n/t n/t n/t n/t n/t n/t Spectrum ID n/t n/t n/t n/t n/t

Theo M+H n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Calc mass

Theoretical MZ n/t FlashLFQ:Theoretical MZ n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Title n/t n/t n/t Spectrum Title n/t n/t n/t Spectrum Title n/t n/t n/t n/t n/t n/t n/t

Total possible number of matched theoretical fragment ions n/t n/t n/t n/t MSFragger:Total possible number of matched theoretical fragment ions n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

TotalFDR n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t q-value n/t n/t

TotalScore n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t pGlyco:TotalScore pGlyco:TotalScore n/t n/t

Unique Siblings n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Unique Siblings

Upstream Amino Acid n/t n/t n/t n/t Sequence Pre AA n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Variable modifications detected n/t n/t n/t n/t Modifications n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

Weighted Probability n/t n/t n/t Amanda:Weighted Probability n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

[M+H] n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Calc mass(Da) n/t n/t n/t n/t

abs_ppm n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t PIPI:abs_ppm n/t

best_locs n/t n/t n/t n/t n/t MSFragger:best_locs MSFragger:best_locs n/t n/t n/t n/t n/t n/t n/t n/t

best_score_with_delta_mass n/t n/t n/t n/t n/t MSFragger:best_score_with_delta_mass MSFragger:best_score_with_delta_mass n/t n/t n/t n/t n/t n/t n/t n/t

calc_neutral_pep_mass n/t n/t n/t n/t n/t MSFragger:Neutral mass of peptide MSFragger:Neutral mass of peptide n/t n/t n/t n/t n/t n/t n/t n/t

charge n/t n/t n/t n/t n/t Charge Charge n/t n/t n/t n/t n/t n/t Charge n/t

delta_C_n n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t PIPI:delta_C_n n/t

delta_score n/t n/t n/t n/t n/t MSFragger:delta_score MSFragger:delta_score n/t n/t n/t n/t n/t n/t n/t n/t

exp_mass n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Exp m/z n/t

expectscore n/t n/t n/t n/t n/t MSFragger:expect score MSFragger:expect score n/t n/t n/t n/t n/t n/t n/t n/t

hit_rank n/t n/t n/t n/t n/t Rank Rank n/t n/t n/t n/t n/t n/t n/t n/t

hyperscore n/t n/t n/t n/t n/t MSFragger:Hyperscore MSFragger:Hyperscore n/t n/t n/t n/t n/t n/t n/t n/t

isotope_correction n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t PIPI:isotope_correction n/t

labelling n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Label n/t

m/z n/t n/t n/t Exp m/z n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

massdiff n/t n/t n/t n/t n/t Mass Difference Mass Difference n/t n/t n/t n/t n/t n/t n/t n/t

modification_info n/t n/t n/t n/t n/t Modifications Modifications n/t n/t n/t n/t n/t n/t n/t n/t

nextscore n/t n/t n/t n/t n/t MSFragger:Next score MSFragger:Next score n/t n/t n/t n/t n/t n/t n/t n/t

num_matched_ions n/t n/t n/t n/t n/t MSFragger:Matched fragment ions MSFragger:Matched fragment ions n/t n/t n/t n/t n/t n/t n/t n/t

num_missed_cleavages n/t n/t n/t n/t n/t MSFragger:Number of missed cleavages MSFragger:Number of missed cleavages n/t n/t n/t n/t n/t n/t n/t n/t

num_tol_term n/t n/t n/t n/t n/t MSFragger:Number of tryptic termini MSFragger:Number of tryptic termini n/t n/t n/t n/t n/t n/t n/t n/t

other_PTM_patterns n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t PIPI:other_PTM_patterns n/t

output_aa_probs n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Pepnovo:aaScore n/t n/t n/t n/t

peptide n/t n/t Sequence n/t n/t Sequence Sequence n/t n/t n/t n/t n/t n/t Sequence n/t

peptide_next_aa n/t n/t n/t n/t n/t Sequence Post AA Sequence Post AA n/t n/t n/t n/t n/t n/t n/t n/t

peptide_prev_aa n/t n/t n/t n/t n/t Sequence Pre AA Sequence Pre AA n/t n/t n/t n/t n/t n/t n/t n/t

posterior_error_prob n/t n/t PEP n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

precursor_charge Charge n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

precursor_mz Exp m/z n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

precursor_neutral_mass n/t n/t n/t n/t n/t MSFragger:Precursor neutral mass (Da) MSFragger:Precursor neutral mass (Da) n/t n/t n/t n/t n/t n/t n/t n/t

predicted_position_score DeepNovo:aaScore n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

predicted_score DeepNovo:score n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

predicted_sequence Sequence n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

protein n/t n/t n/t n/t n/t Protein ID Protein ID n/t n/t n/t n/t n/t n/t n/t n/t

proteinIds n/t n/t Protein ID n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

protein_ID n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Protein ID n/t

q-value n/t n/t q-value n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

retention_time n/t n/t n/t n/t n/t Retention Time (s) Retention Time (s) n/t n/t n/t n/t n/t n/t n/t n/t

scan Spectrum ID n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

scan_list_middle Spectrum ID n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t

scan_num n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Spectrum ID n/t

scannum n/t n/t n/t n/t n/t Spectrum ID Spectrum ID n/t n/t n/t n/t n/t n/t n/t n/t

score n/t n/t Kojak:score n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t PIPI:score n/t

score_without_delta_mass n/t n/t n/t n/t n/t MSFragger:score_without_delta_mass MSFragger:score_without_delta_mass n/t n/t n/t n/t n/t n/t n/t n/t

second_best_score_with_delta_mass n/t n/t n/t n/t n/t MSFragger:second_best_score_with_delta_mass MSFragger:second_best_score_with_delta_mass n/t n/t n/t n/t n/t n/t n/t n/t

theo_mass n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t n/t Calc m/z n/t

tot_num_ions n/t n/t n/t n/t n/t MSFragger:Total possible number of matched theoretical fragment ions MSFragger:Total possible number of matched theoretical fragment ions n/t n/t n/t n/t n/t n/t n/t n/t

heatmap_annotation_field_name¶

The name of the annotation to plot in the heatmap

Default value:	Protein
type:	str
triggers rerun:	True

Available in unodes¶

plot_pygcluster_heatmap_from_csv_1_0_0

Ursgal key translations for heatmap_annotation_field_name¶

Style Translation

heatmap_style_1 heatmap_annotation_field_name

heatmap_box_style¶

Box style for the heatmap

Default value:	classic
type:	str
triggers rerun:	True

Available in unodes¶

plot_pygcluster_heatmap_from_csv_1_0_0

Ursgal key translations for heatmap_box_style¶

Style Translation

heatmap_style_1 heatmap_box_style

heatmap_color_gradient¶

Color gradient for the heatmap

Default value:	Spectral
type:	str
triggers rerun:	True

Available in unodes¶

plot_pygcluster_heatmap_from_csv_1_0_0

Ursgal key translations for heatmap_color_gradient¶

Style Translation

heatmap_style_1 heatmap_color_gradient

heatmap_column_positions¶

The position of each column in the heatmap is given as a dict with keys corresponding to the position and values correspondingto the column name, e.g: {“0” : “Ratio1_2”, “1” : “Ratio2_3”}

Default value:	[]
type:	dict
triggers rerun:	True

Available in unodes¶

plot_pygcluster_heatmap_from_csv_1_0_0

Ursgal key translations for heatmap_column_positions¶

Style Translation

heatmap_style_1 heatmap_column_positions

heatmap_error_suffix¶

The suffix to identify the value error holding columns

Default value:	_std
type:	str
triggers rerun:	True

Available in unodes¶

plot_pygcluster_heatmap_from_csv_1_0_0

Ursgal key translations for heatmap_error_suffix¶

Style Translation

heatmap_style_1 heatmap_error_suffix

heatmap_identifier_field_name¶

The name of the identifier to plot in the heatmap

Default value:	Protein
type:	str
triggers rerun:	True

Available in unodes¶

plot_pygcluster_heatmap_from_csv_1_0_0

Ursgal key translations for heatmap_identifier_field_name¶

Style Translation

heatmap_style_1 heatmap_identifier_field_name

heatmap_max_value¶

Maximum value for the color gradient

Default value:	3
type:	int
triggers rerun:	True

Available in unodes¶

plot_pygcluster_heatmap_from_csv_1_0_0

Ursgal key translations for heatmap_max_value¶

Style Translation

heatmap_style_1 heatmap_max_value

heatmap_min_value¶

Minimum vaue for the color gradient

Default value:	-3
type:	int
triggers rerun:	True

Available in unodes¶

plot_pygcluster_heatmap_from_csv_1_0_0

Ursgal key translations for heatmap_min_value¶

Style Translation

heatmap_style_1 heatmap_min_value

heatmap_value_suffix¶

The suffix to identify the value columns, which should be plotted

Default value:	_mean
type:	str
triggers rerun:	True

Available in unodes¶

plot_pygcluster_heatmap_from_csv_1_0_0

Ursgal key translations for heatmap_value_suffix¶

Style Translation

heatmap_style_1 heatmap_value_suffix

helper_extension¶

Exension for helper files

Default value:	.u.json
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for helper_extension¶

Style Translation

ucontroller_style_1 helper_extension

http_output_folder¶

Default http download path: ‘’ : None

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

get_http_files_1_0_0

Ursgal key translations for http_output_folder¶

Style Translation

get_http_style_1 http_output_folder

http_url¶

http download URL, will fail if it is not set by the user: ‘’ : None

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

get_http_files_1_0_0

Ursgal key translations for http_url¶

Style Translation

get_http_style_1 http_url

identifier_column_names¶

The (combination of) specified csv column name(s) are used as identifiers. E.g. to count the number of peptides for these identifiers. The parameter “count_column_names” defines the countable elements.

Default value:	[‘Protein ID’]
type:	list
triggers rerun:	True

Available in unodes¶

csv2counted_results_1_0_0

Ursgal key translations for identifier_column_names¶

Style Translation

csv2counted_results_style_1 identifier_column_names

infer_proteins¶

Use the picked-protein algorithm to infer protein PEP and FDR in Percolator

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

percolator_2_08
percolator_3_2_1
percolator_3_4_0

Ursgal key translations for infer_proteins¶

Style Translation

percolator_style_1 infer_proteins

instrument¶

Type of mass spectrometer (used to determine the scoring model)

Default value:	q_exactive
type:	select
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
moda_v1_51
moda_v1_61
moda_v1_62
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
novor_1_1beta
novor_1_05

Ursgal key translations for instrument¶

Style Translation

kojak_style_1 instrument

moda_style_1 Instrument

msgfplus_style_1 -inst

novor_style_1 massAnalyzer

Ursgal value translations¶

Ursgal Value Translated Value

. kojak_style_1 moda_style_1 msgfplus_style_1 novor_style_1

FTICR 1 n/t n/t n/t

high_res_ltq 0 ESI-TRAP 1 Trap

low_res_ltq 0 ESI-TRAP 0 Trap

q_exactive 0 ESI-TRAP 3 FT

tof n/t ESI-QTOF 2 TOF

integrate_peak_areas¶

integrate peak areas

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for integrate_peak_areas¶

Style Translation

flash_lfq_style_1 –int

intensity_cutoff¶

Low intensity cutoff as a fraction of max peak

Default value:	0.0
type:	float
triggers rerun:	True

Available in unodes¶

omssa_2_1_9
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
ptmshepherd_0_3_5

Ursgal key translations for intensity_cutoff¶

Style Translation

msfragger_style_1 minimum_ratio

msfragger_style_2 minimum_ratio

msfragger_style_3 minimum_ratio

omssa_style_1 -cl

ptmshepherd_style_1 spectra_condRatio

intensity_cutoff_diagnostic_ions¶

Minimum relative intensity (relative to base peak height) for the sum of all diagnostic fragment ion intensities

Default value:	0.0
type:	float
triggers rerun:	True

Available in unodes¶

msfragger_3_0

Ursgal key translations for intensity_cutoff_diagnostic_ions¶

Style Translation

msfragger_style_3 diagnostic_intensity_filter

intensity_transformation_factor¶

Tranform intensity by this factor for quantification

Default value:	100000.0
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for intensity_transformation_factor¶

Style Translation

pyqms_style_1 INTENSITY_TRANSFORMATION_FACTOR

sugarpy_plot_style_1 INTENSITY_TRANSFORMATION_FACTOR

sugarpy_run_style_1 INTENSITY_TRANSFORMATION_FACTOR

internal_precision¶

Float to int conversion precision

Default value:	1000.0
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
glycopeptide_fragmentor_1_0_0

Ursgal key translations for internal_precision¶

Style Translation

glycopeptide_fragmentor_style_1 internal_precision

pyqms_style_1 INTERNAL_PRECISION

sugarpy_plot_style_1 INTERNAL_PRECISION

sugarpy_run_style_1 INTERNAL_PRECISION

ion_mode¶

The ion mode that has been used for acquiring mass spectra (positive or negative)

Default value:	positive
type:	select
triggers rerun:	True

Available in unodes¶

mzml2mgf_2_0_0

Ursgal key translations for ion_mode¶

Style Translation

mzml2mgf_style_1 ion_mode

Ursgal value translations¶

Ursgal Value Translated Value

. mzml2mgf_style_1

negative

positive

is_open_search¶

specifying whether this is an open search or not

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

ptminer_1_0

Ursgal key translations for is_open_search¶

Style Translation

ptminer_style_1 open_search

Ursgal value translations¶

Ursgal Value Translated Value

. ptminer_style_1

0 0

1 1

isotopic_distribution_tolerance¶

isotopic distribution tolerance in ppm

Default value:	5
type:	float
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for isotopic_distribution_tolerance¶

Style Translation

flash_lfq_style_1 –iso

json_extension¶

Exension for .json files

Default value:	.u.json
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for json_extension¶

Style Translation

ucontroller_style_1 json_extension

keep_asp_pro_broken_peps¶

X!tandem searches for peptides broken between Asp (D) and Pro (P) for every enzyme. Therefore, it reports peptides that are not enzymatically cleaved. Specify, if those should be kept during unify_csv or removed.

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

unify_csv_1_0_0

Ursgal key translations for keep_asp_pro_broken_peps¶

Style Translation

unify_csv_style_1 keep_asp_pro_broken_peps

keep_column_names¶

List of column headers which are are not used as identifiers but kept in the output, e.g. when counting [“Sequence”, “Modifications”] the column [“Protein ID”] could be specified here. Multiple entries for one identifier (e.g. when identifier_column_names = [“Potein ID”] and keep_column_names = [“Sequence”]) are seperated by “<#>”.

