OpenMS
OpenSwathRewriteToFeatureXML

Combines featureXML and mProphet tsv to FDR filtered featureXML.

The command line parameters of this tool are:

OpenSwathRewriteToFeatureXML -- Combines featureXML and mProphet tsv to FDR filtered featureXML.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathRewriteToFeatureXML.html
Version: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
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:
  OpenSwathRewriteToFeatureXML <options>

Options (mandatory options marked with '*'):
  -csv <file>           MProphet tsv output file: "all_peakgroups.xls" (valid formats: 'csv')
  -featureXML <file>*   Input featureXML file (valid formats: 'featureXML')
  -out <file>*          Output featureXML file (valid formats: 'featureXML')
  -FDR_cutoff <double>  FDR cutoff (e.g. to remove all features with a an m_score above 0.05 use 0.05 here) 
                        (default: '-1.0')
                        
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
+OpenSwathRewriteToFeatureXMLCombines featureXML and mProphet tsv to FDR filtered featureXML.
version3.2.0-pre-nightly-2024-07-19 Version of the tool that generated this parameters file.
++1Instance '1' section for 'OpenSwathRewriteToFeatureXML'
csv mProphet tsv output file: "all_peakgroups.xls"input file*.csv
featureXML input featureXML fileinput file*.featureXML
out output featureXML fileoutput file*.featureXML
FDR_cutoff-1.0 FDR cutoff (e.g. to remove all features with a an m_score above 0.05 use 0.05 here)
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