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<div class="title">QCEmbedder </div> </div>
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<div class="textblock"><p>Attaches a table or an image to a given qc parameter.</p>
<center> <table class="doxtable">
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<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> QCEmbedder <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="UTILS_QCExporter.html">QCExporter</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="UTILS_QCMerger.html">QCMerger</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_XTandemAdapter.html">XTandemAdapter</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="UTILS_QCShrinker.html">QCShrinker</a> </td></tr>
</table>
</center><p>If there is additional data from external tools to a certain quality control parameter (qp) in the qcml file at <code>in</code>, it can be attached in tabluar (csv) format or as png image file.</p>
<ul>
<li><code>qp_att_acc</code> defines the qp cv accession of the qp to which the table/image is attached.</li>
<li><code>cv_acc</code> defines the cv accession of the attachment.</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>plot</code> if a plot image is to be attached to a qp, this has to be specified here.</li>
<li><code>table</code> if a table is to be attached to a qp, this has to be specified here.</li>
</ul>
<p>Output is in qcML format (see parameter <code>out</code>) which can be viewed directly in a modern browser (chromium, firefox).</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
QCEmbedder -- Attaches a table or an image to a given qc parameter.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
QCEmbedder <options>
Options (mandatory options marked with '*'):
-in <file> Input qcml file (valid formats: 'qcML')
-qp_att_acc <string> Defines the qp cv accession of the qp to which the table/image is attached.
-cv_acc <string>* Defines the cv accession of the attachment.
-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
formats: 'mzML')
-name <String> If no file for the run was given (or if the target qp is contained in a set), at leas
t a name of the target run/set containing the the qp for the attachment has to be
given.
-plot <file> If a plot image is to be attached to a qp, this has to be specified here. (valid form
ats: 'PNG')
-table <file> If a table is to be attached to a qp, this has to be specified here. (valid formats:
'csv')
-out <file>* Output extended qcML file (valid formats: 'qcML')
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">+QCEmbedder</span><span class="node_description">Attaches a table or an image 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 'QCEmbedder'</span></div>
<div class="item"><span class="item_name" 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" style="padding-left:24px;">qp_att_acc</span><span class="item_value"></span>
<span class="item_description">Defines the qp cv accession of the qp to which the table/image is attached.</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;">cv_acc</span><span class="item_value"></span>
<span class="item_description">Defines the cv accession of the attachment.</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" style="padding-left:24px;">plot</span><span class="item_value"></span>
<span class="item_description">If a plot image is to be attached to a qp, this has to be specified here.</span><span class="item_tags">input file</span><span class="item_restrictions">*.PNG</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">table</span><span class="item_value"></span>
<span class="item_description">If a table is to be attached to a qp, this has to be specified here.</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 extended qcML file</span><span class="item_tags">output file</span><span class="item_restrictions">*.qcML</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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