Converts a featureXML to a mProphet tsv.

potential predecessor tools	→ OpenSwathFeatureXMLToTSV →	potential successor tools
OpenSwathAnalyzer		Downstream data analysis
OpenSwathConfidenceScoring		Downstream data analysis

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: 3.6.0-pre-nightly-2026-03-12 Mar 13 2026, 01:45:58, Revision: 88f2819
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:

Legend:

required parameter

advanced parameter

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+OpenSwathFeatureXMLToTSVConverts a featureXML to a mProphet tsv.

version3.6.0-pre-nightly-2026-03-12 Version of the tool that generated this parameters file.

++1Instance '1' section for 'OpenSwathFeatureXMLToTSV'

in[] Input files separated by blankinput file*.featureXML

tr TraML transition fileinput file*.traML

out tsv output file (mProphet compatible)output file*.csv

short_formatfalse 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)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue, false

forcefalse Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false