<tool id="compare_targets" name="Compare Targets" version="1.3.1">
  <description>Post-processing analysis: compares the target genes from two EMBER runs</description>
  <command interpreter="perl">Compare_Targets.pl -t1 $set1 -t2 $set2 -o $output -of $outtype -n $comptype</command>
  <inputs>
    <param format="txt" name="set1" type="data" label="Targets file 1"/>
    <param format="txt" name="set2" type="data" label="Targets file 2"/>
    <param name="outtype" type="select" label="Output type">
        <option value="0" selected="true">All shared targets</option>
        <option value="1">Targets unique to file 1</option>
        <option value="2">Targets unique to file 2</option>
        <option value="3">Union of targets from files 1 and 2</option>
    </param>
    <param name="comptype" type="select" label="Value to compare">
        <option value="1" selected="true">Gene names</option>
        <option value="0">Probe set IDs</option>
    </param>
  </inputs>
  <outputs>
    <data format="txt" name="output"/>
  </outputs>
  
  <tests>
    <test>
      <param name="set1" value="EMBER/patterns-1.targets"/>
      <param name="set2" value="EMBER/patterns-1.targets"/>
      <param name="outtype" value="0"/>
      <param name="comptype" value="1"/>
      <output name="output" file="EMBER/targets_1-1.txt"/>
    </test>
  </tests>


  <help>

This tool compares the list of gene targets from different EMBER runs.

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Description of inputs:

*Targets files 1 and 2*: the .targets outputs of EMBER (lines start with "PEAK:" or "TGENE:").

*Output type*: This tool compares the gene sets, and you can choose which comparison to print, either the intersection, difference, or union.

*Value to compare*: Choose gene name or probe set ID; some genes have multiple probe sets.

  </help>

</tool>