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<div class="title">IDRipper </div> </div>
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<div class="textblock"><p>IDRipper splits the protein/peptide identification of an idXML file into several idXML files according their annotated file origin.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">potential predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> IDRipper <img class="formulaInl" alt="$ \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_IDFilter.html">IDFilter</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDMapper.html">IDMapper</a> </td></tr>
</table>
</center><p><b>Example</b></p>
<p>Assuming each peptide identification in a given idXML-file is annotated with its file origin (e.g. IDRipper_test.idXML) :</p>
<p><code><code></code> <userParam type="string" name="file_origin" value="IDMerger1_test.idXML"></code> or <br/>
<code><code></code> <userParam type="string" name="file_origin" value="IDMerger2_test.idXML"></code></p>
<p>Obviously the file contains protein/peptide identifications of IDMerger1_test.idXML and IDMerger2_test.idXML.</p>
<p>Calling IDRipper with an input file (here: <code>-in</code> IDRipper_test.idXML) and an output directory (via <code>out</code> or <code>out_path</code>) will result in two idXML-files stored in the specified directory and named according their file origin.</p>
<p>In theory, merging files with <code>IDMerger</code> and rip the resulting file with <code>IDSplitter</code> will result in the original input files.</p>
<p><b>NOTE: The meta value file origin is removed by the <code>IDSplitter</code>!!</b></p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
IDRipper -- Split protein/peptide identification file into several files according annotated file origin.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
IDRipper <options>
Options (mandatory options marked with '*'):
-in <file>* IdXML-file, whereas the protein/peptide identifications must be tagged with file_origin
(valid formats: 'idXML')
-out <file> The path to the file is used as the output directory. (valid formats: 'idXML')
-out_path <file> Directory for the idXML-files after ripping according file_origin tag. If out_path is
set, out is ignored.
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">+IDRipper</span><span class="node_description">Split protein/peptide identification file into several files according annotated file origin.</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 'IDRipper'</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">idXML-file, whereas the protein/peptide identifications must be tagged with file_origin</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">The path to the file is used as the output directory.</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;">out_path</span><span class="item_value"></span>
<span class="item_description">Directory for the idXML-files after ripping according file_origin tag. If out_path is set, out is ignored.</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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