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<div class="title">IDMerger </div> </div>
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<div class="textblock"><p>Merges several idXML files into one idXML file.</p>
<center> <table class="doxtable">
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<td align="center" bgcolor="#EBEBEB">potential predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> IDMerger <img class="formulaInl" alt="$ \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_MascotAdapter.html">MascotAdapter</a> (or other ID engines) </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_ConsensusID.html">ConsensusID</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDFileConverter.html">IDFileConverter</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDMapper.html">IDMapper</a> </td></tr>
</table>
</center><p>The peptide hits and protein hits of the input files will be written into the single output file. In general, the number of idXML files that can be merged into one file is not limited.</p>
<p>The combination of search engine and processing date/time should be unique for every identification run over all input files. If this is not the case, the date/time of a conflicting run will be increased in steps of seconds until the combination is unique.</p>
<p>With the <code>pepxml_protxml</code> option, results from corresponding PeptideProphet and ProteinProphet runs can be combined. In this case, exactly two idXML files are expected as input: one containing data from a pepXML file, and the other containing data from a protXML file that was created based on the pepXML (meaningful results can only be obtained for matching files!). pepXML or protXML can be converted to idXML with the <a class="el" href="TOPP_IDFileConverter.html">IDFileConverter</a> tool.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
IDMerger -- Merges several protein/peptide identification files into one file.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
IDMerger <options>
Options (mandatory options marked with '*'):
-in <files>* Two or more input files separated by blanks (valid formats: 'idXML')
-out <file>* Output file (valid formats: 'idXML')
-annotate_file_origin Store the original filename in each protein/peptide identification (MetaValue: file
_origin).
-pepxml_protxml Merge idXML files derived from a pepXML and corresponding protXML file.
Exactly two input files are expected in this case.
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">+IDMerger</span><span class="node_description">Merges several protein/peptide identification files into one file.</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 'IDMerger'</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">two or more input files separated by blanks</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;">out</span><span class="item_value"></span>
<span class="item_description">output file </span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">annotate_file_origin</span><span class="item_value">false</span>
<span class="item_description">Store the original filename in each protein/peptide identification (MetaValue: file_origin).</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">pepxml_protxml</span><span class="item_value">false</span>
<span class="item_description">Merge idXML files derived from a pepXML and corresponding protXML file.<br>Exactly two input files are expected in this case.</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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