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

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

user@localhost:~/ursgal/docs$ python3.4 uparams_to_sphinx_docu.py
A local server will be created and view the interactive page:

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

Note

This sphinx source file was auto-generated using ursgal/docs/uparams_to_sphinx_docu.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_v9979
  • mzidentml_lib_1_6_10
  • mzidentml_lib_1_6_11
  • mzidentml_lib_1_7
  • msfragger_20170103
  • pipi_1_3_0

Ursgal key translations for -xmx

Style Translation
msfragger_style_1 -Xmx
msgfplus_style_1 -Xmx
mzidentml_style_1 -Xmx
pipi_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)

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

Ursgal key translations for aa_exception_dict

Style Translation
compomics_utilities_style_1 aa_exception_dict
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

allow_multiple_variable_mods_on_residue

Static mods are not considered

Default value:True
type:bool
triggers rerun:True

Available in unodes

  • msfragger_20170103

Ursgal key translations for allow_multiple_variable_mods_on_residue

Style Translation
msfragger_style_1 allow_multiple_variable_mods_on_residue

Ursgal value translations

Ursgal Value Translated Value
. msfragger_style_1
0 0
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
  • omssa_2_1_9
  • pepnovo_3_1
  • pipi_1_3_0

Ursgal key translations for base_mz

Style Translation
moda_style_1 base_mz
omssa_style_1 base_mz
pepnovo_style_1 base_mz
pipi_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

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

Ursgal key translations for batch_size_spectra

Style Translation
msamanda_style_1 LoadedSpectraAtOnce

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
  • qvality_2_02
  • sanitize_csv_1_0_0
  • svm_1_0_0

Ursgal key translations for bigger_scores_better

Style Translation
add_estimated_fdr_style_1 bigger_scores_better
percolator_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
mascot_x_x_x 1 1 1 1 1
moda_v1_51 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_9695 1 1 1 1 1
msamanda_2_0_0_9706 1 1 1 1 1
msfragger_20170103 1 1 1 1 1
msgfplus_v2016_09_16 0 0 0 0 0
msgfplus_v2017_01_27 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
pipi_1_3_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

Ursgal key translations for build_pyqms_result_index

Style Translation
pyqms_style_1 BUILD_RESULT_INDEX

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

Ursgal key translations for clip_nterm_m

Style Translation
msfragger_style_1 clip_nTerm_M

Ursgal value translations

Ursgal Value Translated Value
. msfragger_style_1
0 0
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
kojak_1_5_3 0
mascot_x_x_x 1
moda_v1_51 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_9695 0
msamanda_2_0_0_9706 0
msfragger_20170103 0
msgfplus_v2016_09_16 1
msgfplus_v2017_01_27 1
msgfplus_v9979 1
myrimatch_2_1_138 1
myrimatch_2_2_140 1
novor_1_1beta 0
omssa_2_1_9 0
pepnovo_3_1 0
pipi_1_3_0 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_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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • 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
  • pipi_1_3_0

Ursgal key translations for cpus

Style Translation
kojak_style_1 cpus
msfragger_style_1 num_threads
msgfplus_style_1 -thread
myrimatch_style_1 -cpus
omssa_style_1 -nt
pipi_style_1 thread_num
ucontroller_style_1 cpus
xtandem_style_1 spectrum, threads

Ursgal value translations

Ursgal Value Translated Value
. kojak_style_1 msgfplus_style_1 myrimatch_style_1 omssa_style_1 ucontroller_style_1 xtandem_style_1
-1 max - 1 max - 1 max - 1 max - 1 max - 1 max - 1

csv_filter_rules

Rules are defined as list of lists with three elements:

  1. the column name/csv fieldname,
  2. the rule,
  3. 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
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • 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
  • pipi_1_3_0

Ursgal key translations for database

Style Translation
compomics_utilities_style_1 database
kojak_style_1 database
moda_style_1 Fasta
msamanda_style_1 database
msfragger_style_1 database_name
msgfplus_style_1 -d
myrimatch_style_1 ProteinDatabase
omssa_style_1 -d
pipi_style_1 db
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

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

Ursgal key translations for decoy_tag

Style Translation
generate_target_decoy_style_1 decoy_tag
kojak_style_1 decoy_tag
myrimatch_style_1 DecoyPrefix
mzidentml_style_1 -decoyRegex
unify_csv_style_1 decoy_tag
upeptide_mapper_style_1 decoy_tag
xtandem2csv_style_1 decoy_tag

deisotope_spec

Perform Deisotoping for MS2 spectra

Default value:True
type:bool
triggers rerun:True

Available in unodes

  • msamanda_2_0_0_9695
  • msamanda_2_0_0_9706

Ursgal key translations for deisotope_spec

Style Translation
msamanda_style_1 PerformDeisotoping

Ursgal value translations

Ursgal Value Translated Value
. msamanda_style_1
0 false
1 true

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

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 for PepNovo. If ‘None’, it is supposed to be in :

resources/<platform>/<architecture>/pepnovo_3_1

Default value:None
type:str
triggers rerun:True

Available in unodes

  • pepnovo_3_1

Ursgal key translations for denovo_model_dir

Style Translation
pepnovo_style_1 -model_dir

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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • xtandem_cyclone_2010
  • xtandem_jackhammer
  • xtandem_piledriver
  • xtandem_sledgehammer
  • xtandem_vengeance
  • xtandem_alanine

Ursgal key translations for engine_internal_decoy_generation

Style Translation
msamanda_style_1 generate_decoy
msgfplus_style_1 -tda
xtandem_style_1 scoring, include reverse

