OpenMS
OpenSwathDIAPreScoring

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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: 3.2.0-pre-nightly-2024-07-19 Jul 20 2024, 02:06:43, Revision: f10e72e
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
+OpenSwathDIAPreScoringScoring spectra using the DIA scores.
version3.2.0-pre-nightly-2024-07-19 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