OpenMS
2.6.0
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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: 2.6.0 Sep 30 2020, 12:54:34, Revision: c26f752 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: