<?xml version="1.0"?>

<tool id="extend_bed_regions_1" name="Expand or contract regions">
  <description>in a BED file by a fixed number of bases</description>
  <version_string>echo 1.0.0</version_string>
  <command interpreter="perl">extend_bed_regions $in_bed $extent $strand $out_bed</command>
  <inputs>
    <param format="bed" name="in_bed" type="data" label="BED file whose regions should be modified"/>
    <param name="extent" type="integer" value="50" label="Number of bases to extend each BED region (negative values cause contraction)"/>
    <param name="strand" type="select" display="radio" label="Which end to extend?" help="If the BED file contains strand info, extension will be strand specific. Otherwise, the positive strand is assumed">
      <option value="5">5'</option>
      <option value="3">3'</option>
      <option value="both" selected="true">Both</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_bed" format="bed" type="data" label="BED file with extended/contracted regions"/>
  </outputs>

  <tests/>

  <help>
This tool expands each regions defined in a BED file by the specified amount, at the specified end(s). If expanded regions overlap, they are merged.
 </help>

</tool>