...

SWATH specific parameters only apply if you have full MS2 spectra maps.

The command line parameters of this tool are:

OpenSwathDIAPreScoring -- Scoring spectra using the DIA scores.
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_OpenSwathDIAPreScoring.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
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:
  OpenSwathDIAPreScoring <options>

Options (mandatory options marked with '*'):
  -tr <file>*                    Transition file (valid formats: 'traML')
  -swath_files <files>*          Swath files that were used to extract the transitions. If present, SWATH 
                                 specific scoring will be applied. (valid formats: 'mzML')
  -output_files <files>*         Output files. One per Swath input file. (valid formats: 'tsv')
  -min_upper_edge_dist <double>  Minimal distance to the edge to still consider a precursor, in Thomson (only
                                  in SWATH) (default: '0.0')
                                 
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.

+OpenSwathDIAPreScoringScoring spectra using the DIA scores.

version3.6.0-pre-nightly-2026-03-06 Version of the tool that generated this parameters file.

++1Instance '1' section for 'OpenSwathDIAPreScoring'

tr transition fileinput file*.traML

swath_files[] Swath files that were used to extract the transitions. If present, SWATH specific scoring will be applied.input file*.mzML

output_files[] Output files. One per Swath input file.output file*.tsv

min_upper_edge_dist0.0 Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)

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