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<div class="title">MRMMapper </div> </div>
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<div class="textblock"><p>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">potential predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> MRMMapper <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">potential successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FileFilter.html">FileFilter</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_OpenSwathAnalyzer.html">OpenSwathAnalyzer</a> </td></tr>
</table>
</center><p>This tool reads an mzML containing chromatograms (presumably measured on an SRM instrument) and a TraML file that contains the data that was used to generate the instrument method to measure said data. It then maps the transitions in the TraML file to the chromatograms found in the mzML file and stores the mapping by replacing the "id" paramter in the mzML with the "id" of the transition in the TraML file. It removes chromatograms for which it cannot find a mapping and throws an error if more than one transitions maps to a chromatogram. In strict mode (default) it also throws an error it not all chromatograms could be found in the TraML file.</p>
<p>The thus mapped file can then be used in a downstream analysis.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
MRMMapper -- MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
MRMMapper <options>
Options (mandatory options marked with '*'):
-in <file>* Input file containing chromatograms (converted mzXML file) (valid formats:
'mzML')
-tr <file>* Transition file (valid formats: 'TraML')
-out <file>* Output file containing mapped chromatograms (valid formats: 'mzML')
-precursor_tolerance <double> Precursor tolerance when mapping (in Th) (default: '0.1')
-product_tolerance <double> Product tolerance when mapping (in Th) (default: '0.1')
-no-strict Run in non-strict mode and allow some chromatograms to not be mapped.
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>The algorithm parameters for the Analyzer filter are:</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">+MRMMapper</span><span class="node_description">MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</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 'MRMMapper'</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 containing chromatograms (converted mzXML file)</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;">tr</span><span class="item_value"></span>
<span class="item_description">transition file</span><span class="item_tags">input file</span><span class="item_restrictions">*.TraML</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 file containing mapped chromatograms</span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_tolerance</span><span class="item_value">0.1</span>
<span class="item_description">Precursor tolerance when mapping (in Th)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">product_tolerance</span><span class="item_value">0.1</span>
<span class="item_description">Product tolerance when mapping (in Th)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">no-strict</span><span class="item_value">false</span>
<span class="item_description">run in non-strict mode and allow some chromatograms to not be mapped.</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>
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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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