Default value:	[‘Protein ID’]
type:	list
triggers rerun:	True

Available in unodes¶

csv2counted_results_1_0_0

Ursgal key translations for keep_column_names¶

Style Translation

csv2counted_results_style_1 keep_column_names

kernel¶

The kernel function of the support vector machine used for PSM post-processing (‘rbf’, ‘linear’, ‘poly’ or ‘sigmoid’)

Default value:	rbf
type:	select
triggers rerun:	True

Available in unodes¶

svm_1_0_0

Ursgal key translations for kernel¶

Style Translation

svm_style_1 kernel

kojak_diff_mods_on_xl¶

To search differential modifications on cross-linked peptides: diff_mods_on_xl = 1

Default value:	0
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_diff_mods_on_xl¶

Style Translation

kojak_style_1 kojak_diff_mods_on_xl

kojak_enrichment¶

Values between 0 and 1 to describe 18O APE For example, 0.25 equals 25 APE

Default value:	0
type:	float
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_enrichment¶

Style Translation

kojak_style_1 kojak_enrichment

kojak_export_pepxml¶

Activate (True) or deactivate (False) output as pepXML

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_export_pepxml¶

Style Translation

kojak_style_1 kojak_export_pepXML

Ursgal value translations¶

Ursgal Value Translated Value

. kojak_style_1

0 0

1 1

kojak_export_percolator¶

Activate (True) or deactivate (False) output for percolator

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_export_percolator¶

Style Translation

kojak_style_1 kojak_export_percolator

Ursgal value translations¶

Ursgal Value Translated Value

. kojak_style_1

0 0

1 1

kojak_fragment_bin_offset¶

fragment_bin_offset and fragment_bin_size influence algorithm precision and memory usage. They should be set appropriately for the data analyzed. For ion trap ms/ms: 1.0005 size, 0.4 offset For high res ms/ms: 0.03 size, 0.0 offset

Default value:	0.0
type:	float
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_fragment_bin_offset¶

Style Translation

kojak_style_1 kojak_fragment_bin_offset

kojak_fragment_bin_size¶

fragment_bin_offset and fragment_bin_size influence algorithm precision and memory usage. They should be set appropriately for the data analyzed. For ion trap ms/ms: 1.0005 size, 0.4 offset For high res ms/ms: 0.03 size, 0.0 offset

Default value:	0.03
type:	float
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_fragment_bin_size¶

Style Translation

kojak_style_1 kojak_fragment_bin_size

kojak_mono_links_on_xl¶

To search for mono-linked cross-linker on cross-linked peptides: mono_links_on_xl = 1

Default value:	0
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_mono_links_on_xl¶

Style Translation

kojak_style_1 kojak_mono_links_on_xl

kojak_percolator_version¶

Defines the output format of Kojak for Percolator

Default value:	2.08
type:	str
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_percolator_version¶

Style Translation

kojak_style_1 kojak_percolator_version

kojak_prefer_precursor_pred¶

prefer precursor mono mass predicted by instrument software. Available values:

ignore_previous: previous predictions are ignored

only_previous: only previous predictions are used

supplement: predictions are supplemented with additional analysis

Default value:	supplement
type:	select
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_prefer_precursor_pred¶

Style Translation

kojak_style_1 kojak_prefer_precursor_pred

Ursgal value translations¶

Ursgal Value Translated Value

. kojak_style_1

ignore_previous 0

only_previous 1

supplement 2

kojak_spectrum_processing¶

True, if spectrum should be processed by kojak

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_spectrum_processing¶

Style Translation

kojak_style_1 kojak_spectrum_processing

Ursgal value translations¶

Ursgal Value Translated Value

. kojak_style_1

0 0

1 1

kojak_top_count¶

number of top scoring single peptides to combine in relaxed analysis

Default value:	300
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_top_count¶

Style Translation

kojak_style_1 kojak_top_count

kojak_turbo_button¶

Generally speeds up analysis. Special cases cause reverse effect, thus this is allowed to be disabled. True if it should be used.

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for kojak_turbo_button¶

Style Translation

kojak_style_1 kojak_turbo_button

Ursgal value translations¶

Ursgal Value Translated Value

. kojak_style_1

0 0

1 1

label¶

15N if the corresponding amino acid labeling was applied

Default value:	14N
type:	select
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
pyqms_1_0_0

Ursgal key translations for label¶

Style Translation

moda_style_1 label

msamanda_style_1 label

msfragger_style_1 label

msfragger_style_2 label

msfragger_style_3 label

msgfplus_style_1 label

myrimatch_style_1 label

omssa_style_1 (‘-tem’, ‘-tom’)

pipi_style_1 15N

pyqms_style_1 label

xtandem_style_1 protein, modified residue mass file

Ursgal value translations¶

Ursgal Value Translated Value

. pipi_style_1

14N 0

15N 1

label_percentile¶

Enrichment level of the label

Default value:	[0.0]
type:	list
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0

Ursgal key translations for label_percentile¶

Style Translation

pyqms_style_1 label_percentile

label_percentile_format_string¶

Defines the standard format string when: formatting labeling percentile float

Default value:	{0:.3f}
type:	str
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for label_percentile_format_string¶

Style Translation

pyqms_style_1 PERCENTILE_FORMAT_STRING

sugarpy_plot_style_1 PERCENTILE_FORMAT_STRING

sugarpy_run_style_1 PERCENTILE_FORMAT_STRING

localize_delta_mass¶

Generate and use mass difference fragment index in addition to the regular fragment index for search. This allows shifted fragment ions - fragment ions with mass increased by the calculated mass difference, to be included in scoring.

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for localize_delta_mass¶

Style Translation

msfragger_style_1 localize_delta_mass

msfragger_style_2 localize_delta_mass

msfragger_style_3 localize_delta_mass

Ursgal value translations¶

Ursgal Value Translated Value

. msfragger_style_1 msfragger_style_2 msfragger_style_3

0 0 0 0

1 1 1 1

lower_mz_limit¶

lowest considered mz for quantification

Default value:	150
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for lower_mz_limit¶

Style Translation

pyqms_style_1 LOWER_MZ_LIMIT

sugarpy_plot_style_1 LOWER_MZ_LIMIT

sugarpy_run_style_1 LOWER_MZ_LIMIT

m_score_cutoff¶

minimum required pyQms m_score for a quant event to be evaluated

Default value:	0.7
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for m_score_cutoff¶

Style Translation

pyqms_style_1 M_SCORE_THRESHOLD

sugarpy_plot_style_1 M_SCORE_THRESHOLD

sugarpy_run_style_1 M_SCORE_THRESHOLD

machine_offset_in_ppm¶

Machine offset, m/z values will be corected/shifted by the given value.

Default value:	0.0
type:	float
triggers rerun:	True

Available in unodes¶

mzml2mgf_1_0_0
mzml2mgf_2_0_0
pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for machine_offset_in_ppm¶

Style Translation

mzml2mgf_style_1 machine_offset_in_ppm

pyqms_style_1 MACHINE_OFFSET_IN_PPM

sugarpy_plot_style_1 MACHINE_OFFSET_IN_PPM

sugarpy_run_style_1 MACHINE_OFFSET_IN_PPM

markov_chain_burn_in_iterations¶

number of markov-chain monte carlo burn in iterations for the Bayesian protein fold-change analysis

Default value:	1000
type:	int
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for markov_chain_burn_in_iterations¶

Style Translation

flash_lfq_style_1 –bur

markov_chain_iterations¶

number of markov-chain monte carlo iterations for the Bayesian protein fold-change analysis

Default value:	3000
type:	int
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for markov_chain_iterations¶

Style Translation

flash_lfq_style_1 –mcm

mass_diff_bin_size¶

Number of bins per dalton to be used for mass shift binning. That means 5000 bins correspond to a bin size of 0.0002 Da

Default value:	5000
type:	int
triggers rerun:	True

Available in unodes¶

ptmshepherd_0_3_5

Ursgal key translations for mass_diff_bin_size¶

Style Translation

ptmshepherd_style_1 histo_bindivs

mass_offset_list¶

List of mass offsets at which modification peaks will be checked for (e.g. [0, 79.9663])

Default value:	[]
type:	list
triggers rerun:	True

Available in unodes¶

ptmshepherd_0_3_5

Ursgal key translations for mass_offset_list¶

Style Translation

ptmshepherd_style_1 mass_offsets

match_between_runs¶

Quantify PSMs identified in other runs

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for match_between_runs¶

Style Translation

flash_lfq_style_1 –mbr

match_between_runs_RT_window¶

Max RT differenence in minutes of peptides to be considered for MBR

Default value:	1
type:	float
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for match_between_runs_RT_window¶

Style Translation

flash_lfq_style_1 –mrt

max_accounted_observed_peaks¶

Maximum number of peaks from a spectrum used.

Default value:	150
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
myrimatch_2_1_138
myrimatch_2_2_140
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
deepnovo_pointnovo
ptmshepherd_0_3_5

Ursgal key translations for max_accounted_observed_peaks¶

Style Translation

deepnovo_style_1 MAX_NUM_PEAK

kojak_style_1 max_accounted_observed_peaks

msfragger_style_1 use_topN_peaks

msfragger_style_2 use_topN_peaks

msfragger_style_3 use_topN_peaks

myrimatch_style_1 MaxPeakCount

ptmshepherd_style_1 spectra_condPeaks

xtandem_style_1 spectrum, total peaks

max_glycan_length¶

Maximum number of monosaccharides per glycan

Default value:	15
type:	int
triggers rerun:	False

Available in unodes¶

sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for max_glycan_length¶

Style Translation

sugarpy_plot_style_1 max_tree_length

sugarpy_run_style_1 max_tree_length

max_missed_cleavages¶

Maximum number of missed cleavages per peptide

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
unify_csv_1_0_0
upeptide_mapper_1_0_0
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
pglyco_db_2_2_0
pglyco_db_2_2_2
deepnovo_0_0_1

Ursgal key translations for max_missed_cleavages¶

Style Translation

deepnovo_style_1 num_missed_cleavage

kojak_style_1 max_missed_cleavages

moda_style_1 MissedCleavage

msamanda_style_1 missed_cleavages

msfragger_style_1 allowed_missed_cleavage

msfragger_style_2 allowed_missed_cleavage

msfragger_style_3 allowed_missed_cleavage

msgfplus_style_1 -maxMissedCleavages

myrimatch_style_1 MaxMissedCleavages

omssa_style_1 -v

pglyco_db_style_1 max_miss_cleave

pipi_style_1 missed_cleavage

unify_csv_style_1 max_missed_cleavages

upeptide_mapper_style_1 max_missed_cleavages

xtandem_style_1 scoring, maximum missed cleavage sites

max_mod_alternatives¶

Maximal number of variable modification alternatives, given as C in 2^C

Default value:	6
type:	int
triggers rerun:	True

Available in unodes¶

xtandem_vengeance
xtandem_alanine

Ursgal key translations for max_mod_alternatives¶

Style Translation

xtandem_style_1 protein, ptm complexity

max_mod_size¶

Maximum modification size to consider (in Da)

Default value:	200
type:	int
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62
pipi_1_4_5
pipi_1_4_6
ptminer_1_0

Ursgal key translations for max_mod_size¶

Style Translation

moda_style_1 MaxModSize

pipi_style_1 max_ptm_mass

ptminer_style_1 precursor_matching_tolerance

max_molecules_per_match_bin¶

Max number of molecules in one matching bin.

Default value:	5000
type:	int
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for max_molecules_per_match_bin¶

Style Translation

pyqms_style_1 MAX_MOLECULES_PER_MATCH_BIN

sugarpy_plot_style_1 MAX_MOLECULES_PER_MATCH_BIN

sugarpy_run_style_1 MAX_MOLECULES_PER_MATCH_BIN

max_num_mod_sites¶

Maximum number of potential modification sites for a specific modification per peptide. Peptides with a higher number are discarded, due to a too high complexity.

Default value:	6
type:	int
triggers rerun:	True

Available in unodes¶

msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665

Ursgal key translations for max_num_mod_sites¶

Style Translation

msamanda_style_1 MaxNumberModSites

max_num_mods¶

Maximal number of modifications per peptide

Default value:	3
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
msamanda_2_0_0_9695
msamanda_2_0_0_9706
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
pglyco_db_2_2_0
pglyco_db_2_2_2

Ursgal key translations for max_num_mods¶

Style Translation

kojak_style_1 max_num_mods

msamanda_style_1 MaxNoDynModifs

msgfplus_style_1 NumMods

myrimatch_style_1 MaxDynamicMods

pglyco_db_style_1 max_var_modify_num

max_num_neutral_loss¶

Maximum number of same neutral losses per peptide regarding water and ammonia losses.

Default value:	1
type:	int
triggers rerun:	True

Available in unodes¶

msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665

Ursgal key translations for max_num_neutral_loss¶

Style Translation

msamanda_style_1 MaxNumberNeutralLoss

max_num_neutral_loss_mod¶

Maximum number of same neutral losses per peptide regarding modification specific losses.

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665

Ursgal key translations for max_num_neutral_loss_mod¶

Style Translation

msamanda_style_1 MaxNumberNeutralLossModificati

max_num_of_ions_per_series_to_search¶

Max number of ions in each series being searched: 0 : all

Default value:	0
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for max_num_of_ions_per_series_to_search¶

Style Translation

omssa_style_1 -sp

Ursgal value translations¶

Ursgal Value Translated Value

. omssa_style_1

all 0

max_num_per_mod¶

Maximum number of residues that can be occupied by each variable modification (maximum of 5)

Default value:	3
type:	int
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665

Ursgal key translations for max_num_per_mod¶

Style Translation

msamanda_style_1 MaxNoModifs

msfragger_style_1 max_variable_mods_per_mod

msfragger_style_2 max_variable_mods_per_mod

msfragger_style_3 max_variable_mods_per_peptide

max_num_per_mod_name_specific¶

Maximal number of modification sites per peptide for a specific modification, given as a dictionary:: {unimod_name : number}

Default value:	[]
type:	dict
triggers rerun:	True

Available in unodes¶

xtandem_vengeance
xtandem_alanine

Ursgal key translations for max_num_per_mod_name_specific¶

Style Translation

xtandem_style_1 residue, potential modification mass

max_num_psms_per_spec¶

Maximum number of PSMs retained per spectrum

Default value:	30
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9
sanitize_csv_1_0_0

Ursgal key translations for max_num_psms_per_spec¶

Style Translation

omssa_style_1 -hl

sanitize_csv_style_1 max_output_psms

max_num_substring_mod_pep¶

Maximum number of times a de novo-produced substring can occur in the protein sequence database for TagGraph to consider it as a modified peptide match

Default value:	200
type:	int
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for max_num_substring_mod_pep¶

Style Translation

tag_graph_style_1 modmaxcounts

max_num_substring_pep¶

Maximum number of times a de novo-produced substring can occur in the protein sequence database for TagGraph to consider it as a modified peptide match

Default value:	400
type:	int
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for max_num_substring_pep¶

Style Translation

tag_graph_style_1 maxcounts

max_output_e_value¶

Highest e-value for reported peptides

Default value:	1.0
type:	float
triggers rerun:	True

Available in unodes¶

omssa_2_1_9
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for max_output_e_value¶

