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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. Version: 2.3.0 Jan 9 2018, 17:46:23, Revision: 38ae115 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') 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:
OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:06 using doxygen 1.8.13 |