Ursgal value translations

Ursgal Value Translated Value
. msamanda_style_1 msgfplus_style_1 xtandem_style_1
0 false 0 no
1 true 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
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • novor_1_1beta
  • omssa_2_1_9
  • pepnovo_3_1
  • percolator_2_08
  • unify_csv_1_0_0
  • xtandem_cyclone_2010
  • xtandem_jackhammer
  • xtandem_piledriver
  • xtandem_sledgehammer
  • xtandem_vengeance
  • xtandem_alanine
  • msfragger_20170103
  • pipi_1_3_0

Ursgal key translations for enzyme

Style Translation
generate_target_decoy_style_1 enzyme
kojak_style_1 enzyme
moda_style_1 Enzyme
msamanda_style_1 enzyme specificity
msfragger_style_1 enzyme
msgfplus_style_1 -e
myrimatch_style_1 CleavageRules
novor_style_1 enzyme
omssa_style_1 -e
pepnovo_style_1 -digest
percolator_style_1 enzyme
pipi_style_1 enzyme
unify_csv_style_1 enzyme
xtandem_style_1 protein, cleavage site

Ursgal value translations

Ursgal Value Translated Value
. generate_target_decoy_style_1 kojak_style_1 moda_style_1 msamanda_style_1 msfragger_style_1 msgfplus_style_1 myrimatch_style_1 novor_style_1 omssa_style_1 pepnovo_style_1 percolator_style_1 pipi_style_1 unify_csv_style_1 xtandem_style_1
alpha_lp 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
argc R;C;P n/t argc, R/C R;after;P R;C;P 6 n/t n/t 1 n/t R;C;P n/t R;C;P [R]|{P}
aspn D;N; n/t aspn, D/N; D;before; D;N; 7 Asp-N n/t 12 n/t D;N; AspN;0;D;- D;N; [X]|[D]
aspn_gluc 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
chymotrypsin FMWY;C;P n/t chymotrypsin, FMWY/C FMWY;after;P FMWY;C;P 2 Chymotrypsin n/t 3 n/t FMWY;C;P Chymotrypsin;1;FMWY;P FMWY;C;P [FMWY]|{P}
chymotrypsin_p FMWY;C; n/t chymotrypsin, FMWY/C FMWY;after; FMWY;C; n/t n/t n/t 18 n/t FMWY;C; n/t FMWY;C; [FMWY]|[X]
clostripain R;C; n/t clostripain, R/C R;after; R;C; n/t n/t n/t n/t n/t R;C; n/t R;C; [R]|[X]
cnbr M;C;P n/t cnbr, M/C M;after;P M;C;P n/t CNBr n/t 2 n/t M;C;P n/t M;C;P [M]|{P}
elastase AGILV;C;P n/t elastase, AGILV/C AGILV;after;P AGILV;C;P n/t n/t n/t n/t n/t AGILV;C;P n/t AGILV;C;P [AGILV]|{P}
formic_acid D;C;P n/t formic_acid, D/C D;after;P D;C;P n/t Formic_acid n/t 4 n/t D;C;P n/t D;C;P [D]|{P}
gluc DE;C;P [DE]|{P} gluc, DE/C DE;after;P DE;C;P 5 n/t n/t 13 n/t DE;C;P GluC;1;DE;P DE;C;P [DE]|{P}
gluc_bicarb E;C;P n/t gluc_bicarb, E/C E;after;P E;C;P n/t n/t n/t n/t n/t E;C;P n/t E;C;P [E]|{P}
iodosobenzoate W;C; n/t iodosobenzoate, W/C W;after; W;C; n/t n/t n/t n/t n/t W;C; n/t W;C; [W]|[X]
lysc K;C;P n/t lysc, K/C K;after;P K;C;P 3 Lys-C n/t 5 n/t K;C;P n/t K;C;P [K]|{P}
lysc_gluc DEK;C;P [DEK]|{P} n/t DEK;after;P DEK;C;P n/t n/t n/t n/t n/t DEK;C;P n/t DEK;C;P [DEK]|[X]|{P}
lysc_p K;C; n/t lysc_p, K/C K;after; K;C; n/t Lys-C/P n/t 6 n/t K;C; LysC;1;K;- K;C; [K]|[X]
lysn K;N; |[K] lysn, K/N K;before; K;N; 4 n/t n/t 21 n/t K;N; LysN;0;K;- K;N; [X]|[K]
lysn_promisc AKRS;N; n/t lysn_promisc, AKRS/N AKRS;before; AKRS;N; n/t n/t n/t n/t n/t AKRS;N; n/t AKRS;N; [X]|[AKRS]
no_cleavage n/t n/t NONE n/t n/t 9 n/t n/t 11 n/t n/t n/t n/t n/t
nonspecific n/t n/t n/t ;; n/t 0 n/t n/t 17 NON_SPECIFIC n/t n/t n/t [X]|[X]
pepsina FL;C; n/t pepsina, FL/C FL;after; FL;C; n/t PepsinA n/t 7 n/t FL;C; n/t FL;C; [FL]|[X]
protein_endopeptidase P;C; n/t protein_endopeptidase, P/C P;after; P;C; n/t n/t n/t n/t n/t P;C; n/t P;C; [P]|[X]
staph_protease E;C; n/t staph_protease, E/C E;after; E;C; n/t n/t n/t n/t n/t E;C; 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 [FMWY]|{P},[KR]|{P},[X]|[D]
thermolysin_p 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
top_down 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
trypsin KR;C;P [KR]|{P} trypsin, KR/C KR;after;P KR;C;P 1 Trypsin Trypsin 0 TRYPSIN KR;C;P Trypsin;1;KR;P KR;C;P [KR]|{P}
trypsin_chymotrypsin 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
trypsin_cnbr KRM;C;P n/t trypsin_cnbr, KRM/C KRM;after;P KRM;C;P n/t n/t n/t 8 n/t KRM;C;P n/t KRM;C;P [KR]|{P},[M]|{P}
trypsin_gluc DEKR;C;P n/t trypsin_gluc, DEKR/C DEKR;after;P DEKR;C;P n/t n/t n/t n/t n/t DEKR;C;P n/t DEKR;C;P [DEKR]|{P}
trypsin_p KR;C; [RK]| trypsin_p, KR/C KR;after; KR;C; 1 Trypsin/P n/t 10 n/t KR;C; n/t 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