Style Translation

omssa_style_1 -he

xtandem_style_1 output, maximum valid expectation value

max_pep_length¶

Maximal length of a peptide

Default value:	40
type:	int
triggers rerun:	True

Available in unodes¶

msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
pglyco_db_2_2_0
pglyco_db_2_2_2

Ursgal key translations for max_pep_length¶

Style Translation

msfragger_style_1 digest_max_length

msfragger_style_2 digest_max_length

msfragger_style_3 digest_max_length

msgfplus_style_1 -maxLength

myrimatch_style_1 MaxPeptideLength

omssa_style_1 -nox

pglyco_db_style_1 max_peptide_len

pipi_style_1 max_peptide_length

max_pep_var¶

Maximal peptide variants, new default defined by msfragger

Default value:	1000
type:	int
triggers rerun:	True

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for max_pep_var¶

Style Translation

msfragger_style_1 max_variable_mods_combinations

msfragger_style_2 max_variable_mods_combinations

msfragger_style_3 max_variable_mods_combinations

msgfplus_style_1 -maxLength

myrimatch_style_1 MaxPeptideVariants

omssa_style_1 -nox

max_protein_name¶

Max protein name for output. For kojak, this defines the number of character (0=off), for TagGraph the number of protein names

Default value:	5
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
tag_graph_1_8_0

Ursgal key translations for max_protein_name¶

Style Translation

kojak_style_1 kojak_truncate_prot_names

tag_graph_style_1 DisplayProtNum

max_trees_per_spec¶

Max number of glycoforms reported per spectrum for each peptide

Default value:	5
type:	int
triggers rerun:	True

Available in unodes¶

sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for max_trees_per_spec¶

Style Translation

sugarpy_plot_style_1 max_trees_per_spec

sugarpy_run_style_1 max_trees_per_spec

mgf_input_file¶

Path to input .mgf file: ‘’ : None

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

deepnovo_0_0_1
moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
novor_1_1beta
novor_1_05
omssa_2_1_9
pepnovo_3_1
pglyco_db_2_2_0
pglyco_db_2_2_2
pnovo_3_1_3
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for mgf_input_file¶

Style Translation

deepnovo_style_1 (‘denovo_input_file’, ‘hybrid_input_file’, ‘db_input_file’)

moda_style_1 Spectra

msamanda_style_1 mgf_input_file

msgfplus_style_1 -s

novor_style_1 -f

omssa_style_1 -fm

pepnovo_style_1 -file

pglyco_db_style_1 file1

pnovo_style_1 spec_path1

xtandem_style_1 spectrum, path

mgf_input_files_list¶

List of paths to input .mgf files: ‘’ : None

Default value:	None
type:	list
triggers rerun:	True

Available in unodes¶

ptminer_1_0

Ursgal key translations for mgf_input_files_list¶

Style Translation

ptminer_style_1 mgf_input_files_list

min_element_abundance¶

Set minmal abundance for elements used when building isotopologue library

Default value:	0.001
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for min_element_abundance¶

Style Translation

pyqms_style_1 ELEMENT_MIN_ABUNDANCE

sugarpy_plot_style_1 ELEMENT_MIN_ABUNDANCE

sugarpy_run_style_1 ELEMENT_MIN_ABUNDANCE

min_glycan_length¶

Minimum number of monosaccharides per glycan

Default value:	3
type:	int
triggers rerun:	False

Available in unodes¶

sugarpy_run_1_0_0

Ursgal key translations for min_glycan_length¶

Style Translation

sugarpy_run_style_1 min_tree_length

min_mod_size¶

Minimum modification size to consider (in Da)

Default value:	-200
type:	int
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62
pipi_1_4_5
pipi_1_4_6
ptminer_1_0

Ursgal key translations for min_mod_size¶

Style Translation

moda_style_1 MinModSize

pipi_style_1 min_ptm_mass

ptminer_style_1 precursor_matching_tolerance

min_num_mods¶

Minimal number of modifications per peptide

Default value:	5
type:	int
triggers rerun:	True

Available in unodes¶

ptminer_1_0

Ursgal key translations for min_num_mods¶

Style Translation

ptminer_style_1 min_mod_number

min_number_of_matched_isotopologues¶

Min number of matched isotopologues to consider for quantification

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
flash_lfq_1_1_1

Ursgal key translations for min_number_of_matched_isotopologues¶

Style Translation

flash_lfq_style_1 –nis

pyqms_style_1 MINIMUM_NUMBER_OF_MATCHED_ISOTOPOLOGUES

sugarpy_plot_style_1 MINIMUM_NUMBER_OF_MATCHED_ISOTOPOLOGUES

sugarpy_run_style_1 MINIMUM_NUMBER_OF_MATCHED_ISOTOPOLOGUES

min_number_of_spectra¶

Min number of spectra in which a molecule needs to be matched in order to consider it for further processing

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for min_number_of_spectra¶

Style Translation

sugarpy_plot_style_1 min_spec_number

sugarpy_run_style_1 min_spec_number

min_output_score¶

Lowest score for reported peptides. If set to ‘-1e-10’, default values fo each engine will be used.: -1e-10 = ‘default’

Default value:	-1e-10
type:	float
triggers rerun:	True

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140
pepnovo_3_1

Ursgal key translations for min_output_score¶

Style Translation

myrimatch_style_1 MinResultScore

pepnovo_style_1 -min_filter_prob

Ursgal value translations¶

Ursgal Value Translated Value

. myrimatch_style_1 pepnovo_style_1

-1e-10 1e-07 0.9

min_oxonium_ions¶

Min number of oxonium ions that need to be matched in an MS/MS spectrum, to be accepted as containing oxonium ions (i.e. considered as glycopeptide)

Default value:	3
type:	int
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0
glycopeptide_fragmentor_1_0_0

Ursgal key translations for min_oxonium_ions¶

Style Translation

glycopeptide_fragmentor_style_1 min_oxonium_ions

sugarpy_plot_style_1 min_oxonium_ions

min_pep_length¶

Minimal length of a peptide

Default value:	6
type:	int
triggers rerun:	True

Available in unodes¶

msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
pipi_1_4_5
pipi_1_4_6
pglyco_db_2_2_0
pglyco_db_2_2_2

Ursgal key translations for min_pep_length¶

Style Translation

msamanda_style_1 MinimumPepLength

msfragger_style_1 digest_min_length

msfragger_style_2 digest_min_length

msfragger_style_3 digest_min_length

msgfplus_style_1 -minLength

myrimatch_style_1 MinPeptideLength

omssa_style_1 -no

pglyco_db_style_1 min_peptide_len

pipi_style_1 min_peptide_length

min_precursor_matches¶

Minimum number of precursors that match a spectrum.

Default value:	1
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for min_precursor_matches¶

Style Translation

omssa_style_1 -pc

min_required_matched_peaks¶

Mimimum number of matched ions required for a peptide to be scored, MSFragger default: 4

Default value:	4
type:	int
triggers rerun:	True

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for min_required_matched_peaks¶

Style Translation

msfragger_style_1 min_matched_fragments

msfragger_style_2 min_matched_fragments

msfragger_style_3 min_matched_fragments

myrimatch_style_1 MinMatchedFragments

omssa_style_1 -hm

xtandem_style_1 scoring, minimum ion count

min_required_observed_peaks¶

Mimimum number of peaks in the spectrum to be considered. MSFragger default: 15

Default value:	5
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for min_required_observed_peaks¶

Style Translation

msfragger_style_1 minimum_peaks

msfragger_style_2 minimum_peaks

msfragger_style_3 minimum_peaks

omssa_style_1 -hs

xtandem_style_1 spectrum, minimum peaks

min_subtree_coverage¶

Min subtree coverage to be considered for output

Default value:	0.6
type:	float
triggers rerun:	True

Available in unodes¶

sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for min_subtree_coverage¶

Style Translation

sugarpy_plot_style_1 min_sub_cov

sugarpy_run_style_1 min_sub_cov

min_sugarpy_score¶

Min SugarPy score to be considered for output

Default value:	1.0
type:	float
triggers rerun:	True

Available in unodes¶

sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for min_sugarpy_score¶

Style Translation

sugarpy_plot_style_1 min_sugarpy_score

sugarpy_run_style_1 min_sugarpy_score

min_y_ions¶

Min number of Y-ions that need to be matched in an MS/MS spectrum, to be accepted as containing Y-ions (i.e. considered as glycopeptide)

Default value:	1
type:	int
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0
glycopeptide_fragmentor_1_0_0

Ursgal key translations for min_y_ions¶

Style Translation

glycopeptide_fragmentor_style_1 min_Y_ions

sugarpy_plot_style_1 min_Y_ions

moda_blind_mode¶

Allowed number of modifications per peptide in ModA BlindMode. Available values: no_modification

one_modification no_limit

Default value:	no_limit
type:	select
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62

Ursgal value translations¶

Ursgal Value Translated Value

. moda_style_1

no_limit 2

no_modification 0

one_modification 1

moda_high_res¶

If True, fragment tolerance is set as the same as precursor tolerance, when the peptide mass is significantly small, such that fragment tolerance is larger than precursor tolerance

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62

Ursgal key translations for moda_high_res¶

Style Translation

moda_style_1 HighResolution

Ursgal value translations¶

Ursgal Value Translated Value

. moda_style_1

0 OFF

1 ON

moda_protocol_id¶

MODa specific protocol to enable scoring parameters for labeled samples.

Default value:	None
type:	select
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62

Ursgal key translations for moda_protocol_id¶

Style Translation

moda_style_1 Protocol

Ursgal value translations¶

Ursgal Value Translated Value

. moda_style_1

None NONE

modification_mass_tolerance¶

Maximum absolute deviation (Da) between experimental and database modification mass

Default value:	0.1
type:	float
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for modification_mass_tolerance¶

Style Translation

tag_graph_style_1 modtolerance

modifications¶

Modifications are given as a list of strings, each representing the modification of one amino acid. The string consists of four informations seperated by comma:

‘amino acid, type, position, unimod name or id’

amino acid : specify the modified amino acid as a single letter, use ‘*’ if the amino acid is variable type : specify if it is a fixed (fix) or potential (opt) modification position : specify the position within the protein/peptide (Prot-N-term, Prot-C-term), use ‘any’ if the positon is variable unimod name or id: specify the unimod PSI-MS Name or unimod Accession # (see unimod.org)

Examples:

[ ‘M,opt,any,Oxidation’ ] - potential oxidation of Met at any position within a peptide [ ‘*,opt,Prot-N-term,Acetyl’ ] - potential acetylation of any amino acid at the N-terminus of a protein [ ‘S,opt,any,Phospho’ ] - potential phosphorylation of Serine at any position within a peptide [ ‘C,fix,any,Carbamidomethyl’, ‘N,opt,any,Deamidated’, ‘Q,opt,any,Deamidated’ ] - fixed carbamidomethylation of Cys and potential deamidation of Asn and/or Gln at any position within a peptide

Additionally, userdefined modifications can be given and are written to a userdefined_unimod.xml in ursgal/kb/ext. Userdefined modifications need to have a unique name instead of the unimod name the chemical composition needs to be given as a Hill notation on the fifth position in the string

Example:

[ ‘S,opt,any,New_mod,C2H5N1O3’ ]

Default value:	[’*,opt,Prot-N-term,Acetyl’, ‘M,opt,any,Oxidation’]
type:	list
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
novor_1_1beta
novor_1_05
omssa_2_1_9
pepnovo_3_1
unify_csv_1_0_0
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
pyqms_1_0_0
pglyco_db_2_2_0
ptminer_1_0
pglyco_db_2_2_2
deepnovo_0_0_1
pnovo_3_1_3
tag_graph_1_8_0
flash_lfq_1_1_1
ptmshepherd_0_3_5

Ursgal key translations for modifications¶

Style Translation

deepnovo_style_1 modifications

flash_lfq_style_1 modifications

kojak_style_1 modifications

moda_style_1 ADD

msamanda_style_1 modifications

msfragger_style_1 modifications

msfragger_style_2 modifications

msfragger_style_3 modifications

msgfplus_style_1 -mod

myrimatch_style_1 (‘DynamicMods’, ‘StaticMods’)

novor_style_1 (‘variableModifications’, ‘fixedModifications’)

omssa_style_1 (‘-mv’, ‘mf’)

pepnovo_style_1 -PTMs

pglyco_db_style_1 modifications

pipi_style_1 modifications

pnovo_style_1 modifications

ptminer_style_1 modifications

ptmshepherd_style_1 varmod_masses

pyqms_style_1 modifications

tag_graph_style_1 modifications

unify_csv_style_1 modifications

xtandem_style_1 (‘residue, modification mass’, ‘residue, potential modification mass’, ‘protein, N-terminal residue modification mass’, ‘protein, C-terminal residue modification mass’, ‘protein, C-terminal residue modification mass’, ‘protein, quick acetyl’, ‘protein, quick pyrolidone’)

modifications_offsets¶

Specify molecules (or masses) that will be used as mass offsets in the search. Specify as a dictionary with the keys “chemical_formulas”, “unimods”, “glycans”, “masses”, and lists with the corresponding molecules as values.

Default value:	[‘chemical_formulas’, ‘glycans’, ‘masses’, ‘unimods’]
type:	dict
triggers rerun:	True

Available in unodes¶

msfragger_3_0

Ursgal key translations for modifications_offsets¶

Style Translation

msfragger_style_3 mass_offsets

modifications_y_ion_offsets¶

Specify molecules (or masses) that will be used as mass offsets for Y-ions in the search. Specify as a dictionary with the keys “chemical_formulas”, “unimods”, “glycans”, “masses”, and lists with the corresponding molecules as values.

Default value:	[‘chemical_formulas’, ‘glycans’, ‘masses’, ‘unimods’]
type:	dict
triggers rerun:	True

Available in unodes¶

msfragger_3_0

Ursgal key translations for modifications_y_ion_offsets¶

Style Translation

msfragger_style_3 Y_type_masses

molecules_to_quantify¶

Molecules to quantify. Can be either a list of strings or a csv file

Default value:	None
type:	list
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0

Ursgal key translations for molecules_to_quantify¶

Style Translation

pyqms_style_1 molecules

mono_link_definition¶

Cross-link and mono-link masses allowed. May have more than one of each parameter. Format for mono_link is:

[amino acids] [mass mod]

One or more amino acids (uppercase only!!) can be specified for each linkage moiety. Use lowercase ‘n’ or ‘c’ to indicate protein N-terminus or C-terminus

Default value:	nK 156.0786
type:	str
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for mono_link_definition¶

Style Translation

kojak_style_1 mono_link_definition

monosaccharide_compositions¶

Dictionary defining the chemical formula (hill notation) for each monosaccharide that is used.

