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<div class="title">MRMPairFinder </div> </div>
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<div class="textblock"><p>Util which can be used to evaluate pairs of MRM experiments</p>
<dl class="experimental"><dt><b><a class="el" href="experimental.html#_experimental000027">Experimental classes:</a></b></dt><dd>This software is experimental and might contain bugs!</dd></dl>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
MRMPairFinder -- Util which can be used to evaluate labeled pair ratios on MRM features.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
MRMPairFinder <options>
Options (mandatory options marked with '*'):
-in <file>* Input featureXML file containing the features of the MRM experiment spectra. (valid
formats: 'featureXML')
-pair_in <file>* Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy
rt (valid formats: 'csv')
-out <file>* Output consensusXML file were the pairs of the features will be written to. (valid
formats: 'consensusXML')
-feature_out <file> Output featureXML file, only written if given, skipped otherwise. (valid formats: 'fea
tureXML')
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)
</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">+MRMPairFinder</span><span class="node_description">Util which can be used to evaluate labeled pair ratios on MRM features.</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 'MRMPairFinder'</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 featureXML file containing the features of the MRM experiment spectra.</span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">pair_in</span><span class="item_value"></span>
<span class="item_description">Pair-file in the format: prec-m/z-light prec-m/z-heavy frag-m/z-light frag-m/z-heavy rt</span><span class="item_tags">input file</span><span class="item_restrictions">*.csv</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Output consensusXML file were the pairs of the features will be written to.</span><span class="item_tags">output file</span><span class="item_restrictions">*.consensusXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">feature_out</span><span class="item_value"></span>
<span class="item_description">Output featureXML file, only written if given, skipped otherwise.</span><span class="item_tags">output file</span><span class="item_restrictions">*.featureXML</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">mass_tolerance</span><span class="item_value">0.01</span>
<span class="item_description">Precursor mass tolerance which is used for the pair finding and the matching of the given pair m/z values to the features.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">RT_tolerance</span><span class="item_value">200</span>
<span class="item_description">Maximal deviation in RT dimension in seconds a feature can have when comparing to the RT values given in the pair file.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">RT_pair_tolerance</span><span class="item_value">5</span>
<span class="item_description">Maximal deviation in RT dimension in seconds the two partners of a pair is allowed to have.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</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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