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

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

Ursgal key translations for fixed_label_isotope_enrichment_levels

Style Translation
pyqms_style_1 FIXED_LABEL_ISOTOPE_ENRICHMENT_LEVELS

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

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
  • pipi_1_3_0

Ursgal key translations for frag_clear_mz_range

Style Translation
msfragger_style_1 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
  • 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
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • novor_1_1beta
  • omssa_2_1_9
  • pepnovo_3_1
  • xtandem_cyclone_2010
  • xtandem_jackhammer
  • xtandem_piledriver
  • xtandem_sledgehammer
  • xtandem_vengeance
  • xtandem_alanine
  • msfragger_20170103
  • pipi_1_3_0

Ursgal key translations for frag_mass_tolerance

Style Translation
moda_style_1 FragTolerance
msamanda_style_1 ms2_tol
msfragger_style_1 fragment_mass_tolerance
myrimatch_style_1 FragmentMzTolerance
novor_style_1 fragmentIonErrorTol
omssa_style_1 -to
pepnovo_style_1 -fragment_tolerance
pipi_style_1 ms2_tolerance
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
  • 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
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • novor_1_1beta
  • omssa_2_1_9
  • pepnovo_3_1
  • xtandem_cyclone_2010
  • xtandem_jackhammer
  • xtandem_piledriver
  • xtandem_sledgehammer
  • xtandem_vengeance
  • xtandem_alanine
  • msfragger_20170103
  • pipi_1_3_0

Ursgal key translations for frag_mass_tolerance_unit

Style Translation
moda_style_1 FragTolerance
msamanda_style_1 ms2_tol unit
msfragger_style_1 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
pipi_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 myrimatch_style_1 novor_style_1 omssa_style_1 xtandem_style_1
da Da 0 Da Da Da Daltons
ppm n/t 1 n/t n/t n/t 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
  • pipi_1_3_0

Ursgal key translations for frag_max_charge

Style Translation
msfragger_style_1 max_fragment_charge
omssa_style_1 -zoh
pipi_style_1 max_ms2_charge

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_v9979
  • novor_1_1beta

Ursgal key translations for frag_method

Style Translation
msgfplus_style_1 -m
novor_style_1 fragmentation

Ursgal value translations

Ursgal Value Translated Value
. msgfplus_style_1 novor_style_1
cid 1 CID
etd 2 n/t
hcd 3 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_http_style_1 ftp_blocksize

ftp_folder

ftp folder that should be downloaded
‘’ : None
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_http_style_1 ftp_folder

ftp_include_ext

Only files with the defined file extension are downloaded with ftp download
‘’ : None
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_http_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

Ursgal key translations for ftp_login

Style Translation
get_http_style_1 ftp_login

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_http_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_http_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_http_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_http_style_1 ftp_url

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
  • msgfplus2csv_v2016_09_16
  • msgfplus2csv_v2017_01_27
  • novor_1_1beta
  • omssa_2_1_9
  • pepnovo_3_1
  • msfragger_20170103
  • msgfplus_C_mzid2csv_v2017_07_04
  • pipi_1_3_0

Ursgal key translations for header_translations

Style Translation
kojak_percolator_style_1 header_translations
msamanda_style_1 header_translations
msfragger_style_1 header_translations
msgfplus_style_1 header_translations
novor_style_1 header_translations
omssa_style_1 header_translations
pepnovo_style_1 header_translations
pipi_style_1 header_translations