Default value:	[‘Hex’, ‘HexNAc’, ‘NeuAc’, ‘Pent’, ‘dHex’]
type:	dict
triggers rerun:	True

Available in unodes¶

sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for monosaccharide_compositions¶

Style Translation

sugarpy_plot_style_1 monosaccharides

sugarpy_run_style_1 monosaccharides

ms1_is_centroided¶

MS1 are centroided data: True or False

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for ms1_is_centroided¶

Style Translation

kojak_style_1 kojak_MS1_centroid

Ursgal value translations¶

Ursgal Value Translated Value

. kojak_style_1

0 0

1 1

ms1_resolution¶

MS1 resolution

Default value:	30000
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for ms1_resolution¶

Style Translation

kojak_style_1 kojak_MS1_resolution

ms2_is_centroided¶

MS2 are centroided data: True or False

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for ms2_is_centroided¶

Style Translation

kojak_style_1 kojak_MS2_centroid

Ursgal value translations¶

Ursgal Value Translated Value

. kojak_style_1

0 0

1 1

ms2_resolution¶

MS2 resolution

Default value:	25000
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3

Ursgal key translations for ms2_resolution¶

Style Translation

kojak_style_1 kojak_MS2_resolution

ms_level¶

MS level on which that is taken into account, e.g. for spectrum extraction, matching of evidences, etc.

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
mzml2mgf_1_0_0
mzml2mgf_2_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
pipi_1_4_5
pipi_1_4_6

Ursgal key translations for ms_level¶

Style Translation

mzml2mgf_style_1 ms_level

pipi_style_1 ms_level

pyqms_style_1 ms_level

sugarpy_plot_style_1 ms_level

sugarpy_run_style_1 ms_level

msfragger_add_topN_complementary¶

Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum. Useful for recovery of modified peptides near C-terminal in open search. Should be set to 0 (disabled) otherwise.

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for msfragger_add_topN_complementary¶

Style Translation

msfragger_style_1 add_topN_complementary

msfragger_style_2 add_topN_complementary

msfragger_style_3 add_topN_complementary

Ursgal value translations¶

Ursgal Value Translated Value

. msfragger_style_1 msfragger_style_2 msfragger_style_3

0 0 0 0

1 1 1 1

msfragger_labile_mode¶

“off” corresponds to a standard MSFragger search, “labile” allows to specify delta masses that are searched for, and “nglycan” additionally checks for N-glycosylation motifs

Default value:	off
type:	select
triggers rerun:	True

Available in unodes¶

msfragger_3_0

Ursgal key translations for msfragger_labile_mode¶

Style Translation

msfragger_style_3 labile_search_mode

msfragger_min_fragments_modelling¶

Minimum number of matched peaks in PSM for inclusion in statistical modeling

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for msfragger_min_fragments_modelling¶

Style Translation

msfragger_style_1 min_fragments_modelling

msfragger_style_2 min_fragments_modelling

msfragger_style_3 min_fragments_modelling

msfragger_output_max_expect¶

Suppresses reporting of PSM if top hit has expectation greater than this threshold

Default value:	50
type:	int
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for msfragger_output_max_expect¶

Style Translation

msfragger_style_1 output_max_expect

msfragger_style_2 output_max_expect

msfragger_style_3 output_max_expect

msfragger_track_zero_topN¶

Track top N unmodified peptide results separately from main results internally for boosting features. Should be set to a number greater than output_report_topN if zero bin boosting is desired.

Default value:	0
type:	int
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for msfragger_track_zero_topN¶

Style Translation

msfragger_style_1 track_zero_topN

msfragger_style_2 track_zero_topN

msfragger_style_3 track_zero_topN

msfragger_zero_bin_accept_expect¶

Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value.

Default value:	0.0
type:	float
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for msfragger_zero_bin_accept_expect¶

Style Translation

msfragger_style_1 zero_bin_accept_expect

msfragger_style_2 zero_bin_accept_expect

msfragger_style_3 zero_bin_accept_expect

msfragger_zero_bin_mult_expect¶

Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)

Default value:	1.0
type:	float
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for msfragger_zero_bin_mult_expect¶

Style Translation

msfragger_style_1 zero_bin_mult_expect

msfragger_style_2 zero_bin_mult_expect

msfragger_style_3 zero_bin_mult_expect

msgfplus_mzid_converter_version¶

Determines which msgfplus mzid conversion node should be used e.g. “msgfplus2csv_v2017_07_04”

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for msgfplus_mzid_converter_version¶

Style Translation

ucontroller_style_1 msgfplus_mzid_converter_version

Ursgal value translations¶

Ursgal Value Translated Value

. ucontroller_style_1

msgfplus_v2016_09_16 msgfplus2csv_py_v1_0_0

msgfplus_v2017_01_27 msgfplus2csv_py_v1_0_0

msgfplus_v2018_01_30 msgfplus2csv_py_v1_0_0

msgfplus_v2018_06_28 msgfplus2csv_py_v1_0_0

msgfplus_v2018_09_12 msgfplus2csv_py_v1_0_0

msgfplus_v2019_01_22 msgfplus2csv_py_v1_0_0

msgfplus_v2019_04_18 msgfplus2csv_py_v1_0_0

msgfplus_v2019_07_03 msgfplus2csv_py_v1_0_0

msgfplus_v9979 msgfplus2csv_py_v1_0_0

msgfplus_protocol_id¶

MS-GF+ specific protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples.

Default value:	0
type:	select
triggers rerun:	True

Available in unodes¶

msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979

Ursgal key translations for msgfplus_protocol_id¶

Style Translation

msgfplus_style_1 -protocol

Ursgal value translations¶

Ursgal Value Translated Value

. msgfplus_style_1

0 0

1 1

2 2

3 3

myrimatch_class_size_multiplier¶

Myrimatch ClassSizeMultiplier

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140

Ursgal key translations for myrimatch_class_size_multiplier¶

Style Translation

myrimatch_style_1 ClassSizeMultiplier

myrimatch_num_int_classes¶

Myrimatch NumIntensityClasses

Default value:	3
type:	int
triggers rerun:	True

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140

Ursgal key translations for myrimatch_num_int_classes¶

Style Translation

myrimatch_style_1 NumIntensityClasses

myrimatch_num_mz_fidelity_classes¶

Myrimatch NumMzFidelityClasses

Default value:	3
type:	int
triggers rerun:	True

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140

Ursgal key translations for myrimatch_num_mz_fidelity_classes¶

Style Translation

myrimatch_style_1 NumMzFidelityClasses

myrimatch_prot_sampl_time¶

Myrimatch ProteinSamplingTime

Default value:	15
type:	int
triggers rerun:	True

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140

Ursgal key translations for myrimatch_prot_sampl_time¶

Style Translation

myrimatch_style_1 ProteinSamplingTime

myrimatch_smart_plus_three¶

Use Myrimatch UseSmartPlusThreeModel

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140

Ursgal key translations for myrimatch_smart_plus_three¶

Style Translation

myrimatch_style_1 UseSmartPlusThreeModel

Ursgal value translations¶

Ursgal Value Translated Value

. myrimatch_style_1

0 0

1 1

myrimatch_tic_cutoff¶

Myrimatch TicCutoffPercentage

Default value:	0.98
type:	float
triggers rerun:	True

Available in unodes¶

myrimatch_2_1_138
myrimatch_2_2_140

Ursgal key translations for myrimatch_tic_cutoff¶

Style Translation

myrimatch_style_1 TicCutoffPercentage

mz_score_percentile¶

weighting factor for pyQms mz score

Default value:	0.4
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for mz_score_percentile¶

Style Translation

pyqms_style_1 MZ_SCORE_PERCENTILE

sugarpy_plot_style_1 MZ_SCORE_PERCENTILE

sugarpy_run_style_1 MZ_SCORE_PERCENTILE

mz_transformation_factor¶

Factor which will be multiplied with mz before conversion to integer

Default value:	1000
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for mz_transformation_factor¶

Style Translation

pyqms_style_1 MZ_TRANSFORMATION_FACTOR

sugarpy_plot_style_1 MZ_TRANSFORMATION_FACTOR

sugarpy_run_style_1 MZ_TRANSFORMATION_FACTOR

mzidentml_compress¶

Compress mzidentml_lib output files

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

mzidentml_lib_1_6_10
mzidentml_lib_1_6_11
mzidentml_lib_1_7

Ursgal key translations for mzidentml_compress¶

Style Translation

mzidentml_style_1 -compress

Ursgal value translations¶

Ursgal Value Translated Value

. mzidentml_style_1

0 false

1 true

mzidentml_converter_version¶

mzidentml converter version: version name

Default value:	mzidentml_lib_1_6_10
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for mzidentml_converter_version¶

Style Translation

ucontroller_style_1 mzidentml_converter_version

mzidentml_export_type¶

Defines which paramters shoul be exporte by mzidentml_lib

Default value:	exportPSMs
type:	select
triggers rerun:	True

Available in unodes¶

mzidentml_lib_1_6_10
mzidentml_lib_1_6_11
mzidentml_lib_1_7

Ursgal key translations for mzidentml_export_type¶

Style Translation

mzidentml_style_1 -exportType

mzidentml_function¶

Defines the mzidentml_lib function to be used. Note: only ‘Mzid2Csv’ is supported so far

Default value:	Mzid2Csv
type:	select
triggers rerun:	True

Available in unodes¶

mzidentml_lib_1_6_10
mzidentml_lib_1_6_11
mzidentml_lib_1_7

Ursgal key translations for mzidentml_function¶

Style Translation

mzidentml_style_1 mzidentml_function

mzidentml_output_fragmentation¶

Include fragmentation in mzidentml_lib output

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

mzidentml_lib_1_6_10
mzidentml_lib_1_6_11
mzidentml_lib_1_7

Ursgal key translations for mzidentml_output_fragmentation¶

Style Translation

mzidentml_style_1 -outputFragmentation

Ursgal value translations¶

Ursgal Value Translated Value

. mzidentml_style_1

0 false

1 true

mzidentml_verbose_output¶

Verbose mzidentml_lib output

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

mzidentml_lib_1_6_10
mzidentml_lib_1_6_11
mzidentml_lib_1_7

Ursgal key translations for mzidentml_verbose_output¶

Style Translation

mzidentml_style_1 -verboseOutput

Ursgal value translations¶

Ursgal Value Translated Value

. mzidentml_style_1

0 false

1 true

mzml2mgf_converter_version¶

mzml to mgf converter version: version name

Default value:	mzml2mgf_2_0_0
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for mzml2mgf_converter_version¶

Style Translation

ucontroller_style_1 mzml2mgf_converter_version

mzml_input_files¶

List of paths to the mzML input files

Default value:	None
type:	list
triggers rerun:	True

Available in unodes¶

sugarpy_run_1_0_0
sugarpy_plot_1_0_0
glycopeptide_fragmentor_1_0_0
ptmshepherd_0_3_5

Ursgal key translations for mzml_input_files¶

Style Translation

glycopeptide_fragmentor_style_1 mzml_file_list

ptmshepherd_style_1 dataset

sugarpy_plot_style_1 mzml_file

sugarpy_run_style_1 mzml_file

neutral_loss_enabled¶

Neutral losses enabled for spectrum algorithm: set True or False

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for neutral_loss_enabled¶

Style Translation

xtandem_style_1 spectrum, use neutral loss window

Ursgal value translations¶

Ursgal Value Translated Value

. xtandem_style_1

0 no

1 yes

neutral_loss_mass¶

Sets the centre of the window for ignoring neutral molecule losses.

Default value:	0
type:	int
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for neutral_loss_mass¶

Style Translation

xtandem_style_1 spectrum, neutral loss mass

neutral_loss_window¶

Neutral loss window: sets the width of the window for ignoring neutral molecule losses.

Default value:	0
type:	int
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for neutral_loss_window¶

Style Translation

xtandem_style_1 spectrum, neutral loss window

noise_suppression_enabled¶

Used noise suppresssion

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer

Ursgal key translations for noise_suppression_enabled¶

Style Translation

xtandem_style_1 spectrum, use noise suppression

Ursgal value translations¶

Ursgal Value Translated Value

. xtandem_style_1

0 no

1 yes

normalize_intensities¶

normalize intensity results

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for normalize_intensities¶

Style Translation

flash_lfq_style_1 –nor

num_bins_for_smoothing¶

Number of bins on each side of a bin that the weight of the bin is smoothed across. This smoothing traces a normal distribution.

Default value:	3
type:	int
triggers rerun:	True

Available in unodes¶

ptmshepherd_0_3_5

Ursgal key translations for num_bins_for_smoothing¶

Style Translation

ptmshepherd_style_1 histo_smoothbins

num_compared_psms¶

Maximum number of PSMs (sorted by score, starting with the best scoring PSM) that are compared

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

sanitize_csv_1_0_0

Ursgal key translations for num_compared_psms¶

Style Translation

sanitize_csv_style_1 num_compared_psms

num_i_decimals¶

Number of decimals for intensity (peak)

Default value:	7
type:	int
triggers rerun:	True

Available in unodes¶

mzml2mgf_1_0_0
mzml2mgf_2_0_0

Ursgal key translations for num_i_decimals¶

Style Translation

mzml2mgf_style_1 number_of_i_decimals

num_match_spec¶

Maximum number of peptide spectrum matches to report for each spectrum

Default value:	10
type:	int
triggers rerun:	True

Available in unodes¶

msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
pepnovo_3_1
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pnovo_3_1_3

Ursgal key translations for num_match_spec¶

Style Translation

msamanda_style_1 max_rank

msfragger_style_1 output_report_topN

msfragger_style_2 output_report_topN

msfragger_style_3 output_report_topN

msgfplus_style_1 -n

myrimatch_style_1 MaxResultRank

omssa_style_1 -hc

pepnovo_style_1 -num_solutions

pnovo_style_1 report_pep

num_mz_decimals¶

Number of decimals for m/z mass

Default value:	7
type:	int
triggers rerun:	True

Available in unodes¶

mzml2mgf_1_0_0
mzml2mgf_2_0_0

Ursgal key translations for num_mz_decimals¶

Style Translation

mzml2mgf_style_1 number_of_mz_decimals

omssa_cp¶

Omssa: eliminate charge reduced precursors in spectra

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_cp¶

Style Translation

omssa_style_1 -cp

Ursgal value translations¶

Ursgal Value Translated Value

. omssa_style_1

0 0

1 1

omssa_h1¶

Omssa: number of peaks allowed in single charge window

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_h1¶

Style Translation

omssa_style_1 -h1

omssa_h2¶

Omssa: number of peaks allowed in double charge window

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_h2¶

Style Translation

omssa_style_1 -h2

omssa_ht¶

Omssa: number of m/z values corresponding to the most intense peaks that must include one match to the theoretical peptide

Default value:	6
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_ht¶

Style Translation

omssa_style_1 -ht

omssa_mm¶

Omssa: the maximum number of mass ladders to generate per database peptide

Default value:	128
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_mm¶

Style Translation

omssa_style_1 -mm

omssa_ta¶

Omssa: automatic mass tolerance adjustment fraction

Default value:	1.0
type:	float
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_ta¶

Style Translation

omssa_style_1 -ta

omssa_tex¶

Omssa: threshold in Da above which the mass of neutron should be added in exact mass search

Default value:	1446.94
type:	float
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_tex¶

Style Translation

omssa_style_1 -tex

omssa_verbose¶

Omssa: verbose info print

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_verbose¶

Style Translation

omssa_style_1 -ni

Ursgal value translations¶

Ursgal Value Translated Value

. omssa_style_1

0

1 -ni

omssa_w1¶

Omssa: single charge window in Da

Default value:	27
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_w1¶

Style Translation

omssa_style_1 -w1

omssa_w2¶

Omssa: double charge window in Da

Default value:	14
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_w2¶

Style Translation

omssa_style_1 -w2

omssa_z1¶

Omssa: fraction of peaks below precursor used to determine if spectrum is charge 1

Default value:	0.95
type:	float
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_z1¶

Style Translation

omssa_style_1 -z1

omssa_zc¶

Should charge plus one be determined algorithmically?

