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 |