Ursgal value translations

Ursgal Value Translated Value
. kojak_percolator_style_1 msamanda_style_1 msfragger_style_1 msgfplus_style_1 novor_style_1 omssa_style_1 pepnovo_style_1 pipi_style_1
Accession n/t n/t n/t n/t n/t Accession n/t n/t
Charge n/t n/t n/t n/t n/t Charge n/t n/t
Defline n/t n/t n/t n/t n/t proteinacc_start_stop_pre_post; n/t n/t
E-value n/t n/t n/t n/t n/t OMSSA:evalue n/t n/t
Filename/id n/t n/t n/t n/t n/t Spectrum Title n/t n/t
Mass n/t n/t n/t n/t n/t Exp m/z n/t n/t
Mods n/t n/t n/t n/t n/t Modifications n/t n/t
NIST score n/t n/t n/t n/t n/t NIST score n/t n/t
P-value n/t n/t n/t n/t n/t OMSSA:pvalue n/t n/t
Peptide n/t n/t n/t n/t n/t Sequence n/t n/t
RT n/t n/t n/t n/t Retention Time (s) n/t n/t n/t
Start n/t n/t n/t n/t n/t Start n/t n/t
Stop n/t n/t n/t n/t n/t Stop n/t n/t
Theo Mass n/t n/t n/t n/t n/t Calc m/z n/t n/t
aaScore n/t n/t n/t n/t Novor:aaScore n/t n/t n/t
err(data-denovo) n/t n/t n/t n/t Error (exp-calc) n/t n/t n/t
gi n/t n/t n/t n/t n/t gi n/t n/t
mz(data) n/t n/t n/t n/t Exp m/z n/t n/t n/t
pepMass(denovo) n/t n/t n/t n/t Calc mass n/t n/t n/t
peptide n/t n/t n/t n/t Sequence n/t n/t n/t
ppm(1e6*err/(mz*z)) n/t n/t n/t n/t Error (ppm) n/t n/t n/t
scanNum n/t n/t n/t n/t Spectrum ID n/t n/t n/t
score n/t n/t n/t n/t Novor:score n/t n/t n/t
z n/t n/t n/t n/t Charge n/t n/t n/t
# id n/t n/t n/t n/t Novor:id n/t n/t n/t
#Index n/t n/t n/t n/t n/t n/t Pepnovo:id n/t
#SpecFile n/t n/t n/t Raw data location n/t n/t n/t n/t
Amanda Score n/t Amanda:Score 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 Pepnovo:C-Gap n/t
Charge n/t Charge n/t Charge n/t n/t n/t n/t
CumProb n/t n/t n/t n/t n/t n/t Pepnovo:CumProb n/t
DeNovoScore n/t n/t n/t MS-GF:DeNovoScore n/t n/t n/t n/t
Downstream Amino Acid n/t n/t Sequence Post AA n/t n/t n/t n/t n/t
EValue n/t n/t n/t MS-GF:EValue n/t n/t n/t n/t
Filename n/t Filename n/t n/t n/t n/t n/t n/t
Hit rank n/t n/t Rank n/t n/t n/t n/t n/t
Hyperscore n/t n/t MSFragger:Hyperscore n/t n/t n/t n/t n/t
Intercept of expectation model (expectation in log space) n/t n/t MSFragger:Intercept of expectation model (expectation in log space) 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 Spectrum Title
MSGFScore n/t n/t n/t MS-GF:RawScore n/t n/t n/t n/t
Mass difference n/t n/t Mass Difference n/t n/t n/t n/t n/t
Matched fragment ions n/t n/t MSFragger:Matched fragment ions n/t n/t n/t n/t n/t
Modifications n/t Modifications n/t n/t n/t n/t n/t n/t
N-Gap n/t n/t n/t n/t n/t n/t Pepnovo:N-Gap n/t
Neutral mass of peptide n/t n/t MSFragger:Neutral mass of peptide n/t n/t n/t n/t n/t
Next score n/t n/t MSFragger:Next score n/t n/t n/t n/t n/t
Number of missed cleavages n/t n/t MSFragger:Number of missed cleavages n/t n/t n/t n/t n/t
Number of tryptic termini n/t n/t MSFragger:Number of tryptic termini n/t n/t n/t n/t n/t
PSMId PSMId n/t n/t n/t n/t n/t n/t n/t
Peptide n/t n/t n/t Sequence n/t n/t n/t n/t
Peptide Sequence n/t n/t Sequence n/t n/t n/t n/t n/t
PnvScr n/t n/t n/t n/t n/t n/t Pepnovo:PnvScr n/t
Precursor n/t n/t n/t Exp m/z n/t n/t n/t n/t
Precursor charge n/t n/t Charge n/t n/t n/t n/t n/t
Precursor neutral mass (Da) n/t n/t MSFragger:Precursor neutral mass (Da) n/t n/t n/t n/t n/t
Protein n/t n/t Protein ID proteinacc_start_stop_pre_post; n/t n/t n/t n/t
Protein Accessions n/t proteinacc_start_stop_pre_post; n/t n/t n/t n/t n/t n/t
RT n/t Retention Time (s) n/t n/t n/t n/t n/t n/t
Rank n/t Rank n/t n/t n/t n/t n/t n/t
Retention time (minutes) n/t n/t Retention Time (s) n/t n/t n/t n/t n/t
RnkScr n/t n/t n/t n/t n/t n/t Pepnovo:RnkScr n/t
Scan Number n/t Spectrum ID n/t n/t n/t n/t n/t n/t
ScanID n/t n/t Spectrum ID n/t n/t n/t n/t n/t
ScanNum n/t n/t n/t Spectrum ID n/t n/t n/t n/t
Sequence n/t Sequence n/t n/t n/t n/t n/t n/t
Slope of expectation model (expectation in log space) n/t n/t MSFragger:Slope of expectation model (expectation in log space) n/t n/t n/t n/t n/t
SpecEValue n/t n/t n/t MS-GF:SpecEValue n/t n/t n/t n/t
SpecFile n/t n/t n/t Raw data location n/t n/t n/t n/t
Spectrum number n/t n/t n/t n/t n/t Spectrum ID n/t n/t
Title n/t Spectrum Title n/t Spectrum Title n/t n/t n/t n/t
Total possible number of matched theoretical fragment ions n/t n/t MSFragger:Total possible number of matched theoretical fragment ions n/t n/t n/t n/t n/t
Upstream Amino Acid n/t n/t Sequence Pre AA n/t n/t n/t n/t n/t
Variable modifications detected n/t n/t Modifications n/t n/t n/t n/t n/t
Weighted Probability n/t Amanda:Weighted Probability 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 Calc mass(Da) n/t
abs_ppm n/t n/t n/t n/t n/t n/t n/t PIPI:abs_ppm
charge n/t n/t n/t n/t n/t n/t n/t Charge
delta_C n/t n/t n/t n/t n/t n/t n/t PIPI:delta_C
exp_mass n/t n/t n/t n/t n/t n/t n/t Exp m/z
m/z n/t Exp m/z n/t n/t n/t n/t n/t n/t
naive_q_value n/t n/t n/t n/t n/t n/t n/t PIPI:naive_q_value
other_PTM_patterns n/t n/t n/t n/t n/t n/t n/t PIPI:other_PTM_patterns
output_aa_probs n/t n/t n/t n/t n/t n/t Pepnovo:aaScore n/t
peptide Sequence n/t n/t n/t n/t n/t n/t Sequence
percolator_q_value n/t n/t n/t n/t n/t n/t n/t PIPI:percolator_q_value
percolator_score n/t n/t n/t n/t n/t n/t n/t PIPI:percolator_score
posterior_error_prob PEP n/t n/t n/t n/t n/t n/t PIPI:posterior_error_prob
proteinIds Protein ID 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 Protein ID
ptm_delta_score n/t n/t n/t n/t n/t n/t n/t PIPI:ptm_delta_score protein_ID
q-value q-value 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 Spectrum ID
score Kojak:score n/t n/t n/t n/t n/t n/t PIPI:score
theo_mass n/t n/t n/t n/t n/t n/t n/t Calc m/z