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_zc¶

Style Translation

omssa_style_1 -zc

Ursgal value translations¶

Ursgal Value Translated Value

. omssa_style_1

0 0

1 1

omssa_zcc¶

Omssa: how should precursor charges be determined?, use a range

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_zcc¶

Style Translation

omssa_style_1 -zcc

omssa_zt¶

Minimum precursor charge to start considering multiply charged products

Default value:	3
type:	int
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for omssa_zt¶

Style Translation

omssa_style_1 -zt

only_precursor_charge¶

use only precursor charge state

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for only_precursor_charge¶

Style Translation

flash_lfq_style_1 –chg

output_aa_probs¶

Output probabilities for each amino acid.

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

pepnovo_3_1

Ursgal key translations for output_aa_probs¶

Style Translation

pepnovo_style_1 -output_aa_probs

output_add_features¶

Add features to the output of MSGF+

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979

Ursgal key translations for output_add_features¶

Style Translation

msgfplus_style_1 -addFeatures

Ursgal value translations¶

Ursgal Value Translated Value

. msgfplus_style_1

0 0

1 1

output_cum_probs¶

Output cumulative probabilities.

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

pepnovo_3_1

Ursgal key translations for output_cum_probs¶

Style Translation

pepnovo_style_1 -output_cum_probs

output_file_incl_path¶

Path to output file: ‘None’ : None

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

generate_target_decoy_1_0_0
merge_csvs_1_0_0
moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
mzidentml_lib_1_6_10
mzidentml_lib_1_6_11
mzidentml_lib_1_7
novor_1_1beta
novor_1_05
omssa_2_1_9
pepnovo_3_1
percolator_2_08
percolator_3_2_1
percolator_3_4_0
qvality_2_02
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
venndiagram_1_0_0
venndiagram_1_1_0
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
ptminer_1_0

Ursgal key translations for output_file_incl_path¶

Style Translation

generate_target_decoy_style_1 output_file

merge_csvs_style_1 output

moda_style_1 -o

msamanda_style_1 output_file_incl_path

msgfplus_style_1 -o

myrimatch_style_1 output_file_incl_path

mzidentml_style_1 output_file_incl_path

novor_style_1 output_file_incl_path

omssa_style_1 output_file_incl_path

pepnovo_style_1 output_file_incl_path

percolator_style_1 output_file_incl_path

ptminer_style_1 output_file_incl_path

qvality_style_1 -o

sugarpy_plot_style_1 output_file

sugarpy_run_style_1 output_file

venndiagram_style_1 output_file

xtandem_style_1 output, path

output_file_type¶

Output file type. If set to ‘default’, default output file tzpes for each engine are used. Note: not every file type is supported by every engine and usin non-default types might cause problems during conversion to .csv.

Default value:	default
type:	select
triggers rerun:	True

Available in unodes¶

omssa_2_1_9
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
thermo_raw_file_parser_1_1_2
tag_graph_1_8_0

Ursgal key translations for output_file_type¶

Style Translation

omssa_style_1 (‘-oc’, ‘-ox’)

tag_graph_style_1 generatePepXML

thermo_raw_file_parser_style_1 -f

xtandem_style_1 output, mzid

Ursgal value translations¶

Ursgal Value Translated Value

. omssa_style_1 tag_graph_style_1 thermo_raw_file_parser_style_1 xtandem_style_1

.csv -oc n/t n/t n/t

.mgf n/t n/t 0 n/t

.mzid n/t n/t n/t yes

.mzml n/t n/t 1 n/t

.omx -ox n/t n/t n/t

.pepXML n/t 1 n/t n/t

default -oc 0 1 no

indexed_mzml n/t n/t 2 n/t

parquet n/t n/t 3 n/t

output_prm¶

Only print spectrum graph nodes with scores.

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

pepnovo_3_1

Ursgal key translations for output_prm¶

Style Translation

pepnovo_style_1 -prm

output_prm_norm¶

Prints spectrum graph scores after normalization and removal of negative scores.

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

pepnovo_3_1

Ursgal key translations for output_prm_norm¶

Style Translation

pepnovo_style_1 -prm_norm

output_q_values¶

Output Q-values

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

msgfplus2csv_v2016_09_16
msgfplus2csv_v2017_01_27

Ursgal key translations for output_q_values¶

Style Translation

msgfplus_style_1 -showQValue

Ursgal value translations¶

Ursgal Value Translated Value

. msgfplus_style_1

0 0

1 1

peak_colors¶

The dict defines the colors of “matched”, “unmatched”, “raw” peaks and “labels”

Default value:	[‘labels’, ‘matched’, ‘raw’, ‘unmatched’]
type:	dict
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for peak_colors¶

Style Translation

sugarpy_plot_style_1 peak_colors

pepnovo_tag_length¶

Returns peptide sequences of the specified length (only lengths 3-6 are allowed): 0 : None

Default value:	None
type:	int
triggers rerun:	True

Available in unodes¶

pepnovo_3_1

Ursgal key translations for pepnovo_tag_length¶

Style Translation

pepnovo_style_1 -tag_length

peptide_mapper_class_version¶

version 3 and 4 are the fastest and most memory efficient class versions, version 2 is the classic approach

Default value:	UPeptideMapper_v4
type:	str
triggers rerun:	True

Available in unodes¶

upeptide_mapper_1_0_0

Ursgal key translations for peptide_mapper_class_version¶

Style Translation

upeptide_mapper_style_1 peptide_mapper_class_version

peptide_mapper_converter_version¶

determines which upeptide mapper node should be used

Default value:	upeptide_mapper_1_0_0
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for peptide_mapper_converter_version¶

Style Translation

ucontroller_style_1 peptide_mapper_converter_version

percolator_post_processing¶

Method to assign FDR and PEP to PSMs

Default value:	tdc
type:	select
triggers rerun:	True

Available in unodes¶

percolator_3_2_1
percolator_3_4_0

Ursgal key translations for percolator_post_processing¶

Style Translation

percolator_style_1 (‘-y’, ‘-Y’)

pipi_mz_bin_offset¶

PIPI mz_bin_offset

Default value:	0.0
type:	float
triggers rerun:	True

Available in unodes¶

pipi_1_4_5
pipi_1_4_6

Ursgal key translations for pipi_mz_bin_offset¶

Style Translation

pipi_style_1 mz_bin_offset

plotly_layout¶

The dict defines plotly layout options. Checkout https://plot.ly/python/reference/#layout for all available options

Default value:	[]
type:	dict
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for plotly_layout¶

Style Translation

sugarpy_plot_style_1 plotly_layout

pparse_options¶

Dictionary to specify options and their value for pParse. For available options see http://pfind.ict.ac.cn/software/pParse/#

Default value:	[‘-F’, ‘-m’, ‘-p’]
type:	dict
triggers rerun:	True

Available in unodes¶

pparse_2_0
pparse_2_2_1

Ursgal key translations for pparse_options¶

Style Translation

pparse_style_1 pparse_options

precursor_charge_dependency¶

charge dependency of precursor mass tolerance (none or linear)

Default value:	linear
type:	select
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for precursor_charge_dependency¶

Style Translation

omssa_style_1 -tez

Ursgal value translations¶

Ursgal Value Translated Value

. omssa_style_1

linear 1

none 0

precursor_isotope_range¶

Error range for incorrect carbon isotope parent ion assignment

Default value:	0,1
type:	select
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
pepnovo_3_1
unify_csv_1_0_0
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
ptmshepherd_0_3_5

Ursgal key translations for precursor_isotope_range¶

Style Translation

kojak_style_1 precursor_isotope_range

msfragger_style_1 isotope_error

msfragger_style_2 isotope_error

msfragger_style_3 isotope_error

msgfplus_style_1 -ti

myrimatch_style_1 MonoisotopeAdjustmentSet

omssa_style_1 -ti

pepnovo_style_1 -correct_pm

ptmshepherd_style_1 isotope_error

unify_csv_style_1 precursor_isotope_range

xtandem_style_1 spectrum, parent monoisotopic mass isotope error

Ursgal value translations¶

Ursgal Value Translated Value

. kojak_style_1 msfragger_style_1 msfragger_style_2 msfragger_style_3 myrimatch_style_1 omssa_style_1 ptmshepherd_style_1 xtandem_style_1

0 0 0 0 0 [0,] 0 0 no

0,1 1 0/1 0/1 0/1 [0,1] 1 0/1 yes

0,1,2 n/t n/t n/t n/t [0,1,2] n/t n/t n/t

0,2 2 0/1/2 0/1/2 0/1/2 n/t 2 0/1/2 yes

precursor_mass_tolerance_minus¶

Lower precursor mass tolerance; maximum negative deviation of measured from calculated parent ion mass.

Default value:	5
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
novor_1_1beta
novor_1_05
omssa_2_1_9
pepnovo_3_1
unify_csv_1_0_0
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
pglyco_db_2_2_0
ptminer_1_0
pglyco_db_2_2_2
deepnovo_0_0_1
deepnovo_pointnovo
pnovo_3_1_3
ptmshepherd_0_3_5

Ursgal key translations for precursor_mass_tolerance_minus¶

Style Translation

deepnovo_style_1 (‘precursor_mass_tolerance’, ‘precursor_mass_ppm’)

kojak_style_1 ppm_tolerance_pre

moda_style_1 PPMTolerance

msamanda_style_1 ms1_tol

msfragger_style_1 precursor_mass_lower

msfragger_style_2 precursor_mass_lower

msfragger_style_3 precursor_mass_lower

msgfplus_style_1 -t

myrimatch_style_1 MonoPrecursorMzTolerance

novor_style_1 precursorErrorTol

omssa_style_1 -te

pepnovo_style_1 -pm_tolerance

pglyco_db_style_1 search_precursor_tolerance

pipi_style_1 ms1_tolerance

pnovo_style_1 pep_tol

ptminer_style_1 precursor_tol

ptmshepherd_style_1 precursor_tol

pyqms_style_1 REL_MZ_RANGE

sugarpy_plot_style_1 REL_MZ_RANGE

sugarpy_run_style_1 REL_MZ_RANGE

unify_csv_style_1 precursor_mass_tolerance_minus

xtandem_style_1 spectrum, parent monoisotopic mass error minus

precursor_mass_tolerance_plus¶

Upper precursor mass tolerance; maximum positive deviation of measured from calculated parent ion mass.

Default value:	5
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
novor_1_1beta
novor_1_05
omssa_2_1_9
pepnovo_3_1
unify_csv_1_0_0
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
pglyco_db_2_2_0
ptminer_1_0
pglyco_db_2_2_2
deepnovo_0_0_1
deepnovo_pointnovo
pnovo_3_1_3
flash_lfq_1_1_1
ptmshepherd_0_3_5

Ursgal key translations for precursor_mass_tolerance_plus¶

Style Translation

deepnovo_style_1 (‘precursor_mass_tolerance’, ‘precursor_mass_ppm’)

flash_lfq_style_1 –ppm

kojak_style_1 ppm_tolerance_pre

moda_style_1 PPMTolerance

msamanda_style_1 ms1_tol

msfragger_style_1 precursor_mass_upper

msfragger_style_2 precursor_mass_upper

msfragger_style_3 precursor_mass_upper

msgfplus_style_1 -t

myrimatch_style_1 MonoPrecursorMzTolerance

novor_style_1 precursorErrorTol

omssa_style_1 -te

pepnovo_style_1 -pm_tolerance

pglyco_db_style_1 search_precursor_tolerance

pipi_style_1 ms1_tolerance

pnovo_style_1 pep_tol

ptminer_style_1 precursor_tol

ptmshepherd_style_1 precursor_tol

pyqms_style_1 REL_MZ_RANGE

sugarpy_plot_style_1 REL_MZ_RANGE

sugarpy_run_style_1 REL_MZ_RANGE

unify_csv_style_1 precursor_mass_tolerance_minus

xtandem_style_1 spectrum, parent monoisotopic mass error plus

precursor_mass_tolerance_unit¶

Precursor mass tolerance unit: available in ppm (parts-per-millon), da (Dalton) or mmu (Milli mass unit)

Default value:	ppm
type:	select
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
novor_1_1beta
novor_1_05
omssa_2_1_9
pepnovo_3_1
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pipi_1_4_5
pipi_1_4_6
pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
pglyco_db_2_2_0
ptminer_1_0
pglyco_db_2_2_2
deepnovo_0_0_1
deepnovo_pointnovo
pnovo_3_1_3
ptmshepherd_0_3_5

Ursgal key translations for precursor_mass_tolerance_unit¶

Style Translation

deepnovo_style_1 (‘precursor_mass_tolerance’, ‘precursor_mass_ppm’)

moda_style_1 PPMTolerance

msamanda_style_1 ms1_tol unit

msfragger_style_1 precursor_mass_units

msfragger_style_2 precursor_mass_units

msfragger_style_3 precursor_mass_units

msgfplus_style_1 -t

myrimatch_style_1 MonoPrecursorMzTolerance

novor_style_1 precursorErrorTol

omssa_style_1 -teppm

pepnovo_style_1 precursor_mass_tolerance_unit

pglyco_db_style_1 search_precursor_tolerance_type

pipi_style_1 ms1_tolerance_unit

pnovo_style_1 pep_tol_type_ppm

ptminer_style_1 precursor_tol_type

ptmshepherd_style_1 precursor_mass_units

pyqms_style_1 REL_MZ_RANGE

sugarpy_plot_style_1 REL_MZ_RANGE

sugarpy_run_style_1 REL_MZ_RANGE

xtandem_style_1 spectrum, parent monoisotopic mass error units

Ursgal value translations¶

Ursgal Value Translated Value

. msamanda_style_1 msfragger_style_1 msfragger_style_2 msfragger_style_3 msgfplus_style_1 myrimatch_style_1 novor_style_1 omssa_style_1 pglyco_db_style_1 pipi_style_1 pnovo_style_1 ptminer_style_1 ptmshepherd_style_1 xtandem_style_1

da Da 0 0 0 Da Da Da Da 0 0 0 0 Daltons

ppm n/t 1 1 1 n/t n/t n/t -teppm n/t 1 1 1 1 n/t

precursor_mass_type¶

Precursor mass type: monoisotopic or average

Default value:	monoisotopic
type:	select
triggers rerun:	True

Available in unodes¶

msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9

Ursgal key translations for precursor_mass_type¶

Style Translation

msamanda_style_1 monoisotopic

myrimatch_style_1 PrecursorMzToleranceRule

omssa_style_1 -tem

Ursgal value translations¶

Ursgal Value Translated Value

. msamanda_style_1 myrimatch_style_1 omssa_style_1

average false average 1

monoisotopic true mono 0

precursor_max_charge¶

Maximal accepted parent ion charge

Default value:	5
type:	int
triggers rerun:	True

Available in unodes¶

msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
mzml2mgf_2_0_0
omssa_2_1_9
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for precursor_max_charge¶

