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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/documentation/UTILS_OpenSwathDIAPreScoring.html
Version: 2.5.0-nightly-2020-03-06 Mar  7 2020, 01:22:16, Revision: 84b1398
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:
  OpenSwathDIAPreScoring <options>

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

version2.5.0-nightly-2020-03-06 Version of the tool that generated this parameters file.

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

tr transition fileinput file*.TraML

out output fileoutput file*.tsv

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

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 Overwrite tool specific checks.true,false

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