| OpenMS 2.5.0

OpenSwathDIAPreScoring

...

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-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:

      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
+OpenSwathDIAPreScoring Scoring spectra using the DIA scores.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'OpenSwathDIAPreScoring'
tr transition file input file*.TraML
out output file output 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_dist 0.0 Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)
log Name of log file (created only when specified)
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