Style Translation

msamanda_style_1 considered_charges

msfragger_style_1 precursor_max_charge

msfragger_style_2 precursor_max_charge

msfragger_style_3 precursor_max_charge

msgfplus_style_1 -maxCharge

myrimatch_style_1 NumChargeStates

mzml2mgf_style_1 precursor_max_charge

omssa_style_1 -zh

pyqms_style_1 precursor_max_charge

sugarpy_plot_style_1 max_charge

sugarpy_run_style_1 max_charge

precursor_max_mass¶

Maximal parent ion mass in Da. Adjusted to default used by MSFragger

Default value:	7000
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
myrimatch_2_1_138
myrimatch_2_2_140
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pglyco_db_2_2_0
pglyco_db_2_2_2
pnovo_3_1_3
deepnovo_pointnovo

Ursgal key translations for precursor_max_mass¶

Style Translation

deepnovo_style_1 MZ_MAX

kojak_style_1 precursor_max_mass

msfragger_style_1 precursor_max_mass

msfragger_style_2 precursor_max_mass

msfragger_style_3 precursor_max_mass

myrimatch_style_1 MaxPeptideMass

pglyco_db_style_1 max_peptide_weight

pnovo_style_1 mass_upper_bound

xtandem_style_1 spectrum, minimum parent m+h

precursor_min_charge¶

Minimal accepted parent ion charge

Default value:	1
type:	int
triggers rerun:	True

Available in unodes¶

msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
mzml2mgf_2_0_0
omssa_2_1_9
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for precursor_min_charge¶

Style Translation

msamanda_style_1 considered_charges

msfragger_style_1 precursor_min_charge

msfragger_style_2 precursor_min_charge

msfragger_style_3 precursor_min_charge

msgfplus_style_1 -minCharge

mzml2mgf_style_1 precursor_min_charge

omssa_style_1 -zl

pyqms_style_1 precursor_min_charge

sugarpy_plot_style_1 min_charge

sugarpy_run_style_1 min_charge

precursor_min_mass¶

Minimal parent ion mass

Default value:	400
type:	int
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
myrimatch_2_1_138
myrimatch_2_2_140
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0
pglyco_db_2_2_0
pglyco_db_2_2_2
pnovo_3_1_3

Ursgal key translations for precursor_min_mass¶

Style Translation

kojak_style_1 precursor_min_mass

msfragger_style_1 precursor_min_mass

msfragger_style_2 precursor_min_mass

msfragger_style_3 precursor_min_mass

myrimatch_style_1 MinPeptideMass

pglyco_db_style_1 min_peptide_weight

pnovo_style_1 mass_lower_bound

xtandem_style_1 spectrum, minimum parent m+h

precursor_true_tolerance¶

True precursor mass tolerance (window is +/- this value). Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches.

Default value:	5
type:	int
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for precursor_true_tolerance¶

Style Translation

msfragger_style_1 precursor_true_tolerance

msfragger_style_2 precursor_true_tolerance

msfragger_style_3 precursor_true_tolerance

precursor_true_units¶

Mass tolerance units fo precursor_true_tolerance

Default value:	ppm
type:	str
triggers rerun:	True

Available in unodes¶

msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for precursor_true_units¶

Style Translation

msfragger_style_1 precursor_true_units

msfragger_style_2 precursor_true_units

msfragger_style_3 precursor_true_units

Ursgal value translations¶

Ursgal Value Translated Value

. msfragger_style_1 msfragger_style_2 msfragger_style_3

da 0 0 0

ppm 1 1 1

preferred_engines¶

List of engines that should be preferred when sanitizing results. In combination with “accept_conflicting_psms”=True, conflicting PSMs for only the preferred engine are selected. If no PSMs for that engine exist, the second preferred engine is used, and so on

Default value:	[]
type:	list
triggers rerun:	True

Available in unodes¶

sanitize_csv_1_0_0

Ursgal key translations for preferred_engines¶

Style Translation

sanitize_csv_style_1 preferred_engines

prefix¶

‘None’ : None

Default value:	None
type:	None
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for prefix¶

Style Translation

ucontroller_style_1 prefix

protein_delimiter¶

This delimiter seperates protein IDs/names in the unified csv

Default value:	<\|>
type:	str
triggers rerun:	True

Available in unodes¶

percolator_2_08
percolator_3_2_1
percolator_3_4_0
unify_csv_1_0_0
upeptide_mapper_1_0_0

Ursgal key translations for protein_delimiter¶

Style Translation

percolator_style_1 protein_delimiter

unify_csv_style_1 protein_delimiter

upeptide_mapper_style_1 protein_delimiter

psm_colnames_to_merge_multiple_values¶

Defines the column names which should have their different values merged into a single value when merging rows corresponding the same PSM Formatted as a dictionary with keys as the column names and values as a parameter to specify which one of the different values to take Available values: max_value: min_value most_frequent avg_value

Default value:	[]
type:	dict
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for psm_colnames_to_merge_multiple_values¶

Style Translation

ucontroller_style_1 colnames_to_merge_multiple_values

psm_defining_colnames¶

List of column names that are used to define unique PSMs and to merge multiple lines of the same PSM (if specified). The validation_score_field is automatically added to this list.

Default value:	[‘Spectrum Title’, ‘Sequence’, ‘Modifications’, ‘Mass Difference’, ‘Charge’, ‘Is decoy’]
type:	list
triggers rerun:	True

Available in unodes¶

ucontroller
sanitize_csv_1_0_0
combine_pep_1_0_0
unify_csv_1_0_0

Ursgal key translations for psm_defining_colnames¶

Style Translation

combine_pep_style_1 columns_for_grouping

sanitize_csv_style_1 psm_defining_colnames

ucontroller_style_1 psm_defining_colnames

unify_csv_style_1 psm_defining_colnames

psm_merge_delimiter¶

This delimiter seperates differing values for merged rows in the unified csv

Default value:	;
type:	str
triggers rerun:	True

Available in unodes¶

unify_csv_1_0_0
ucontroller

Ursgal key translations for psm_merge_delimiter¶

Style Translation

ucontroller_style_1 psm_merge_delimiter

unify_csv_style_1 psm_merge_delimiter

ptmshepherd_localization_background¶

Background of peptides against which localization enrichment scores are calculated

Default value:	peptides_entire_dataset
type:	select
triggers rerun:	True

Available in unodes¶

ptmshepherd_0_3_5

Ursgal key translations for ptmshepherd_localization_background¶

Style Translation

ptmshepherd_style_1 localization_background

Ursgal value translations¶

Ursgal Value Translated Value

. ptmshepherd_style_1

peptides_entire_dataset 3

peptides_same_bin 1

psms_entire_dataset 3

psms_same_bin 2

ptmshepherd_peak_picking_params¶

Dictionary to specify options for peak picking for PTM-Shepherd.

Default value:	[‘peakpicking_mass_units’, ‘peakpicking_promRatio’, ‘peakpicking_topN’, ‘peakpicking_width’]
type:	dict
triggers rerun:	True

Available in unodes¶

ptmshepherd_0_3_5

Ursgal key translations for ptmshepherd_peak_picking_params¶

Style Translation

ptmshepherd_style_1 (‘peakpicking_promRatio’, ‘peakpicking_mass_units’, ‘peakpicking_width’, ‘peakpicking_topN’)

pymzml_spec_id_attribute¶

Specify the spectrum ID attribute to be used to access the spectrum ID (ID, id_dict or index). Given as a dict (key = attribute, value = key in id_dict). For .wiff files, during conversion to mzML, spectrum IDs are formatted differently; pymzml can deal with this by returning an id_dict or accessing the index.

Default value:	[‘ID’]
type:	dict
triggers rerun:	True

Available in unodes¶

mzml2mgf_2_0_0

Ursgal key translations for pymzml_spec_id_attribute¶

Style Translation

mzml2mgf_style_1 spec_id_attribute

pyqms_min_rel_isotope_peak_intensity¶

Defines the relative minimum peak intensity within an isotopologue to be considered for matching

Default value:	0.01
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for pyqms_min_rel_isotope_peak_intensity¶

Style Translation

pyqms_style_1 MIN_REL_PEAK_INTENSITY_FOR_MATCHING

sugarpy_plot_style_1 MIN_REL_PEAK_INTENSITY_FOR_MATCHING

sugarpy_run_style_1 MIN_REL_PEAK_INTENSITY_FOR_MATCHING

pyqms_trivial_names¶

Trivial name lookup mapping molecules to a trivial name

Default value:	None
type:	dict
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0

Ursgal key translations for pyqms_trivial_names¶

Style Translation

pyqms_style_1 trivial_names

pyqms_verbosity¶

verbosity for pyqms

Default value:	True
type:	bool
triggers rerun:	False

Available in unodes¶

pyqms_1_0_0

Ursgal key translations for pyqms_verbosity¶

Style Translation

pyqms_style_1 pyqms_verbosity

quantification_evidences¶

Molecules to quantify. Can be either a list of strings or a csv file

Default value:	None
type:	list
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
flash_lfq_1_1_1

Ursgal key translations for quantification_evidences¶

Style Translation

flash_lfq_style_1 evidences

pyqms_style_1 evidences

qvality_cross_validation¶

The relative crossvalidation step size used as treshhold before ending the iterations, qvality determines step size automatically when set to 0

Default value:	0
type:	int
triggers rerun:	True

Available in unodes¶

qvality_2_02

Ursgal key translations for qvality_cross_validation¶

Style Translation

qvality_style_1 -c

qvality_epsilon_step¶

The relative step size used as treshhold before cross validation error is calculated, qvality determines step size automatically when set to 0

Default value:	0
type:	int
triggers rerun:	True

Available in unodes¶

qvality_2_02

Ursgal key translations for qvality_epsilon_step¶

Style Translation

qvality_style_1 -s

qvality_number_of_bins¶

Number of bins used in qvality

Default value:	500
type:	int
triggers rerun:	True

Available in unodes¶

qvality_2_02

Ursgal key translations for qvality_number_of_bins¶

Style Translation

qvality_style_1 -n

qvality_verbose¶

Verbose qvality output (range from 0 = no processing info to 5 = all)

Default value:	2
type:	select
triggers rerun:	True

Available in unodes¶

qvality_2_02

Ursgal key translations for qvality_verbose¶

Style Translation

qvality_style_1 -v

Ursgal value translations¶

Ursgal Value Translated Value

. qvality_style_1

1 1

2 2

3 3

4 4

5 5

random_seed¶

Random seed for random number generators

Default value:	10
type:	int
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for random_seed¶

Style Translation

flash_lfq_style_1 –rns

raw_ident_csv_suffix¶

CSV suffix of raw indentification: this is the conversion result after CSV conversion but before adding retention time

Default value:	.csv
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for raw_ident_csv_suffix¶

Style Translation

ucontroller_style_1 raw_ident_csv_suffix

rel_intensity_error¶

Relative intensity error range (for the most intense peak)

Default value:	0.2
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for rel_intensity_error¶

Style Translation

pyqms_style_1 REL_I_RANGE

sugarpy_plot_style_1 REL_I_RANGE

sugarpy_run_style_1 REL_I_RANGE

remove_precursor_peak¶

Remove precursor peaks from spectrum. Options are: “off”, “remove_precursor_charge” (removes peaks with same charge as precursor), “remove_all_charges” (removes peaks of all charges)

Default value:	off
type:	select
triggers rerun:	True

Available in unodes¶

msfragger_2_3
msfragger_3_0

Ursgal key translations for remove_precursor_peak¶

Style Translation

msfragger_style_3 remove_precursor_peak

Ursgal value translations¶

Ursgal Value Translated Value

. msfragger_style_3

off 0

remove_all_charges 2

remove_precursor_charge 1

remove_precursor_range¶

The given mass range is used to remove precursor peaks.

Default value:	[-1.5, 1.5]
type:	list
triggers rerun:	True

Available in unodes¶

msfragger_2_3
msfragger_3_0

Ursgal key translations for remove_precursor_range¶

Style Translation

msfragger_style_3 remove_precursor_range

remove_redundant_psms¶

If True, redundant PSMs (e.g. the same identification reported by multiple engines) for the same spectrum are removed. An identification is defined by psm_defining_colnames

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

sanitize_csv_1_0_0

Ursgal key translations for remove_redundant_psms¶

Style Translation

sanitize_csv_style_1 remove_redundant_psms

remove_temporary_files¶

Remove temporary files: True or False

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

ucontroller
tag_graph_1_8_0

Ursgal key translations for remove_temporary_files¶

Style Translation

tag_graph_style_1 (‘cleanInputDataFilesFromOutput’, ‘cleanIntermediateFiles’)

ucontroller_style_1 remove_temporary_files

require_msms_id¶

Require MS/MS match in condition to consider quantification

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for require_msms_id¶

Style Translation

flash_lfq_style_1 –rmc

required_percentile_peak_overlap¶

Minimum percentile overlap for matching labeled peaks

Default value:	0.5
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for required_percentile_peak_overlap¶

Style Translation

pyqms_style_1 REQUIRED_PERCENTILE_PEAK_OVERLAP

sugarpy_plot_style_1 REQUIRED_PERCENTILE_PEAK_OVERLAP

sugarpy_run_style_1 REQUIRED_PERCENTILE_PEAK_OVERLAP

rounded_mass_decimals¶

Masses of modifications are rounded in order to match them to their corresponding unimod name. Use this parameter to set the number of decimal places after rounding.

