OpenMS
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Converts a featureXML to a mProphet tsv
potential predecessor tools | → OpenSwathFeatureXMLToTSV → | potential successor tools |
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OpenSwathAnalyzer | Downstream data analysis | |
OpenSwathConfidenceScoring |
Creates a tsv that is compatible as input to mProphet. Furthermore it creates the columns "decoy" and "transition_group_id" which are required by mProphet.
The command line parameters of this tool are:
OpenSwathFeatureXMLToTSV -- Converts a featureXML to a mProphet tsv. Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathFeatureXMLToTSV.html Version: 3.4.0-pre-nightly-2024-11-30 Nov 30 2024, 02:33:34, Revision: 7ff3f2e 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: OpenSwathFeatureXMLToTSV <options> Options (mandatory options marked with '*'): -in <files>* Input files separated by blank (valid formats: 'featureXML') -tr <file>* TraML transition file (valid formats: 'traML') -out <file>* Tsv output file (mProphet compatible) (valid formats: 'csv') -short_format Whether to write short (one peptide per line) or long format (one transiti on per line). -best_scoring_peptide <varname> If only the best scoring feature per peptide should be printed, give the variable name 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: