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 |