Default value:	3
type:	int
triggers rerun:	True

Available in unodes¶

unify_csv_1_0_0

Ursgal key translations for rounded_mass_decimals¶

Style Translation

unify_csv_style_1 rounded_mass_decimals

rt_border_tolerance¶

Retention time border tolerance (in min) for curating RT windows

Default value:	1
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for rt_border_tolerance¶

Style Translation

pyqms_style_1 rt_border_tolerance

sugarpy_plot_style_1 rt_border_tolerance

sugarpy_run_style_1 rt_border_tolerance

rt_pickle_name¶

name of the pickle that is used to map the retention time

Default value:	_ursgal_lookup.pkl
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller
sugarpy_run_1_0_0
sugarpy_plot_1_0_0
mgf_to_rt_lookup_1_0_0
unify_csv_1_0_0

Ursgal key translations for rt_pickle_name¶

Style Translation

mgf_to_rt_lookup_style_1 rt_pickle_name

sugarpy_plot_style_1 scan_rt_lookup

sugarpy_run_style_1 scan_rt_lookup

ucontroller_style_1 rt_pickle_name

unify_csv_style_1 scan_rt_lookup_path

scan_exclusion_list¶

Spectra rejected during mzml2mgf conversion

Default value:	[]
type:	list
triggers rerun:	True

Available in unodes¶

mzml2mgf_1_0_0
mzml2mgf_2_0_0

Ursgal key translations for scan_exclusion_list¶

Style Translation

mzml2mgf_style_1 scan_exclusion_list

scan_inclusion_list¶

Exclusively spectra included during mzml2mgf conversion

Default value:	None
type:	list
triggers rerun:	True

Available in unodes¶

mzml2mgf_1_0_0
mzml2mgf_2_0_0

Ursgal key translations for scan_inclusion_list¶

Style Translation

mzml2mgf_style_1 scan_inclusion_list

scan_skip_modulo_step¶

Include only the n-th spectrum during mzml2mgf conversion: 1 : None

Default value:	None
type:	int
triggers rerun:	True

Available in unodes¶

mzml2mgf_1_0_0
mzml2mgf_2_0_0

Ursgal key translations for scan_skip_modulo_step¶

Style Translation

mzml2mgf_style_1 scan_skip_modulo_step

Ursgal value translations¶

Ursgal Value Translated Value

. mzml2mgf_style_1

score_correlation_corr¶

Use correlation correction to score?

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

omssa_2_1_9

Ursgal key translations for score_correlation_corr¶

Style Translation

omssa_style_1 -scorr

Ursgal value translations¶

Ursgal Value Translated Value

. omssa_style_1

0 1

1 0

score_diff_threshold¶

Minimum score difference between the best PSM and the first rejected PSM of one spectrum, default: 0.01

Default value:	0.01
type:	float
triggers rerun:	True

Available in unodes¶

sanitize_csv_1_0_0

Ursgal key translations for score_diff_threshold¶

Style Translation

sanitize_csv_style_1 score_diff_threshold

score_ion_list¶

List of ion types that are taken into account by the respective search engine.Availabel ion types: a, b, c, x, y, z, -h2o, -nh3, b1, c_terminal, imm (immonium),int (internal), z+1, z+2, b~ (b+HexNAx), y~ (y+HexNAc), Y

Default value:	[‘b’, ‘y’]
type:	list
triggers rerun:	True

Available in unodes¶

kojak_1_5_3
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_3_0

Ursgal key translations for score_ion_list¶

Style Translation

kojak_style_1 (‘ion_series_X’, ‘ion_series_Y’, ‘ion_series_Z’, ‘ion_series_A’, ‘ion_series_B’, ‘ion_series_C’)

msamanda_style_1 series

msfragger_style_3 fragment_ion_series

myrimatch_style_1 FragmentationRule

omssa_style_1 (‘-i’, ‘-sct’, ‘-sb1’)

xtandem_style_1 (‘scoring, x ions’, ‘scoring, y ions’, ‘scoring, z ions’, ‘scoring, a ions’, ‘scoring, b ions’, ‘scoring, c ions’)

search_for_saps¶

Search for potential single amino acid polymorphisms. ‘True’ might cause problems in the downstream processing of th result files (unify_csv, …)

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for search_for_saps¶

Style Translation

xtandem_style_1 protein, saps

Ursgal value translations¶

Ursgal Value Translated Value

. xtandem_style_1

0 no

1 yes

semi_enzyme¶

Allows semi-enzymatic peptide ends

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62
msamanda_1_0_0_5242
msamanda_1_0_0_5243
msamanda_1_0_0_6299
msamanda_1_0_0_6300
msamanda_1_0_0_7503
msamanda_1_0_0_7504
msamanda_2_0_0_9706
msamanda_2_0_0_9695
msamanda_2_0_0_10695
msamanda_2_0_0_11219
msamanda_2_0_0_13723
msamanda_2_0_0_14665
msgfplus_v2016_09_16
msgfplus_v2017_01_27
msgfplus_v2018_01_30
msgfplus_v2018_06_28
msgfplus_v2018_09_12
msgfplus_v2019_01_22
msgfplus_v2019_04_18
msgfplus_v2019_07_03
msgfplus_v9979
myrimatch_2_1_138
myrimatch_2_2_140
omssa_2_1_9
unify_csv_1_0_0
xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for semi_enzyme¶

Style Translation

moda_style_1 enzyme_constraint_min_number_termini

msamanda_style_1 enzyme specificity

msfragger_style_1 num_enzyme_termini

msfragger_style_2 num_enzyme_termini

msfragger_style_3 num_enzyme_termini

msgfplus_style_1 -ntt

myrimatch_style_1 MinTerminiCleavages

omssa_style_1 semi_enzyme

unify_csv_style_1 semi_enzyme

xtandem_style_1 protein, cleavage semi

Ursgal value translations¶

Ursgal Value Translated Value

. moda_style_1 msamanda_style_1 msfragger_style_1 msfragger_style_2 msfragger_style_3 msgfplus_style_1 myrimatch_style_1 xtandem_style_1

0 2 Full 2 2 2 2 2 no

1 1 Semi 1 1 1 1 1 yes

show_unodes_in_development¶

Show ursgal nodes that are in development: False or True

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for show_unodes_in_development¶

Style Translation

ucontroller_style_1 show_unodes_in_development

signal_to_noise_threshold¶

Only peaks above the given signal to noise (S/N) threshold will be accepted

Default value:	0.0
type:	float
triggers rerun:	True

Available in unodes¶

mzml2mgf_2_0_0

Ursgal key translations for signal_to_noise_threshold¶

Style Translation

mzml2mgf_style_1 signal_to_noise_threshold

silac_aas_locked_in_experiment¶

AA which are always SILAC labeled and not considered for calculating partially labeling percentile

Default value:	None
type:	list
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for silac_aas_locked_in_experiment¶

Style Translation

pyqms_style_1 SILAC_AAS_LOCKED_IN_EXPERIMENT

sugarpy_plot_style_1 SILAC_AAS_LOCKED_IN_EXPERIMENT

sugarpy_run_style_1 SILAC_AAS_LOCKED_IN_EXPERIMENT

spec_dynamic_range¶

Internal normalization for MS/MS spectrum: The highest peak (intensity) within a spectrum is set to given value and all other peaks are normalized to this peak. If the normalized value is less than 1 the peak is rejected.

Default value:	100
type:	int
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal key translations for spec_dynamic_range¶

Style Translation

xtandem_style_1 spectrum, dynamic range

ssl_score_column_name¶

Name of the column that includes the scores that should be used for the .ssl file

Default value:	q-value
type:	str
triggers rerun:	True

Available in unodes¶

csv2ssl_1_0_0

Ursgal key translations for ssl_score_column_name¶

Style Translation

csv2ssl_style_1 score_column_name

ssl_score_type¶

Type of scores used for the .ssl file

Default value:	PERCOLATOR QVALUE
type:	select
triggers rerun:	True

Available in unodes¶

csv2ssl_1_0_0

Ursgal key translations for ssl_score_type¶

Style Translation

csv2ssl_style_1 score_type

sugarpy_decoy_glycan¶

Glycan (given in the SugarPy Hill noation format) that will be used for matching glycopeptide fragment ions in MS2 spectra from non-glycosylated peptides

Default value:	End(HexNAc)Hex(5)HexNAc(3)NeuAc(1)dHex(1)
type:	str
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0
glycopeptide_fragmentor_1_0_0

Ursgal key translations for sugarpy_decoy_glycan¶

Style Translation

glycopeptide_fragmentor_style_1 decoy_glycan

sugarpy_plot_style_1 decoy_glycan

sugarpy_include_subtrees¶

Defines if/how subtrees should be taken into account for plotting molecule elution profiles in SugarPy. Available are: “no_subtrees”, “sum_subtrees”, “individual_subtrees”

Default value:	no_subtrees
type:	select
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for sugarpy_include_subtrees¶

Style Translation

sugarpy_plot_style_1 include_subtrees

sugarpy_plot_molecule_dict¶

The dict contains all peptidoforms (Peptide#Unimod:Pos) as keys and a dict with the glycans (keys) and {‘charges’:set(), ‘file_names’:set()} (value) as values. It can be auto generated from a SugarPy results .csv (use uparam sugarpy_results_file to specify). Don’t use sugarpy_results_file and sugarpy_plot_molecule_dict at the same time!

Default value:	[]
type:	dict
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for sugarpy_plot_molecule_dict¶

Style Translation

sugarpy_plot_style_1 plot_molecule_dict

sugarpy_plot_peak_types¶

List of peak types that should be plotted by the SugarPy plot spectrum function. Available are: “matched” (peaks matched by pyQms), “unmatched” (unmatched peaks from matched formulas), “labels@ (for monoisotopic peaks)

Default value:	[‘matched’, ‘unmatched’, ‘labels’]
type:	list
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for sugarpy_plot_peak_types¶

Style Translation

sugarpy_plot_style_1 plot_peak_types

sugarpy_plot_types¶

List of plot types that should be created by the SugarPy plotting function. Available are: “plot_molecule_elution_profile”, “plot_glycan_elution_profile”, “plot_annotated_spectra”, “check_peak_presence”, “check_frag_specs”

Default value:	[‘plot_glycan_elution_profile’]
type:	list
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for sugarpy_plot_types¶

Style Translation

sugarpy_plot_style_1 plot_types

sugarpy_remove_subtrees¶

List of subtree formulas (hill notation) that should not be plotted. Formulas include the complete molecule, i.e. peptide and glycan

Default value:	[]
type:	list
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for sugarpy_remove_subtrees¶

Style Translation

sugarpy_plot_style_1 remove_subtrees

sugarpy_results_csv¶

Path to the SugarPy results .csv

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for sugarpy_results_csv¶

Style Translation

sugarpy_plot_style_1 result_file

sugarpy_results_pkl¶

Path to the SugarPy results .pkl

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for sugarpy_results_pkl¶

Style Translation

sugarpy_plot_style_1 validated_results_pkl

sugarpy_score_type¶

Defines the score type used for the y-axis. Available are: “top_scores”, “sum_scores”

Default value:	top_scores
type:	select
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for sugarpy_score_type¶

Style Translation

sugarpy_plot_style_1 score_type

svm_c_param¶

Penalty parameter C of the error term of the post-processing SVM

Default value:	1.0
type:	float
triggers rerun:	True

Available in unodes¶

svm_1_0_0

Ursgal key translations for svm_c_param¶

Style Translation

svm_style_1 c

tag_graph_config_file¶

Path to pickled (python-serialized) model configuration file. Use “default” for the default file location in the resources

Default value:	default
type:	str
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for tag_graph_config_file¶

Style Translation

tag_graph_style_1 config

tag_graph_fdr_threshold¶

FDR threshold applied to output by TagGraph

Default value:	0.01
type:	float
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for tag_graph_fdr_threshold¶

Style Translation

tag_graph_style_1 FDRCutoff

tag_graph_init_iterations¶

Number of iterations in initial EM over all results

Default value:	20
type:	int
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for tag_graph_init_iterations¶

Style Translation

tag_graph_style_1 initIterations

tag_graph_log_em_threshold¶

p-value threshold applied to output by TagGraph

Default value:	2
type:	int
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for tag_graph_log_em_threshold¶

Style Translation

tag_graph_style_1 logEMCutoff

tag_graph_max_iterations¶

Maximum number of expectation maximization iterations for FDR assignment

Default value:	100
type:	int
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for tag_graph_max_iterations¶

Style Translation

tag_graph_style_1 maxIterations

tag_graph_model_file¶

Path to pickled (python-serialized) probabilistic model file. Use “default” for the default file location in the resources

Default value:	default
type:	str
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for tag_graph_model_file¶

Style Translation

tag_graph_style_1 model

tag_graph_unimod_file¶

Path to pickled (python-serialized) unimod dictionary. Use “default” for the default file location in the resources

Default value:	default
type:	str
triggers rerun:	True

Available in unodes¶

tag_graph_1_8_0

Ursgal key translations for tag_graph_unimod_file¶

Style Translation

tag_graph_style_1 unimoddict

test_param1¶

TEST/DEBUG: Internal Ursgal parameter 1 for debugging and testing.

Default value:	b
type:	select
triggers rerun:	True

Available in unodes¶

_test_node

Ursgal key translations for test_param1¶

Style Translation

_test_node_style_1 test_param1

Ursgal value translations¶

Ursgal Value Translated Value

. _test_node_style_1

a A

b B

c C

d D

e E

test_param2¶

TEST/DEBUG: Internal Ursgal parameter 2 for debugging and testing.

Default value:	three
type:	select
triggers rerun:	True

Available in unodes¶

_test_node

Ursgal key translations for test_param2¶

Style Translation

_test_node_style_1 test_param2

Ursgal value translations¶

Ursgal Value Translated Value

. _test_node_style_1

five 5

four 4

one 1

three 3

two 2

thermo_raw_file_parser_options¶

Dictionary to specify options and their value for ThermoRawFileParser. If options are given as a flag only, specify ‘None’ as their value. For available options see https://github.com/compomics/ThermoRawFileParser

Default value:	[‘-e’, ‘-m’]
type:	dict
triggers rerun:	True

Available in unodes¶

thermo_raw_file_parser_1_1_2

Ursgal key translations for thermo_raw_file_parser_options¶

Style Translation

thermo_raw_file_parser_style_1 (‘-h’, ‘-m’, ‘-g’, ‘-u’, ‘-k’, ‘-t’, ‘-n’, ‘-v’, ‘-e’)

threshold_is_log10¶

True, if log10 scale has been used for score_diff_threshold.

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

sanitize_csv_1_0_0

Ursgal key translations for threshold_is_log10¶

Style Translation

sanitize_csv_style_1 threshold_is_log10

unify_csv_converter_version¶

unify csv converter version: version name

Default value:	unify_csv_1_0_0
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for unify_csv_converter_version¶

Style Translation

ucontroller_style_1 unify_csv_converter_version

upper_mz_limit¶

Highest considered mz for quantification

Default value:	2000
type:	float
triggers rerun:	True

Available in unodes¶

pyqms_1_0_0
sugarpy_run_1_0_0
sugarpy_plot_1_0_0

Ursgal key translations for upper_mz_limit¶

Style Translation

pyqms_style_1 UPPER_MZ_LIMIT

sugarpy_plot_style_1 UPPER_MZ_LIMIT

sugarpy_run_style_1 UPPER_MZ_LIMIT

ursgal_resource_url¶

URL that is used to prepare and install resources via corresponding scripts (prepare_resources.py and install_resources.py)

Default value:	https://www.sas.upenn.edu/~sschulze/ursgal_resources/
type:	str
triggers rerun:	False

Available in unodes¶

ucontroller

Ursgal key translations for ursgal_resource_url¶

Style Translation

ucontroller_style_1 ursgal_resource_url

ursgal_results_csv¶

Path to the Ursgal results .csv containing all PSMs in the unified format

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

sugarpy_plot_1_0_0

Ursgal key translations for ursgal_results_csv¶

Style Translation

sugarpy_plot_style_1 ursgal_ident_file

use_median_accuracy¶

Accuracy of identifications (ident_file) are used to calculate the machine_offset_in_ppm. If “all” is selected, the median of all identifications will be used, for “peptide” the median of each peptide will be used.

