Converts a featureXML to a mProphet tsv
| potential predecessor tools |  FeatureXMLToTSV   | 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: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
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 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |