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<div class="title">IDEvaluator </div> </div>
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<div class="textblock"><p>Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.</p>
<p>An arbitrary number of idXML files resulting from a target+decoy search can be provided as input.</p>
<p>Since the q-value can be computed independently from a scoring scheme, no further preprocessing (like IDPep or FDR) is required, apart from a target-decoy annotation! I.e., apply PeptideIndexer to the immediate output of a search engine (or ConsensusID) and use this as input to this tool.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
IDEvaluator -- Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifi
cations for a certain q-value.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
IDEvaluator <options>
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.
Options (mandatory options marked with '*'):
-in <file> Input file(s) (valid formats: 'idXML')
-out <file> Output file (if given, no GUI will be displayed) (valid formats: 'png', 'jpg', 'svg'
)
-out_type <file type> The image format. Set this if you want to force a format not reflected by the 'out'
filename. (valid: 'png', 'jpg', 'svg')
-out_csv <file> Optional output of points as table for manual post-processing. (valid formats: 'csv'
)
-q_min <float> Minimal q-value in plot. (default: '0' min: '0' max: '1')
-q_max <float> Maximal q-value in plot. (default: '0.4' min: '0' max: '1')
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)
The following configuration subsections are valid:
- algorithm Additional parameters for FDR and image sizes.
You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.
</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">+IDEvaluator</span><span class="node_description">Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.</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 'IDEvaluator'</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 file(s)</span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Output file (if given, no GUI will be displayed)</span><span class="item_tags">output file</span><span class="item_restrictions">*.png,*.jpg,*.svg</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out_type</span><span class="item_value"></span>
<span class="item_description">The image format. Set this if you want to force a format not reflected by the 'out' filename.</span><span class="item_tags"></span><span class="item_restrictions">png,jpg,svg</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out_csv</span><span class="item_value"></span>
<span class="item_description">Optional output of points as table for manual post-processing.</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;">q_min</span><span class="item_value">0</span>
<span class="item_description">Minimal q-value in plot.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">q_max</span><span class="item_value">0.4</span>
<span class="item_description">Maximal q-value in plot.</span><span class="item_tags"></span><span class="item_restrictions">0:1</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 class="node"><span class="node_name">+++algorithm</span><span class="node_description">Additional parameters for FDR and image sizes.</span></div>
<div class="node"><span class="node_name">++++fdr</span><span class="node_description"></span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">use_all_hits</span><span class="item_value">false</span>
<span class="item_description">If 'true' not only the first hit, but all are used (peptides only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">++++image</span><span class="node_description"></span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">height</span><span class="item_value">800</span>
<span class="item_description">Height of raster images (e.g., PNG).</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:40px;">width</span><span class="item_value">1024</span>
<span class="item_description">Width of raster images (e.g., PNG).</span><span class="item_tags"></span><span class="item_restrictions"> </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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