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<?xml version='1.0' encoding='UTF-8'?>
<tool id="IDEvaluator" name="IDEvaluator" version="1.12.0">
  <description>Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.</description>
  <macros>
    <token name="@EXECUTABLE@">IDEvaluator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IDEvaluator

-in ${param_in}
-out ${param_out}
-out_type ${param_out_type}
-out_csv ${param_out_csv}
-q_min ${param_q_min}
-q_max ${param_q_max}
-threads \${GALAXY_SLOTS:-24} 
${param_use_all_hits}
-algorithm:image:height ${param_height}
-algorithm:image:width ${param_width}
</command>
  <inputs>
    <param name="param_in" type="data" format="idXML" optional="True" size="20" label="Input file(s)" help="(-in)"/>
    <param name="param_out_type" type="select" optional="True" label="The image format. Set this if you want to force a format not reflected by the 'out' filename." help="(-out_type)">
      <option value="png">png</option>
      <option value="jpg">jpg</option>
      <option value="svg">svg</option>
    </param>
    <param name="param_q_min" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimal q-value in plot." help="(-q_min)"/>
    <param name="param_q_max" type="float" min="0.0" max="1.0" optional="True" value="0.4" label="Maximal q-value in plot." help="(-q_max)"/>
    <param name="param_use_all_hits" type="boolean" truevalue="-algorithm:fdr:use_all_hits true" falsevalue="-algorithm:fdr:use_all_hits false" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits)"/>
    <param name="param_height" type="integer" value="800" label="Height of raster images (e.g., PNG)." help="(-height)"/>
    <param name="param_width" type="integer" value="1024" label="Width of raster images (e.g., PNG)." help="(-width)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file (if given, no GUI will be displayed)" format="svg">
      <change_format>
        <when input="param_out_type" value="png" format="png"/>
        <when input="param_out_type" value="jpg" format="jpg"/>
      </change_format>
    </data>
    <data name="param_out_csv" label="Optional output of points as table for manual post-processing." format="tabular"/>
  </outputs>
  <help>**What it does**

Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDEvaluator.html

@REFERENCES@
</help>
</tool>