Welcome to ursgal’s documentation!

The latest Documentation was generated on: May 14, 2021

• Introduction
  • Summary
  • Abstract
  • Documentation
  • Download and Installation
  • Tests
  • Update to v0.6.0 Warning
  • Questions and Participation
  • Disclaimer
  • Copyrights
  • Contact
  • Citation

Quick Start

• Quick Start Tutorial
  • 1. Getting Started
  • 2. Running a Simple Search
  • 3. Adjusting Parameters
  • 4. Available Workflow Functions
  • 5. Building Custom workflows
  • 6. JSONs, Force and File Names
  • 7. Example Scripts

Module structure

• General Structure
  • Schematic Overview
  • Resources
  • Wrapper Python class
  • Grouped parameters - uparams.py

Ursgal module contents

• UController
• UNode
• UCore
• UMapMaster
• Chemical Composition
• Unimod Mapper
• Ursgal Results

Parameters

• Ursgal Parameters

Engines

Ursgal allows existing programs to be incorporated with ease. We call those programs or scripts engines. Currently, ursgal comes with these engines:

Included engines

• Available Search Engines
  • Protein Database Search Engines
    • MS Amanda
    • MS-GF+
    • MSFragger
    • MODa
    • MyriMatch
    • TagGraph
    • OMSSA
    • PIPI
    • X!Tandem
  • De Novo Search Engines
    • DeepNovo
    • Novor
    • PepNovo
    • pNovo
  • Cross Link Search Engines
    • Kojak
  • Glycosylation Search Engines
    • pGlyco
• Converter Engines
  • Convert CSV to SSL 1_0_0
  • Convert CSV to Counted Results
  • Convert Mascot DAT to CSV
  • Convert MS-GF+ MZID to CSV
  • Convert MZML to MGF
  • Convert X!Tandem XML to CSV 1_0_0
  • MzidLib
  • pParse 2.0
  • ThermoRawFileParser
• Other Engines
  • Fetcher
    • Get FTP Files 1_0_0
    • Get HTTP Files 1_0_0
  • Meta Engines
    • Combine FDR 0_1
    • Combine PEP 1_0_0
  • Misc Engines
    • Filter CSV 1_0_0
    • Generate Target Decoy 1_0_0
    • Merge CSVS 1_0_0
    • Sanitize CSV 1_0_0
    • SugarPy v1_0_0
    • Unify CSV 1_0_0
    • Upeptide mapper v1_0_0
  • Quantification Engines
    • pyQms 1_0_0
    • FlashLFQ 1_1_1
  • Validation Engines
    • Kojak tailored Percolator 2_08
    • Percolator
    • PTMiner 1.0
    • PTM-Sheperd 0.3.5
    • pGlyco FDR 2.2.0
    • qvality 2_02
  • Visualizer
    • Plot pyGCluster heatmap from CSV 1_0_0
    • Venn Diagram v1_0_0

How to extend and create new engines ?

• Create/Implement your own UNode
  • 1. Integration into Resources
  • 2. Integration into uparams.py
  • 3. Implementation of the wrapper class

Examples

Ursgal comes with multiple example scripts which can be used to test its functionality. Example scripts can also be used as templates for your own scripts.

• Example Scripts
  • Simple Example Scripts
  • Complete Workflow Scripts
  • Open Modification Search Scripts
  • Version Comparison Scripts
  • Parameter Optimization Scripts
  • Filter CSV Examples
  • SugarPy Example Scripts
  • Cascade Search
  • Upeptide Mapper Example Scripts

Changelog

Record of released Ursgal versions with all notable changes

• Changelog

Contribution Guidelines

• Contribution Guidelines

FAQ

• Frequently Asked Questions

Known Issues

• Known Issues