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<div class="title">ExecutePipeline </div>  </div>
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<div class="textblock"><p>Executes workflows created by TOPPAS.</p>
<p>This tool is the non-GUI, i.e. command line version for non-interactive execution of TOPPAS pipelines. In order to really use this tool in batch-mode, you can provide a TOPPAS resource file (.trf) which specifies the input files for the input nodes in your pipeline.</p>
<p><b> *.trf files </b></p>
<p>A TOPPAS resource file (<code>*.trf</code>) specifies the locations of input files for a pipeline. It is an XML file following the normal TOPP INI file schema, i.e. it can be edited using the INIFileEditor or filled using a script (we do NOT provide one - sorry). It can be exported from TOPPAS (<code>File -&gt; Save TOPPAS resource file</code>). For two input nodes 1 and 2 with files (<code>dataA.mzML</code>, <code>dataB.mzML</code>) and (<code>dataC.mzML</code>) respectively it has the following format.</p>
<div class="fragment"><div class="line">&lt;?xml version=<span class="stringliteral">&quot;1.0&quot;</span> encoding=<span class="stringliteral">&quot;ISO-8859-1&quot;</span>?&gt;</div>
<div class="line">&lt;PARAMETERS version=<span class="stringliteral">&quot;1.3&quot;</span> xsi:noNamespaceSchemaLocation=<span class="stringliteral">&quot;http://open-ms.sourceforge.net/schemas/Param_1_3.xsd&quot;</span> xmlns:xsi=<span class="stringliteral">&quot;http://www.w3.org/2001/XMLSchema-instance&quot;</span>&gt;</div>
<div class="line">  &lt;NODE name=<span class="stringliteral">&quot;1&quot;</span> description=<span class="stringliteral">&quot;&quot;</span>&gt;</div>
<div class="line">    &lt;ITEMLIST name=<span class="stringliteral">&quot;url_list&quot;</span> type=<span class="stringliteral">&quot;string&quot;</span> description=<span class="stringliteral">&quot;&quot;</span>&gt;</div>
<div class="line">      &lt;LISTITEM value=<span class="stringliteral">&quot;file:///Users/jeff/dataA.mzML&quot;</span>/&gt;</div>
<div class="line">      &lt;LISTITEM value=<span class="stringliteral">&quot;file:///Users/jeff/dataB.mzML&quot;</span>/&gt;</div>
<div class="line">    &lt;/ITEMLIST&gt;</div>
<div class="line">  &lt;/NODE&gt;</div>
<div class="line">  &lt;NODE name=<span class="stringliteral">&quot;2&quot;</span> description=<span class="stringliteral">&quot;&quot;</span>&gt;</div>
<div class="line">    &lt;ITEMLIST name=<span class="stringliteral">&quot;url_list&quot;</span> type=<span class="stringliteral">&quot;string&quot;</span> description=<span class="stringliteral">&quot;&quot;</span>&gt;</div>
<div class="line">      &lt;LISTITEM value=<span class="stringliteral">&quot;file:///Users/jeff/dataC.mzML&quot;</span>/&gt;</div>
<div class="line">    &lt;/ITEMLIST&gt;</div>
<div class="line">  &lt;/NODE&gt;</div>
<div class="line">&lt;/PARAMETERS&gt;</div>
</div><!-- fragment --><p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
ExecutePipeline -- Executes workflows created by TOPPAS.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  ExecutePipeline &lt;options&gt;

Options (mandatory options marked with '*'):
  -in &lt;file&gt;*            The workflow to be executed. (valid formats: 'toppas')
  -out_dir &lt;directory&gt;   Directory for output files (default: user's home directory)
  -resource_file &lt;file&gt;  A TOPPAS resource file (*.trf) specifying the files this workflow is to be applied 
                         to
  -num_jobs &lt;integer&gt;    Maximum number of jobs running in parallel (default: '1' min: '1')
                         
Common TOPP options:
  -ini &lt;file&gt;            Use the given TOPP INI file
  -threads &lt;n&gt;           Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini &lt;file&gt;      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">+ExecutePipeline</span><span class="node_description">Executes workflows created by TOPPAS.</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 'ExecutePipeline'</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">The workflow to be executed.</span><span class="item_tags">input file</span><span class="item_restrictions">*.toppas</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">out_dir</span><span class="item_value"></span>
<span class="item_description">Directory for output files (default: user's home directory)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">resource_file</span><span class="item_value"></span>
<span class="item_description">A TOPPAS resource file (*.trf) specifying the files this workflow is to be applied to</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">num_jobs</span><span class="item_value">1</span>
<span class="item_description">Maximum number of jobs running in parallel</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</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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