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 |