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_order

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

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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • novor_1_1beta

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

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

Ursgal key translations for intensity_cutoff

Style Translation
msfragger_style_1 minimum_ratio
omssa_style_1 -cl

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

Ursgal key translations for intensity_transformation_factor

Style Translation
pyqms_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

Ursgal key translations for internal_precision

Style Translation
pyqms_style_1 INTERNAL_PRECISION

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_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_truncate_prot_names

Max protein name character to export, 0=off

Default value:0
type:int
triggers rerun:True

Available in unodes

  • kojak_1_5_3

Ursgal key translations for kojak_truncate_prot_names

Style Translation
kojak_style_1 kojak_truncate_prot_names

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
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • 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
  • pipi_1_3_0
  • pyqms_1_0_0

Ursgal key translations for label

Style Translation
moda_style_1 label
msamanda_style_1 label
msfragger_style_1 label
msgfplus_style_1 label
myrimatch_style_1 label
omssa_style_1 (‘-tem’, ‘-tom’)
pipi_style_1 label
pyqms_style_1 label
xtandem_style_1 protein, modified residue mass file

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

Ursgal key translations for label_percentile_format_string

Style Translation
pyqms_style_1 PECENTILE_FORMAT_STRING

lower_mz_limit

lowest considered mz for quantification

Default value:150
type:float
triggers rerun:True

Available in unodes

  • pyqms_1_0_0

Ursgal key translations for lower_mz_limit

Style Translation
pyqms_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

Ursgal key translations for m_score_cutoff

Style Translation
pyqms_style_1 m_score_cutoff

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
  • pyqms_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

max_accounted_observed_peaks

Maximum number of peaks from a spectrum used.

Default value:100
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

Ursgal key translations for max_accounted_observed_peaks

Style Translation
kojak_style_1 max_accounted_observed_peaks
msfragger_style_1 use_topN_peaks
myrimatch_style_1 MaxPeakCount
xtandem_style_1 spectrum, total peaks

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
  • 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
  • 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
  • pipi_1_3_0

Ursgal key translations for max_missed_cleavages

Style Translation
kojak_style_1 max_missed_cleavages
moda_style_1 MissedCleavage
msamanda_style_1 missed_cleavages
msfragger_style_1 allowed_missed_cleavage
myrimatch_style_1 MaxMissedCleavages
omssa_style_1 -v
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
  • pipi_1_3_0

Ursgal key translations for max_mod_size

Style Translation
moda_style_1 MaxModSize
pipi_style_1 max_ptm_mass

max_molecules_per_match_bin

Max number of molecules in one matching bin.

Default value:20
type:int
triggers rerun:True

Available in unodes

  • pyqms_1_0_0

Ursgal key translations for max_molecules_per_match_bin

Style Translation
pyqms_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

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_v9979
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • msamanda_2_0_0_9695
  • msamanda_2_0_0_9706

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

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

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

Ursgal key translations for max_num_neutral_loss_mod

Style Translation
msamanda_style_1 MaxNumberNeutralLossModificati

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
  • msamanda_2_0_0_9706
  • msamanda_2_0_0_9695

Ursgal key translations for max_num_per_mod

Style Translation
msamanda_style_1 MaxNoModifs
msfragger_style_1 max_variable_mods_per_mod

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_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_v9979
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • omssa_2_1_9
  • msfragger_20170103

Ursgal key translations for max_pep_length

Style Translation
msfragger_style_1 digest_max_length
msgfplus_style_1 -maxLength
myrimatch_style_1 MaxPeptideLength
omssa_style_1 -nox

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

Ursgal key translations for max_pep_var

Style Translation
msfragger_style_1 max_variable_mods_combinations
msgfplus_style_1 -maxLength
myrimatch_style_1 MaxPeptideVariants
omssa_style_1 -nox

mgf_input_file

Path to input .mgf file
‘’ : None
Default value:None
type:str
triggers rerun:True

Available in unodes

  • moda_v1_51
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • novor_1_1beta
  • omssa_2_1_9
  • pepnovo_3_1
  • xtandem_cyclone_2010
  • xtandem_jackhammer
  • xtandem_piledriver
  • xtandem_sledgehammer
  • xtandem_vengeance
  • xtandem_alanine

Ursgal key translations for mgf_input_file

Style Translation
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
xtandem_style_1 spectrum, path

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

Ursgal key translations for min_element_abundance

Style Translation
pyqms_style_1 ELEMENT_MIN_ABUNDANCE

min_mod_size

Minimum modification size to consider (in Da)

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

Available in unodes

  • moda_v1_51
  • pipi_1_3_0

Ursgal key translations for min_mod_size

Style Translation
moda_style_1 MinModSize
pipi_style_1 min_ptm_mass

min_number_of_matched_isotopologues

Min number of matched isotopologues for pyqms to consider for quantification

Default value:2
type:int
triggers rerun:True

Available in unodes

  • pyqms_1_0_0

Ursgal key translations for min_number_of_matched_isotopologues

Style Translation
pyqms_style_1 MININUM_NUMBER_OF_MATCHES_ISOTOPOLOGUES

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_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_v9979
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • omssa_2_1_9
  • msfragger_20170103
  • msamanda_2_0_0_9706
  • msamanda_2_0_0_9695

Ursgal key translations for min_pep_length

Style Translation
msamanda_style_1 MinimumPepLength
msfragger_style_1 digest_min_length
msgfplus_style_1 -minLength
myrimatch_style_1 MinPeptideLength
omssa_style_1 -no

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_rel_peak_intensity_for_matching

Minimum required intensity for pyqms peak matching

Default value:0.01
type:float
triggers rerun:True

Available in unodes

  • pyqms_1_0_0

Ursgal key translations for min_rel_peak_intensity_for_matching

Style Translation
pyqms_style_1 MIN_REL_PEAK_INTENSITY_FOR_MATCHING

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

Ursgal key translations for min_required_matched_peaks

Style Translation
msfragger_style_1 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
  • pipi_1_3_0

Ursgal key translations for min_required_observed_peaks

Style Translation
msfragger_style_1 minimum_peaks
omssa_style_1 -hs
pipi_style_1 min_peak_num
xtandem_style_1 spectrum, minimum peaks

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

Ursgal key translations for moda_blind_mode

Style Translation
moda_style_1 BlindMode

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

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

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

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
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • novor_1_1beta
  • omssa_2_1_9
  • pepnovo_3_1
  • 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
  • pipi_1_3_0
  • pyqms_1_0_0

Ursgal key translations for modifications

Style Translation
kojak_style_1 modifications
moda_style_1 ADD
msamanda_style_1 modifications
msfragger_style_1 modifications
msgfplus_style_1 -mod
myrimatch_style_1 (‘DynamicMods’, ‘StaticMods’)
novor_style_1 (‘variableModifications’, ‘fixedModifications’)
omssa_style_1 (‘-mv’, ‘mf’)
pepnovo_style_1 -PTMs
pipi_style_1 modifications
pyqms_style_1 modifications
unify_csv_style_1 modifications
upeptide_mapper_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’)

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

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

Ursgal key translations for ms_level

Style Translation
mzml2mgf_style_1 ms_level
pyqms_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

Ursgal key translations for msfragger_add_topN_complementary

Style Translation
msfragger_style_1 add_topN_complementary

Ursgal value translations

Ursgal Value Translated Value
. msfragger_style_1
0 0
1 1

msfragger_min_fragments_modelling

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

Default value:3
type:int
triggers rerun:True

Available in unodes

  • msfragger_20170103

Ursgal key translations for msfragger_min_fragments_modelling

Style Translation
msfragger_style_1 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

Ursgal key translations for msfragger_output_max_expect

Style Translation
msfragger_style_1 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

Ursgal key translations for msfragger_track_zero_topN

Style Translation
msfragger_style_1 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

Ursgal key translations for msfragger_zero_bin_accept_expect

Style Translation
msfragger_style_1 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

Ursgal key translations for msfragger_zero_bin_mult_expect

Style Translation
msfragger_style_1 zero_bin_mult_expect

msgfplus_mzid_converter_version

Determines which msgfplus mzid conversion node should be used e.g. “msgfplus_C_mzid2csv_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_v2016_09_16
msgfplus_v2017_01_27 msgfplus2csv_v2017_01_27
msgfplus_v9979 mzidentml_lib_1_6_10

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_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

Ursgal key translations for mz_score_percentile

Style Translation
pyqms_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

Ursgal key translations for mz_transformation_factor

Style Translation
pyqms_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_1_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

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

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_hits_retain_spec

Maximum number of hits retained per precursor charge state per spectrum during the search

Default value:30
type:int
triggers rerun:True

Available in unodes

  • omssa_2_1_9

Ursgal key translations for num_hits_retain_spec

Style Translation
omssa_style_1 -hl

num_i_decimals

Number of decimals for intensity (peak)

Default value:5
type:int
triggers rerun:True

Available in unodes

  • mzml2mgf_1_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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • omssa_2_1_9
  • pepnovo_3_1
  • msfragger_20170103

Ursgal key translations for num_match_spec

Style Translation
msamanda_style_1 max_rank
msfragger_style_1 output_report_topN
msgfplus_style_1 -n
myrimatch_style_1 MaxResultRank
omssa_style_1 -hc
pepnovo_style_1 -num_solutions

num_mz_decimals

Number of decimals for m/z mass

Default value:5
type:int
triggers rerun:True

Available in unodes

  • mzml2mgf_1_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

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

Number of decimals for intensity (peak)

Default value:True
type:bool
triggers rerun:True

Available in unodes

  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • 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
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • 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
  • omssa_2_1_9
  • pepnovo_3_1
  • percolator_2_08
  • qvality_2_02
  • venndiagram_1_0_0
  • xtandem_cyclone_2010
  • xtandem_jackhammer
  • xtandem_piledriver
  • xtandem_sledgehammer
  • xtandem_vengeance
  • xtandem_alanine

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
qvality_style_1 -o
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

Ursgal key translations for output_file_type

Style Translation
omssa_style_1 (‘-oc’, ‘-ox’)
xtandem_style_1 output, mzid

Ursgal value translations

Ursgal Value Translated Value
. omssa_style_1 xtandem_style_1
.csv -oc n/t
.mzid n/t yes
.omx -ox n/t
default -oc no

