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: 3.6.0-pre-nightly-2026-03-12 Mar 13 2026, 01:45:58, Revision: 88f2819
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

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+OpenSwathRewriteToFeatureXMLCombines featureXML and mProphet tsv to FDR filtered featureXML.

version3.6.0-pre-nightly-2026-03-12 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