| OpenMS 2.5.0

OpenSwathFeatureXMLToTSV

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.

    Full documentation: http://www.openms.de/documentation/TOPP_OpenSwathFeatureXMLToTSV.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    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:

      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:

Legend:
required parameter
advanced parameter
+OpenSwathFeatureXMLToTSV Converts a featureXML to a mProphet tsv.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'OpenSwathFeatureXMLToTSV'
in[] Input files separated by blank input file*.featureXML
tr TraML transition file input file*.traML
out tsv output file (mProphet compatible)output file*.csv
short_format false Whether to write short (one peptide per line) or long format (one transition per line).true,false
best_scoring_peptide If only the best scoring feature per peptide should be printed, give the variable name
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false