Can be used to calibrate the RTs of peptide hits linearly to standards.
| pot. predecessor tools |  IDRTCalibration   | pot. successor tools | 
| MascotAdapter (or other ID engines) | PeptideIndexer (or other tools operating with identifications (in idXML format)) | 
This tool can be used to linearly align RTs of the idXML-File to a reference. If only calibrant_1_input and calibrant_2_input are given, the first calibrant will result at RT 0.1 and calibrant_2_input will be at 0.9. If one wants to align the RTs of this idXML file to the IDs of a reference file one can also give the RTs of the same calibrant in the reference file (calibrant_1_reference, calibrant_2_reference). If these calibrants are given, the linear transformation (shift and scale) will be calculated such that calibrant_1_input will be at the same RT as calibrant_1_reference and calibrant_2_input will be at the same RT as calibrant_2_reference. This only applies if calibrant_1* has a smaller RT than calibrant_2*. Otherwise the values are swapped.
The command line parameters of this tool are:
IDRTCalibration -- Can be used to calibrate RTs of peptide hits linearly to standards.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
  IDRTCalibration <options>
Options (mandatory options marked with '*'):
  -in <file>*                  Input file  (valid formats: 'idXML')
  -out <file>*                 Output file  (valid formats: 'idXML')
  -calibrant_1_reference <RT>  The RT of the first calibrant in the reference file. (default: '0.1')
  -calibrant_2_reference <RT>  The RT of the second calibrant in the reference file. (default: '0.9')
  -calibrant_1_input <RT>      The RT of the first calibrant in the input file. Please note that this value 
                               needs to be set. The default value -1.0 is not allowed. (default: '-1')
  -calibrant_2_input <RT>      The RT of the second calibrant in the input file. Please note that this value 
                               needs to be set. The default value -1.0 is not allowed. (default: '-1')
                               
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)
INI file documentation of this tool:
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |