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<div class="title">QCExtractor </div> </div>
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<div class="textblock"><p>Extracts a table attachment to a given qc parameter.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> QCExtractor <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="2"><a class="el" href="UTILS_QCEmbedder.html">QCEmbedder</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="UTILS_QCShrinker.html">QCShrinker</a> </td></tr>
</table>
</center><p>If there is a table attached to a qp that is needed as a single file. The qcml file to extract from is given with <code>in</code>.</p>
<ul>
<li><code>qp</code> defines the qp name to which the table is attached;</li>
<li><code>run</code> the file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name.</li>
<li><code>name</code> if no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given.</li>
<li><code>set/run</code> if the target qp is contained in a set, this has to be set here;</li>
</ul>
<p>Output is in csv format (see parameter <code>out_csv</code>) which can be easily parsed by many programs.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
QCExtractor -- Extracts a table attachment to a given qc parameter.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
QCExtractor <options>
Options (mandatory options marked with '*'):
-in <file>* Input qcml file (valid formats: 'qcML')
-qp <string>* Target attachment qp.
-run <file> The file that defined the run under which the qp for the attachment is aggregated as
mzML file. The file is only used to extract the run name from the file name. (valid form
ats: 'mzML')
-name <string> If no file for the run was given (or if the target qp is contained in a set), at least
a name of the target run/set containing the the qp for the attachment has to be given.
-out_csv <file>* Output csv formatted table. (valid formats: 'csv')
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">+QCExtractor</span><span class="node_description">Extracts a table attachment to a given qc parameter.</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 'QCExtractor'</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 qcml file</span><span class="item_tags">input file</span><span class="item_restrictions">*.qcML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">qp</span><span class="item_value"></span>
<span class="item_description">Target attachment qp.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">run</span><span class="item_value"></span>
<span class="item_description">The file that defined the run under which the qp for the attachment is aggregated as mzML file. The file is only used to extract the run name from the file name.</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">name</span><span class="item_value"></span>
<span class="item_description">If no file for the run was given (or if the target qp is contained in a set), at least a name of the target run/set containing the the qp for the attachment has to be given.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out_csv</span><span class="item_value"></span>
<span class="item_description">Output csv formatted table.</span><span class="item_tags">output file</span><span class="item_restrictions">*.csv</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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