<tool id="collapseBed" name="collapse">
  <description>intervals</description>
  <command interpreter="python">collapseBed2.py $input $strand $score > $outfile </command>
  <inputs>
    <param name="input" format="interval" type="data" label="Original file"/>
    <param name="strand" size="10" type="integer" value="6" label="strand column" help="set 0 to ignore strand information" />
    <param name="score" size="10" type="integer" value="5" label="for duplicate lines, keep the one with max value in column" help="set 0 to ignore score information" />
    </inputs>
  <outputs>
    <data format="input" name="outfile" />
  </outputs>
  <help>

**What it does**

This tool collapses genomic intervals that have the same position (and strandness if specified) and output a set of unique intervals.  

  </help>
</tool>