Converts a featureXML to a mProphet tsv
potential predecessor tools | OpenSwathFeatureXMLToTSV | potential successor tools |
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. Version: 2.3.0 Jan 9 2018, 17:46:23, Revision: 38ae115 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)
The algorithm parameters for the Analyzer filter are:
OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:06 using doxygen 1.8.13 |