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<div class="title">SvmTheoreticalSpectrumGeneratorTrainer </div> </div>
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<div class="textblock"><p>Trainer for SVM model as input for SvmTheoreticalSpectrumGenerator.</p>
<p>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 <a class="el" href="classOpenMS_1_1SvmTheoreticalSpectrumGeneratorTrainer.html">OpenMS::SvmTheoreticalSpectrumGeneratorTrainer</a></p>
<dl class="section note"><dt>Note</dt><dd>This tool is experimental!</dd></dl>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
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.
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+SvmTheoreticalSpectrumGeneratorTrainer</span><span class="node_description">Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'SvmTheoreticalSpectrumGeneratorTrainer'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in_spectra</span><span class="item_value"></span>
<span class="item_description">Input Training Spectra in mzML</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">in_identifications</span><span class="item_value"></span>
<span class="item_description">Input file with corresponding sequences in idXML</span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">model_output_file</span><span class="item_value"></span>
<span class="item_description">Name for output files. For each ion_type one file <filename>_residue_loss_charge.svm and one <filename>.info which has to be passed to the SvmTheoretical SpectrumGenerator</span><span class="item_tags">output file</span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_charge</span><span class="item_value">2</span>
<span class="item_description">Precursor charge state used for model training</span><span class="item_tags"></span><span class="item_restrictions">1:3</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">write_training_files</span><span class="item_value">false</span>
<span class="item_description">No models are trained but input training files for libSVM command line tools are produced</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">+++algorithm</span><span class="node_description"></span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">number_intensity_levels</span><span class="item_value">7</span>
<span class="item_description">The number of intensity bins (for secondary type models)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">number_regions</span><span class="item_value">3</span>
<span class="item_description">The number of regions each spectrum is split to (for secondary type models)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">parent_tolerance</span><span class="item_value">2.5</span>
<span class="item_description">The maximum difference between theoretical and experimental parent mass to accept training spectrum</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">peak_tolerance</span><span class="item_value">0.5</span>
<span class="item_description">The maximum mass error for a peak to the expected mass of some ion type</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">add_b_ions</span><span class="item_value">true</span>
<span class="item_description">Train simulator for b-ions</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">add_y_ions</span><span class="item_value">true</span>
<span class="item_description">Train simulator for y-ions</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">add_a_ions</span><span class="item_value">false</span>
<span class="item_description">Train simulator for a-ions</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">add_c_ions</span><span class="item_value">false</span>
<span class="item_description">Train simulator for c-ions</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">add_x_ions</span><span class="item_value">false</span>
<span class="item_description">Train simulator for x-ions</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">add_z_ions</span><span class="item_value">false</span>
<span class="item_description">Train simulator for z-ions</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">add_losses</span><span class="item_value">false</span>
<span class="item_description">Train simulator for neutral losses of H2O and NH3 for b-ions and y-ions</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">add_b2_ions</span><span class="item_value">false</span>
<span class="item_description">Train simulator for doubly charged b-ions</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">add_y2_ions</span><span class="item_value">false</span>
<span class="item_description">Train simulator for double charged y-ions</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">++++svm</span><span class="node_description">Parameters controlling SVM trainig behaviour. All parameter names are chosen as in the libSVM library. Please refer to libSVM documentation for explanation</span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">svc_type</span><span class="item_value">0</span>
<span class="item_description">Type of the SVC: 0=C_SVC 1=NU_SVC</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">svr_type</span><span class="item_value">1</span>
<span class="item_description">Type of the SVR: 0=EPSILON_SVR 1=NU_SVR</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">scaling</span><span class="item_value">true</span>
<span class="item_description">Apply scaling of feature values</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">scaling_lower</span><span class="item_value">0</span>
<span class="item_description">Lower bound for scaling</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">scaling_upper</span><span class="item_value">1</span>
<span class="item_description">Upper bound for scaling</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">n_fold</span><span class="item_value">5</span>
<span class="item_description">n_fold cross validation is performed</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">grid</span><span class="item_value">false</span>
<span class="item_description">Perform grid search</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">additive_cv</span><span class="item_value">false</span>
<span class="item_description">Additive step size (if false multiplicative)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">+++++svc</span><span class="node_description">Parameters for svm - classification of missing/abundant</span></div>
<div class="item"><span class="item_name" style="padding-left:48px;">kernel_type</span><span class="item_value">2</span>