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

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_v3
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

pipi_mz_bin_offset

PIPI mz_bin_offset

Default value:0.0
type:float
triggers rerun:True

Available in unodes

  • pipi_1_3_0

Ursgal key translations for pipi_mz_bin_offset

Style Translation
pipi_style_1 mz_bin_offset

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_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

Ursgal key translations for precursor_isotope_range

Style Translation
kojak_style_1 precursor_isotope_range
msfragger_style_1 isotope_error
msgfplus_style_1 -ti
myrimatch_style_1 MonoisotopeAdjustmentSet
omssa_style_1 -ti
pepnovo_style_1 -correct_pm
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 myrimatch_style_1 omssa_style_1 xtandem_style_1
0 0 0 [0,] 0 no
0,1 1 0/1 [0,1] 1 yes
0,1,2 n/t n/t [0,1,2] n/t n/t
0,2 2 0/1/2 n/t 2 yes

precursor_mass_tolerance_minus

Precursor mass tolerance: lower mass tolerance of measured and calculated parent ion M+H

Default value:5
type:int
triggers rerun:True

Available in unodes

  • kojak_1_5_3
  • moda_v1_51
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • novor_1_1beta
  • 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
  • pipi_1_3_0

Ursgal key translations for precursor_mass_tolerance_minus

Style Translation
kojak_style_1 ppm_tolerance_pre
moda_style_1 PPMTolerance
msamanda_style_1 ms1_tol
msfragger_style_1 precursor_mass_tolerance
msgfplus_style_1 -t
myrimatch_style_1 MonoPrecursorMzTolerance
novor_style_1 precursorErrorTol
omssa_style_1 -te
pepnovo_style_1 -pm_tolerance
pipi_style_1 ms1_tolerance
unify_csv_style_1 precursor_mass_tolerance_minus
xtandem_style_1 spectrum, parent monoisotopic mass error minus

precursor_mass_tolerance_plus

Precursor mass tolerance: higher mass tolerance of measured and calculated parent ion M+H

Default value:5
type:int
triggers rerun:True

Available in unodes

  • kojak_1_5_3
  • moda_v1_51
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • novor_1_1beta
  • 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
  • pipi_1_3_0

Ursgal key translations for precursor_mass_tolerance_plus

Style Translation
kojak_style_1 ppm_tolerance_pre
moda_style_1 PPMTolerance
msamanda_style_1 ms1_tol
msfragger_style_1 precursor_mass_tolerance
msgfplus_style_1 -t
myrimatch_style_1 MonoPrecursorMzTolerance
novor_style_1 precursorErrorTol
omssa_style_1 -te
pepnovo_style_1 -pm_tolerance
pipi_style_1 ms1_tolerance
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
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • novor_1_1beta
  • omssa_2_1_9
  • pepnovo_3_1
  • xtandem_cyclone_2010
  • xtandem_jackhammer
  • xtandem_piledriver
  • xtandem_sledgehammer
  • xtandem_vengeance
  • xtandem_alanine
  • msfragger_20170103
  • pipi_1_3_0

Ursgal key translations for precursor_mass_tolerance_unit

Style Translation
moda_style_1 PPMTolerance
msamanda_style_1 ms1_tol unit
msfragger_style_1 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
pipi_style_1 ms1_tolerance_unit
xtandem_style_1 spectrum, parent monoisotopic mass error units

Ursgal value translations

Ursgal Value Translated Value
. msamanda_style_1 msfragger_style_1 msgfplus_style_1 myrimatch_style_1 novor_style_1 omssa_style_1 pipi_style_1 xtandem_style_1
da Da 0 Da Da Da   0 Daltons
ppm n/t 1 n/t n/t n/t -teppm 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
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • myrimatch_2_1_138
  • myrimatch_2_2_140
  • omssa_2_1_9
  • msfragger_20170103
  • pipi_1_3_0
  • pyqms_1_0_0

Ursgal key translations for precursor_max_charge

Style Translation
msamanda_style_1 considered_charges
msfragger_style_1 precursor_max_charge
msgfplus_style_1 -maxCharge
myrimatch_style_1 NumChargeStates
omssa_style_1 -zh
pipi_style_1 (‘max_ms1_charge’, ‘max_potential_charge’)
pyqms_style_1 precursor_max_charge

precursor_max_mass

Maximal parent ion mass. 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
  • pipi_1_3_0

Ursgal key translations for precursor_max_mass

Style Translation
kojak_style_1 precursor_max_mass
msfragger_style_1 precursor_max_mass
myrimatch_style_1 MaxPeptideMass
pipi_style_1 max_precursor_mass
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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • msgfplus_v9979
  • omssa_2_1_9
  • msfragger_20170103
  • pipi_1_3_0
  • pyqms_1_0_0

Ursgal key translations for precursor_min_charge

Style Translation
msamanda_style_1 considered_charges
msfragger_style_1 precursor_min_charge
msgfplus_style_1 -minCharge
omssa_style_1 -zl
pipi_style_1 (‘min_ms1_charge’, ‘min_potential_charge’)
pyqms_style_1 precursor_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
  • pipi_1_3_0

Ursgal key translations for precursor_min_mass

Style Translation
kojak_style_1 precursor_min_mass
msfragger_style_1 precursor_min_mass
myrimatch_style_1 MinPeptideMass
pipi_style_1 min_precursor_mass
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

Ursgal key translations for precursor_true_tolerance

Style Translation
msfragger_style_1 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

Ursgal key translations for precursor_true_units

Style Translation
msfragger_style_1 precursor_true_units

Ursgal value translations

Ursgal Value Translated Value
. msfragger_style_1
da 0
ppm 1

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
  • 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_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

Ursgal key translations for psm_defining_colnames

Style Translation
ucontroller_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

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

Ursgal key translations for quantification_evidences

Style Translation
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

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_range

rel Intensity Error

Default value:0.2
type:float
triggers rerun:True

Available in unodes

  • pyqms_1_0_0

Ursgal key translations for rel_intensity_range

Style Translation
pyqms_style_1 REL_I_RANGE

rel_mz_range

relative mz error

Default value:5e-06
type:float
triggers rerun:True

Available in unodes

  • pyqms_1_0_0

Ursgal key translations for rel_mz_range

Style Translation
pyqms_style_1 REL_MZ_RANGE

remove_redundant_psms

If True, redundant PSMs (e.g. the same identification reported by multiple engined) for the same spectrum are removed. An identification is defined by the combination of ‘Sequence’, ‘Modifications’ and ‘Charge’.

