view mytools/collapseBed.xml @ 9:87eb5c5ddfe9

author xuebing
date Fri, 09 Mar 2012 20:01:43 -0500
parents f0dc65e7f6c0
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<tool id="collapseBed" name="collapse">
  <command interpreter="python"> $input $strand $score > $outfile </command>
    <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" />
    <data format="input" name="outfile" />

**What it does**

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