OpenMS  3.0.0
OpenSwathFeatureXMLToTSV

Converts a featureXML to a mProphet tsv

potential predecessor tools $ \longrightarrow $ OpenSwathFeatureXMLToTSV $ \longrightarrow $ potential successor tools
OpenSwathAnalyzer Downstream data analysis
OpenSwathConfidenceScoring

Creates a tsv that is compatible as input to mProphet. Furthermore it creates the columns "decoy" and "transition_group_id" which are required by mProphet.

The command line parameters of this tool are:

OpenSwathFeatureXMLToTSV -- Converts a featureXML to a mProphet tsv.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathFeatureXMLToTSV.html
Version: 3.0.0-pre-nightly-2022-07-20 Jul 21 2022, 00:07:28, Revision: ea0316e
To cite OpenMS:
  Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

Usage:
  OpenSwathFeatureXMLToTSV <options>

Options (mandatory options marked with '*'):
  -in <files>*                     Input files separated by blank (valid formats: 'featureXML')
  -tr <file>*                      TraML transition file (valid formats: 'traML')
  -out <file>*                     Tsv output file (mProphet compatible) (valid formats: 'csv')
  -short_format                    Whether to write short (one peptide per line) or long format (one transiti
                                   on per line).
  -best_scoring_peptide <varname>  If only the best scoring feature per peptide should be printed, give the 
                                   variable name
                                   
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 (default: 
                                   '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
+OpenSwathFeatureXMLToTSVConverts a featureXML to a mProphet tsv.
version3.0.0-pre-nightly-2022-07-20 Version of the tool that generated this parameters file.
++1Instance '1' section for 'OpenSwathFeatureXMLToTSV'
in[] Input files separated by blankinput file*.featureXML
tr TraML transition fileinput file*.traML
out tsv output file (mProphet compatible)output file*.csv
short_formatfalse Whether to write short (one peptide per line) or long format (one transition per line).true,false
best_scoring_peptide If only the best scoring feature per peptide should be printed, give the variable name
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