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

Ursgal key translations for remove_temporary_files

Style Translation
ucontroller_style_1 remove_temporary_files

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

Ursgal key translations for required_percentile_peak_overlap

Style Translation
pyqms_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 for curating RT windows

Default value:1
type:float
triggers rerun:True

Available in unodes

  • pyqms_1_0_0

Ursgal key translations for rt_border_tolerance

Style Translation
pyqms_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

Ursgal key translations for rt_pickle_name

Style Translation
ucontroller_style_1 rt_pickle_name

scan_exclusion_list

Spectra rejected during mzml2mgf conversion

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

Available in unodes

  • mzml2mgf_1_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

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

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

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
  • 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

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
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
  • 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
  • msgfplus_v2016_09_16
  • msgfplus_v2017_01_27
  • 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

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
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 msgfplus_style_1 myrimatch_style_1 xtandem_style_1
0 2 Full 2 2 2 no
1 1 Semi 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

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

Ursgal key translations for silac_aas_locked_in_experiment

Style Translation
pyqms_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

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

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

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

Ursgal key translations for upper_mz_limit

Style Translation
pyqms_style_1 UPPER_MZ_LIMIT

ursgal_resource_url

URL that is used to install and prepare_resources.py

Default value:http://plan-a.uni-muenster.de/
type:str
triggers rerun:False

Available in unodes

  • ucontroller

Ursgal key translations for ursgal_resource_url

Style Translation
ucontroller_style_1 ursgal_resource_url

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 key translations for use_refinement

Style Translation
xtandem_style_1 refine

Ursgal value translations

Ursgal Value Translated Value
. xtandem_style_1
0 no
1 yes

use_spectrum_charge

Does not correct precursor charge.

Default value:True
type:bool
triggers rerun:True

Available in unodes

  • pepnovo_3_1
  • msfragger_20170103

Ursgal key translations for use_spectrum_charge

Style Translation
msfragger_style_1 override_charge
pepnovo_style_1 -use_spectrum_charge

Ursgal value translations

Ursgal Value Translated Value
. msfragger_style_1
0 1
1 0

use_spectrum_mz

Does not correct precusor m/z.

Default value:True
type:bool
triggers rerun:True

Available in unodes

  • moda_v1_51
  • 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
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_9695 0
msamanda_2_0_0_9706 0
msfragger_20170103 0
msgfplus_v2016_09_16 1e-100
msgfplus_v2017_01_27 1e-100
msgfplus_v9979 1e-100
myrimatch_2_1_138 0
myrimatch_2_2_140 0
omssa_2_1_9 1e-30
pipi_1_3_0 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
  • qvality_2_02
  • sanitize_csv_1_0_0
  • svm_1_0_0
  • ucontroller
  • unify_csv_1_0_0

Ursgal key translations for validation_score_field

Style Translation
add_estimated_fdr_style_1 validation_score_field
percolator_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
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
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_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
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_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_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
pipi_1_3_0 PIPI:score PIPI:score PIPI:score PIPI:score PIPI:score PIPI:score PIPI:score
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_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

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

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:ursgal Venn Diagram
type:str
triggers rerun:True

Available in unodes

  • venndiagram_1_0_0

Ursgal key translations for visualization_header

Style Translation
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

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

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

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

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

Available in unodes

  • venndiagram_1_0_0

Ursgal key translations for visualization_stroke_width

Style Translation
venndiagram_style_1 stroke-width

window_size

Combined PEPs are computed by iterating a sliding window over the sorted PSMs. Each PSM receives a PEP based on the target/decoy ratio of the surrounding PEPs. This parameter defines the window size.

Default value:249
type:int
triggers rerun:True

Available in unodes

  • combine_pep_1_0_0

Ursgal key translations for window_size

Style Translation
combine_pep_style_1 window_size

word_len

word length used to index peptide mapper, smaller word len requires more memory

Default value:6
type:int
triggers rerun:False

Available in unodes

  • unify_csv_1_0_0
  • upeptide_mapper_1_0_0

Ursgal key translations for word_len

Style Translation
unify_csv_style_1 word_len
upeptide_mapper_style_1 word_len

write_unfiltered_results

Writes rejected results if True

Default value:False
type:bool
triggers rerun:True

Available in unodes

  • filter_csv_1_0_0

Ursgal key translations for write_unfiltered_results

Style Translation
filter_csv_style_1 write_unfiltered_results

xtandem_converter_version

Determines which X!tandem conversion node should be used e.g. “xtandem2csv_1_0_0”

Default value:xtandem2csv_1_0_0
type:str
triggers rerun:True

Available in unodes

  • ucontroller

Ursgal key translations for xtandem_converter_version

Style Translation
ucontroller_style_1 xtandem_converter_version

xtandem_stp_bias

Interpretation of peptide phosphorylation models.

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 xtandem_stp_bias

Style Translation
xtandem_style_1 protein, stP bias

Ursgal value translations

Ursgal Value Translated Value
. xtandem_style_1
0 no
1 yes