<span class="item_description">Type of the kernel: 0=LINEAR 1=POLY 2=RBF 3=SIGMOID</span><span class="item_tags"></span><span class="item_restrictions">0:3</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">degree</span><span class="item_value">3</span>
<span class="item_description">For POLY</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">gamma</span><span class="item_value">0</span>
<span class="item_description">For POLY/RBF/SIGMOID</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">C</span><span class="item_value">1</span>
<span class="item_description">Cost of constraint violation</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">nu</span><span class="item_value">0.5</span>
<span class="item_description">For NU_SVC, ONE_CLASS and NU_SVR</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">balancing</span><span class="item_value">true</span>
<span class="item_description">Use class balanced SVC training</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">degree_start</span><span class="item_value">1</span>
<span class="item_description">starting point of degree</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">degree_step_size</span><span class="item_value">2</span>
<span class="item_description">step size point of degree</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">degree_stop</span><span class="item_value">4</span>
<span class="item_description">stopping point of degree</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">gamma_start</span><span class="item_value">1e-05</span>
<span class="item_description">starting point of gamma</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">gamma_step_size</span><span class="item_value">100</span>
<span class="item_description">step size point of gamma</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">gamma_stop</span><span class="item_value">0.1</span>
<span class="item_description">stopping point of gamma</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">c_start</span><span class="item_value">0.1</span>
<span class="item_description">starting point of c</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">c_step_size</span><span class="item_value">100</span>
<span class="item_description">step size of c</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">c_stop</span><span class="item_value">1000</span>
<span class="item_description">stopping point of c</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">nu_start</span><span class="item_value">0.3</span>
<span class="item_description">starting point of nu</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">nu_step_size</span><span class="item_value">2</span>
<span class="item_description">step size of nu</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">nu_stop</span><span class="item_value">0.6</span>
<span class="item_description">stopping point of nu</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="node"><span class="node_name">+++++svr</span><span class="node_description">Parameters for svm - regression of peak intensities</span></div>
<div class="item"><span class="item_name" style="padding-left:48px;">kernel_type</span><span class="item_value">2</span>
<span class="item_description">Type of the kernel: 0=LINEAR 1=POLY 2=RBF 3=SIGMOID</span><span class="item_tags"></span><span class="item_restrictions">0:3</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">degree</span><span class="item_value">3</span>
<span class="item_description">For POLY</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">gamma</span><span class="item_value">0</span>
<span class="item_description">For POLY/RBF/SIGMOID</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">C</span><span class="item_value">1</span>
<span class="item_description">Cost of constraint violation</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">p</span><span class="item_value">0.1</span>
<span class="item_description">The epsilon for the loss function in epsilon-SVR</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">nu</span><span class="item_value">0.5</span>
<span class="item_description">For NU_SVC, ONE_CLASS and NU_SVR</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">degree_start</span><span class="item_value">1</span>
<span class="item_description">starting point of degree</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">degree_step_size</span><span class="item_value">2</span>
<span class="item_description">step size point of degree</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">degree_stop</span><span class="item_value">4</span>
<span class="item_description">stopping point of degree</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">gamma_start</span><span class="item_value">1e-05</span>
<span class="item_description">starting point of gamma</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">gamma_step_size</span><span class="item_value">100</span>
<span class="item_description">step size point of gamma</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">gamma_stop</span><span class="item_value">0.1</span>
<span class="item_description">stopping point of gamma</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">p_start</span><span class="item_value">1e-05</span>
<span class="item_description">starting point of p</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">p_step_size</span><span class="item_value">100</span>
<span class="item_description">step size point of p</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">p_stop</span><span class="item_value">0.1</span>
<span class="item_description">stopping point of p</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">c_start</span><span class="item_value">0.1</span>
<span class="item_description">starting point of c</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">c_step_size</span><span class="item_value">100</span>
<span class="item_description">step size of c</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">c_stop</span><span class="item_value">1000</span>
<span class="item_description">stopping point of c</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">nu_start</span><span class="item_value">0.3</span>
<span class="item_description">starting point of nu</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item"><span class="item_name" style="padding-left:48px;">nu_step_size</span><span class="item_value">2</span>
<span class="item_description">step size of nu</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:48px;">nu_stop</span><span class="item_value">0.6</span>
<span class="item_description">stopping point of nu</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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