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<div class="title">CVInspector </div>  </div>
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<div class="textblock"><p>A tool for visualization and validation of PSI mapping and CV files.</p>
<p>This tool is used to validate the correct use of mapping files and CV files.</p>
<p>It can also generate a HTML representation of mapping file and CV.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
CVInspector -- A tool for visualization and validation of PSI mapping and CV files.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  CVInspector &lt;options&gt;

Options (mandatory options marked with '*'):
  -cv_files &lt;files&gt;*    List of ontology files in OBO format. (valid formats: 'obo')
  -cv_names &lt;names&gt;*    List of identifiers (one for each ontology file).
  -mapping_file &lt;file&gt;  Mapping file in CVMapping (XML) format. (valid formats: 'XML')
  -ignore_cv &lt;list&gt;     A list of CV identifiers which should be ignored. (default: '[UO PATO BTO]')
  -html &lt;file&gt;          Writes an HTML version of the mapping file with annotated CV terms (valid formats: 
                        'HTML')
                        
Common UTIL 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">+CVInspector</span><span class="node_description">A tool for visualization and validation of PSI mapping and CV files.</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 'CVInspector'</span></div>
      <div class="item"><span class="item_name item_required" style="padding-left:24px;">cv_files</span><span class="item_value">[]</span>
<span class="item_description">List of ontology files in OBO format.</span><span class="item_tags">input file</span><span class="item_restrictions">*.obo</span></div>      <div class="item"><span class="item_name item_required" style="padding-left:24px;">cv_names</span><span class="item_value">[]</span>
<span class="item_description">List of identifiers (one for each ontology file).</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">mapping_file</span><span class="item_value"></span>
<span class="item_description">Mapping file in CVMapping (XML) format.</span><span class="item_tags">input file</span><span class="item_restrictions">*.XML</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">ignore_cv</span><span class="item_value">[UO, PATO, BTO]</span>
<span class="item_description">A list of CV identifiers which should be ignored.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">html</span><span class="item_value"></span>
<span class="item_description">Writes an HTML version of the mapping file with annotated CV terms</span><span class="item_tags">output file</span><span class="item_restrictions">*.HTML</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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