Trainer for SVM model as input for SvmTheoreticalSpectrumGenerator.
This application requires mzML file with ms2 spectra and annotations in an idXml file and trains a SVM model usable by SvmTheoreticalSpectrumGenerator. Please refer to the documentation of the corresponding class OpenMS::SvmTheoreticalSpectrumGeneratorTrainer
The command line parameters of this tool are:
SvmTheoreticalSpectrumGeneratorTrainer -- Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
  SvmTheoreticalSpectrumGeneratorTrainer <options>
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.
Options (mandatory options marked with '*'):
  -in_spectra <file>*          Input Training Spectra in mzML (valid formats: 'mzML')
  -in_identifications <file>*  Input file with corresponding sequences in idXML (valid formats: 'idXML')
  -model_output_file <file>*   Name for output files. For each ion_type one file <filename>_residue_loss_char
                               ge.svm and one <filename>.info which has to be passed to the SvmTheoretical
                               SpectrumGenerator
  -precursor_charge <Int>      Precursor charge state used for model training (default: '2' min: '1' max: 
                               '3')
  -write_training_files        No models are trained but input training files for libSVM command line tools 
                               are produced
                               
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)
The following configuration subsections are valid:
 - algorithm   
You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.
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 |