TriqlerConverter

Converter to input for Triqler

This util consumes an ID-mapped consensusXML file and OpenMS experimental design in TSV format to create a CSV file which can subsequently be used as input for the python tool Triqler [1].

[1] The, M. & Käll, L. (2019). Integrated identification and quantification error probabilities for shotgun proteomics. Molecular & Cellular Proteomics, 18 (3), 561-570.

The command line parameters of this tool are:

TriqlerConverter -- Converter to input for Triqler
Full documentation: http://www.openms.de/doxygen/release/3.3.0/html/TOPP_TriqlerConverter.html
Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  TriqlerConverter <options>

Options (mandatory options marked with '*'):
  -in <in>*                               Input consensusXML with peptide intensities (valid formats: 'consen
                                          susXML')
  -in_design <in_design>*                 Experimental Design file (valid formats: 'tsv')
  -Triqler_condition <Triqler_condition>  Which column in the condition table should be used for Triqler 'Con
                                          dition' (default: 'Triqler_Condition')
  -out <out>*                             Input CSV file for Triqler. (valid formats: 'csv')
                                          
Common TOPP options:
  -ini <file>                             Use the given TOPP INI file
  -threads <n>                            Sets the number of threads allowed to be used by the TOPP tool (def
                                          ault: '1')
  -write_ini <file>                       Writes the default configuration file
  --help                                  Shows options
  --helphelp                              Shows all options (including advanced)

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+TriqlerConverterConverter to input for Triqler

version3.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'TriqlerConverter'

in Input consensusXML with peptide intensitiesinput file*.consensusXML

in_design Experimental Design fileinput file*.tsv

Triqler_conditionTriqler_Condition Which column in the condition table should be used for Triqler 'Condition'

reannotate_filenames[] Overwrite MS file names in consensusXMLinput file*.mzML

out Input CSV file for Triqler.output file*.csv

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false