The OpenSwathRTNormalizer will find retention time peptides in data.
This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transoform the RT space into the normalized space.
The command line parameters of this tool are:
OpenSwathRTNormalizer -- This tool will take a description of RT peptides and their normalized retention time
to write out a transformation file on how to transoform the RT space into the normalized space.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
  OpenSwathRTNormalizer <options>
Options (mandatory options marked with '*'):
  -in <files>*            Input files separated by blank (valid formats: 'mzML')
  -tr <file>*             Transition file with the RT peptides ('TraML' or 'csv') (valid formats: 'csv', 'tra
                          ML')
  -out <file>*            Output file (valid formats: 'trafoXML')
  -rt_norm <file>         RT normalization file (how to map the RTs of this run to the ones stored in the 
                          library) (valid formats: 'trafoXML')
  -min_rsq <double>       Minimum r-squared of RT peptides regression (default: '0.95')
  -min_coverage <double>  Minimum relative amount of RT peptides to keep (default: '0.6')
                          
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)
The algorithm parameters for the Analyzer filter are:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |