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OpenSwathRTNormalizer

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:

Legend:
required parameter
advanced parameter
+OpenSwathRTNormalizerThis 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.
version1.11.1 Version of the tool that generated this parameters file.
++1Instance '1' section for 'OpenSwathRTNormalizer'
in[] Input files separated by blankinput file*.mzML
tr transition file with the RT peptides ('TraML' or 'csv')input file*.csv,*.traML
out output fileoutput file*.trafoXML
rt_norm RT normalization file (how to map the RTs of this run to the ones stored in the library)input file*.trafoXML
min_rsq0.95 Minimum r-squared of RT peptides regression
min_coverage0.6 Minimum relative amount of RT peptides to keep
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
testfalse Enables the test mode (needed for internal use only)true,false

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5