<!--
Usage of THIS SCRIPT: ./idrPlotWrapper.sh em uri outputfile 
-->

<tool id="batch_consistency_plot" name="IDR-Plot">
  <requirements>
    <requirement type="set_environment">SCRIPT_PATH</requirement>
  </requirements>
  <description>Plot Consistency Analysis on IDR output files</description>
  <command interpreter="bash">idrPlotWrapper.sh $em $uri $outputfile \$SCRIPT_PATH</command>
  <inputs>
    <param name="uri" type="data" label="uri.sav file (output from IDR consistency analysis)"/>
    <param name="em" type="data" label="em.sav file (output from IDR consistency analysis)"/>
  </inputs>
  <outputs>
    <data format="pdf" name="outputfile" label="IDR-plot.pdf"/>
  </outputs>

  <tests>
    <test>
<!--
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
-->
    </test>
  </tests>

  <help>
Plots the correspondence curve and IDR threshold (i.e. number of selected peaks vs IDR) for each pair of samples.
Uses the output of IDR consistency analysis and produces a downloadable PDF file containing the graphical analysis.
This is a part of the IDR package.  For more information about IDR, see https://sites.google.com/site/anshulkundaje/projects/idr.
  </help>

</tool>