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<div class="title">PTPredict </div> </div>
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<div class="textblock"><p>This application is used to predict the likelihood of peptides to be proteotypic.</p>
<p>This method has been described in the publication</p>
<p>Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher and Knut Reinert LC-MSsim - a simulation software for Liquid ChromatographyMass Spectrometry data BMC Bioinformatics 2008, 9:423.</p>
<p>The input of this application is an svm model and an idXML file with peptide identifications. The svm model file is specified by the <b>svm_model</b> parameter in the command line or the ini file. This file should have been produced by the <a class="el" href="TOPP_PTModel.html">PTModel</a> application.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
PTPredict -- predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
PTPredict <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'idXML')
-out <file> Output file
(valid formats: 'idXML')
-svm_model <file>* Svm model in libsvm format (can be produced by PTModel) (valid formats: 'txt
')
-max_number_of_peptides <int> The maximum number of peptides considered at once (bigger number will lead
to faster results but needs more memory).
(default: '100000')
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)
</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">+PTPredict</span><span class="node_description">predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel</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 'PTPredict'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">input file </span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">output file<br></span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">svm_model</span><span class="item_value"></span>
<span class="item_description">svm model in libsvm format (can be produced by PTModel)</span><span class="item_tags">input file</span><span class="item_restrictions">*.txt</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">max_number_of_peptides</span><span class="item_value">100000</span>
<span class="item_description">the maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory).<br></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;">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>
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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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