Default value:	None
type:	select
triggers rerun:	True

Available in unodes¶

sugarpy_run_1_0_0

Ursgal key translations for use_median_accuracy¶

Style Translation

sugarpy_run_style_1 use_median_accuracy

use_prior_probability¶

specifying whether the prior probability should be used or not

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

ptminer_1_0

Ursgal key translations for use_prior_probability¶

Style Translation

ptminer_style_1 use_prior

Ursgal value translations¶

Ursgal Value Translated Value

. ptminer_style_1

0 0

1 1

use_pyqms_for_mz_calculation¶

Use pyQms for accurate calculation of isotopologue m/z. This will affect the accuracy (ppm) calculation as well. If True, unify_csv will be significantly slower. Please note that this does not work for any type of labeling yet.

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

unify_csv_1_0_0

Ursgal key translations for use_pyqms_for_mz_calculation¶

Style Translation

unify_csv_style_1 use_pyqms_for_mz_calculation

use_quality_filter¶

Use filter for low quality spectra.

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

pepnovo_3_1

Ursgal key translations for use_quality_filter¶

Style Translation

pepnovo_style_1 -no_quality_filter

Ursgal value translations¶

Ursgal Value Translated Value

. pepnovo_style_1

0 1

1 0

use_refinement¶

X! TANDEM can use ‘refinement’ to improve the speed and accuracy of peptide modelling. This is not included in Ursgal, yet. See further: http://www.thegpm.org/TANDEM/api/refine.html

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

xtandem_cyclone_2010
xtandem_jackhammer
xtandem_piledriver
xtandem_sledgehammer
xtandem_vengeance
xtandem_alanine

Ursgal value translations¶

Ursgal Value Translated Value

. xtandem_style_1

0 no

1 yes

use_shared_peptides¶

use shared peptides for protein quantification

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

flash_lfq_1_1_1

Ursgal key translations for use_shared_peptides¶

Style Translation

flash_lfq_style_1 –sha

use_spectrum_charge¶

Does not correct precursor charge.

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

pepnovo_3_1
msfragger_20170103
msfragger_20171106
msfragger_20190222
msfragger_20190628
msfragger_2_3
msfragger_3_0

Ursgal key translations for use_spectrum_charge¶

Style Translation

msfragger_style_1 override_charge

msfragger_style_2 override_charge

msfragger_style_3 override_charge

pepnovo_style_1 -use_spectrum_charge

Ursgal value translations¶

Ursgal Value Translated Value

. msfragger_style_1 msfragger_style_2 msfragger_style_3

0 1 1 1

1 0 0 0

use_spectrum_mz¶

Does not correct precusor m/z.

Default value:	True
type:	bool
triggers rerun:	True

Available in unodes¶

moda_v1_51
moda_v1_61
moda_v1_62
pepnovo_3_1

Ursgal key translations for use_spectrum_mz¶

Style Translation

moda_style_1 AutoPMCorrection

pepnovo_style_1 -use_spectrum_mz

Ursgal value translations¶

Ursgal Value Translated Value

. moda_style_1

0 1

1 0

validated_ident_csv_suffix¶

CSV suffix of validated identification files: string, CSV-file which contains PSMs validated with validation tools

Default value:	validated.csv
type:	str
triggers rerun:	True

Available in unodes¶

ucontroller

Ursgal key translations for validated_ident_csv_suffix¶

Style Translation

ucontroller_style_1 validated_ident_csv_suffix

validation_generalized¶

Generalized target decoy competition, situations where PSMs known to more frequently be incorrect are mixed in with the correct PSMs

Default value:	False
type:	bool
triggers rerun:	True

Available in unodes¶

qvality_2_02

Ursgal key translations for validation_generalized¶

Style Translation

qvality_style_1 -g

Ursgal value translations¶

Ursgal Value Translated Value

. qvality_style_1

0 None

1

validation_minimum_score¶

Defines the minimum score used for validation. If scores lower than this are produced, they are set to the minimum score. This is used to avoid huge gaps/jumps in the score distribution: ‘None’ : None

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

qvality_2_02

Ursgal key translations for validation_minimum_score¶

Style Translation

qvality_style_1 validation_minimum_score

Ursgal value translations¶

Ursgal Value Translated Value

. qvality_style_1

moda_v1_51 0

moda_v1_61 0

moda_v1_62 0

msamanda_1_0_0_5242 0

msamanda_1_0_0_5243 0

msamanda_1_0_0_6299 0

msamanda_1_0_0_6300 0

msamanda_1_0_0_7503 0

msamanda_1_0_0_7504 0

msamanda_2_0_0_10695 0

msamanda_2_0_0_11219 0

msamanda_2_0_0_13723 0

msamanda_2_0_0_14665 0

msamanda_2_0_0_9695 0

msamanda_2_0_0_9706 0

msfragger_20170103 0

msfragger_20171106 0

msfragger_20190222 0

msfragger_20190628 0

msfragger_2_3 0

msfragger_3_0 0

msgfplus_v2016_09_16 1e-100

msgfplus_v2017_01_27 1e-100

msgfplus_v2018_01_30 1e-100

msgfplus_v2018_06_28 1e-100

msgfplus_v2018_09_12 1e-100

msgfplus_v2019_01_22 1e-100

msgfplus_v2019_04_18 1e-100

msgfplus_v2019_07_03 1e-100

msgfplus_v9979 1e-100

myrimatch_2_1_138 0

myrimatch_2_2_140 0

omssa_2_1_9 1e-30

pipi_1_4_5 0

pipi_1_4_6 0

xtandem_alanine 0

xtandem_cyclone_2010 0

xtandem_jackhammer 0

xtandem_piledriver 0

xtandem_sledgehammer 0

xtandem_vengeance 0

validation_score_field¶

Name of the column that is used for validation, e.g. by qvality and percolator. If None is defined, default values are used: ‘None’ : None

Default value:	None
type:	str
triggers rerun:	True

Available in unodes¶

add_estimated_fdr_1_0_0
percolator_2_08
percolator_3_2_1
percolator_3_4_0
qvality_2_02
sanitize_csv_1_0_0
svm_1_0_0
ucontroller
unify_csv_1_0_0
ptminer_1_0

Ursgal key translations for validation_score_field¶

Style Translation

add_estimated_fdr_style_1 validation_score_field

percolator_style_1 validation_score_field

ptminer_style_1 validation_score_field

qvality_style_1 validation_score_field

sanitize_csv_style_1 validation_score_field

svm_style_1 validation_score_field

ucontroller_style_1 validation_score_field

unify_csv_style_1 validation_score_field

Ursgal value translations¶

Ursgal Value Translated Value

. add_estimated_fdr_style_1 percolator_style_1 qvality_style_1 sanitize_csv_style_1 svm_style_1 ucontroller_style_1 unify_csv_style_1

deepnovo_0_0_1 DeepNovo:score DeepNovo:score DeepNovo:score DeepNovo:score DeepNovo:score DeepNovo:score DeepNovo:score

deepnovo_pointnovo DeepNovo:score DeepNovo:score DeepNovo:score DeepNovo:score DeepNovo:score DeepNovo:score DeepNovo:score

mascot_x_x_x Mascot:Score Mascot:Score Mascot:Score Mascot:Score Mascot:Score Mascot:Score Mascot:Score

moda_v1_51 ModA:probability ModA:probability ModA:probability ModA:probability ModA:probability ModA:probability ModA:probability

moda_v1_61 ModA:probability ModA:probability ModA:probability ModA:probability ModA:probability ModA:probability ModA:probability

moda_v1_62 ModA:probability ModA:probability ModA:probability ModA:probability ModA:probability ModA:probability ModA:probability

msamanda_1_0_0_5242 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_1_0_0_5243 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_1_0_0_6299 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_1_0_0_6300 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_1_0_0_7503 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_1_0_0_7504 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_2_0_0_10695 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_2_0_0_11219 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_2_0_0_13723 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_2_0_0_14665 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_2_0_0_9695 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msamanda_2_0_0_9706 Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score Amanda:Score

msfragger_20170103 MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore

msfragger_20171106 MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore

msfragger_20190222 MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore

msfragger_20190628 MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore

msfragger_2_3 MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore

msfragger_3_0 MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore MSFragger:Hyperscore

msgfplus_v2016_09_16 MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue

msgfplus_v2017_01_27 MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue

msgfplus_v2018_01_30 MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue

msgfplus_v2018_06_28 MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue

msgfplus_v2018_09_12 MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue

msgfplus_v2019_01_22 MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue

msgfplus_v2019_04_18 MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue

msgfplus_v2019_07_03 MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue

msgfplus_v9979 MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue MS-GF:SpecEValue

myrimatch_2_1_138 MyriMatch:MVH MyriMatch:MVH MyriMatch:MVH MyriMatch:MVH MyriMatch:MVH MyriMatch:MVH MyriMatch:MVH

myrimatch_2_2_140 MyriMatch:MVH MyriMatch:MVH MyriMatch:MVH MyriMatch:MVH MyriMatch:MVH MyriMatch:MVH MyriMatch:MVH

novor_1_05 Novor:score Novor:score Novor:score Novor:score Novor:score Novor:score Novor:score

novor_1_1beta Novor:score Novor:score Novor:score Novor:score Novor:score Novor:score Novor:score

omssa_2_1_9 OMSSA:pvalue OMSSA:pvalue OMSSA:pvalue OMSSA:pvalue OMSSA:pvalue OMSSA:pvalue OMSSA:pvalue

pepnovo_3_1 Pepnovo:PnvScr Pepnovo:PnvScr Pepnovo:PnvScr Pepnovo:PnvScr Pepnovo:PnvScr Pepnovo:PnvScr Pepnovo:PnvScr

pglyco_db_2_2_0 pGlyco:TotalScore pGlyco:TotalScore pGlyco:TotalScore pGlyco:TotalScore pGlyco:TotalScore pGlyco:TotalScore pGlyco:TotalScore

pglyco_db_2_2_2 pGlyco:TotalScore pGlyco:TotalScore pGlyco:TotalScore pGlyco:TotalScore pGlyco:TotalScore pGlyco:TotalScore n/t

pipi_1_4_5 PIPI:score PIPI:score PIPI:score PIPI:score PIPI:score PIPI:score PIPI:score

pipi_1_4_6 PIPI:score PIPI:score PIPI:score PIPI:score PIPI:score PIPI:score PIPI:score

pnovo_3_1_3 pNovo:Score pNovo:Score pNovo:Score pNovo:Score pNovo:Score pNovo:Score n/t

tag_graph_1_8_0 TagGraph:: 1-log10 EM TagGraph:: 1-log10 EM TagGraph:: 1-log10 EM TagGraph:: 1-log10 EM TagGraph:: 1-log10 EM TagGraph:: 1-log10 EM TagGraph:: 1-log10 EM

unknown n/t n/t n/t n/t n/t n/t

xtandem_alanine X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore

xtandem_cyclone_2010 X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore

xtandem_jackhammer X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore

xtandem_piledriver X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore

xtandem_sledgehammer X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore

xtandem_vengeance X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore X!Tandem:hyperscore

visualization_color_positions¶

Specifies colors for the datasets that should be visualized. Given as a dict in which the key represents the position of the corresponding dataset in the list, e.g.: {“0” : “#e41a1c”, “1” : “#377eb8”}

Default value:	[]
type:	dict
triggers rerun:	True

Available in unodes¶

venndiagram_1_1_0

Ursgal key translations for visualization_color_positions¶

Style Translation

venndiagram_style_1 visualization_color_position

visualization_column_names¶

The specified csv column names are used for the visualization. E.g. for a Venn diagram the entries of these columns are used (merged) to determine overlapping results.

Default value:	[‘Modifications’, ‘Sequence’]
type:	list
triggers rerun:	True

Available in unodes¶

venndiagram_1_0_0
venndiagram_1_1_0

Ursgal key translations for visualization_column_names¶

Style Translation

venndiagram_style_1 visualization_column_names

visualization_font¶

Font used for visualization plots (e.g. Venn diagram), given as dict with keys: font_type, font_size_header, font_size_major, font_size_minor, font_size_venn

Default value:	[‘font_size_header’, ‘font_size_major’, ‘font_size_minor’, ‘font_size_venn’, ‘font_type’]
type:	dict
triggers rerun:	True

Available in unodes¶

venndiagram_1_0_0
venndiagram_1_1_0

Ursgal key translations for visualization_font¶

Style Translation

venndiagram_style_1 visualization_font

visualization_header¶

Header of visualization output (e.g. Venn diagram)

Default value:
type:	str
triggers rerun:	True

Available in unodes¶

venndiagram_1_0_0
venndiagram_1_1_0
sugarpy_plot_1_0_0

Ursgal key translations for visualization_header¶

Style Translation

sugarpy_plot_style_1 title

venndiagram_style_1 header

visualization_label_positions¶

Specifies labels for the datasets that should be visualized. Given as a dict in which the key represents the position of the corresponding dataset in the list, e.g.: {“0” : “LabelA”, “1” : “LabelB”}

Default value:	[]
type:	dict
triggers rerun:	True

Available in unodes¶

venndiagram_1_0_0
venndiagram_1_1_0

Ursgal key translations for visualization_label_positions¶

Style Translation

venndiagram_style_1 visualization_label_position

visualization_opacity¶

Opacity used in visualization plots (e.g. Venn diagram)

Default value:	0.35
type:	float
triggers rerun:	True

Available in unodes¶

venndiagram_1_0_0
venndiagram_1_1_0

Ursgal key translations for visualization_opacity¶

Style Translation

venndiagram_style_1 opacity

visualization_scaling_factors¶

Scaling factor for visualization plots (e.g. Venn diagram), given as dict with keys: x_axis, y_axis

Default value:	[‘x_axis’, ‘y_axis’]
type:	dict
triggers rerun:	True

Available in unodes¶

venndiagram_1_0_0
venndiagram_1_1_0

Ursgal key translations for visualization_scaling_factors¶

Style Translation

venndiagram_style_1 visualization_scaling_factors

visualization_size¶

Size of visualization plots (e.g. Venn diagram), given as dict with keys: width, height

Default value:	[‘height’, ‘width’]
type:	dict
triggers rerun:	True

Available in unodes¶

venndiagram_1_0_0
venndiagram_1_1_0

Ursgal key translations for visualization_size¶

Style Translation

venndiagram_style_1 visualization_size

visualization_stroke_width¶

Stroke width used in visualization plots (e.g. Venn diagram)

Default value:	2.0
type:	float
triggers rerun:	True