| OpenMS 2.5.0

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/documentation/UTILS_OpenSwathRewriteToFeatureXML.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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:

      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 UTIL 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
+OpenSwathRewriteToFeatureXML Combines featureXML and mProphet tsv to FDR filtered featureXML.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'OpenSwathRewriteToFeatureXML'
csv mProphet tsv output file: "all_peakgroups.xls"input file*.csv
featureXML input featureXML file input file*.featureXML
out output featureXML file output 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)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false