OpenSwathRewriteToFeatureXML

Combines featureXML and mProphet tsv to FDR filtered featureXML.

The command line parameters of this tool are:

stty: 'standard input': Inappropriate ioctl for device

OpenSwathRewriteToFeatureXML -- Combines featureXML and mProphet tsv to FDR filtered featureXML.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathRewriteToFeatureXML.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry 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.

version3.4.0-pre-nightly-2024-12-16 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