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<div class="title">OpenSwathFeatureXMLToTSV </div> </div>
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<div class="textblock"><p>Converts a featureXML to a mProphet tsv</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 $" src="form_91.png"/> FeatureXMLToTSV <img class="formulaInl" alt="$ \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_OpenSwathAnalyzer.html">OpenSwathAnalyzer</a> </td><td valign="middle" align="center" rowspan="2">Downstream data analysis </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_OpenSwathConfidenceScoring.html">OpenSwathConfidenceScoring</a> </td></tr>
</table>
</center><p>Creates a tsv that is compatible as input to mProphet. Furthermore it creates the columns "decoy" and "transition_group_id" which are required by mProphet.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
OpenSwathFeatureXMLToTSV -- Converts a featureXML to a mProphet tsv.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
OpenSwathFeatureXMLToTSV <options>
Options (mandatory options marked with '*'):
-in <files>* Input files separated by blank (valid formats: 'featureXML')
-tr <file>* TraML transition file (valid formats: 'traML')
-out <file>* Tsv output file (mProphet compatible) (valid formats: 'csv')
-short_format Whether to write short (one peptide per line) or long format (one transiti
on per line).
-best_scoring_peptide <varname> If only the best scoring feature per peptide should be printed, give the
variable name
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>The algorithm parameters for the Analyzer filter are:</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">+OpenSwathFeatureXMLToTSV</span><span class="node_description">Converts a featureXML to a mProphet tsv.</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 'OpenSwathFeatureXMLToTSV'</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 files separated by blank</span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">tr</span><span class="item_value"></span>
<span class="item_description">TraML transition file</span><span class="item_tags">input file</span><span class="item_restrictions">*.traML</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">tsv output file (mProphet compatible)</span><span class="item_tags">output file</span><span class="item_restrictions">*.csv</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">short_format</span><span class="item_value">false</span>
<span class="item_description">Whether to write short (one peptide per line) or long format (one transition per line).</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">best_scoring_peptide</span><span class="item_value"></span>
<span class="item_description">If only the best scoring feature per peptide should be printed, give the variable name</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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