<tool id="region_motif_intersect" name="Region Motif Intersect">
  <description>for computing the motifs that lie inside a region set</description>
  <command interpreter="bash">
    /usr/bin/R --slave --vanilla -f $GALAXY_ROOT_DIR/tools/my_tools/region_motif_intersect.r --args $GALAXY_ROOT_DIR $db_type $in_bed $out_tab
  </command>
  <inputs>
    <param name="in_bed" type="data" format="bed" label="Input BED File" />
    <param name="db_type" type="select" label="Select Motif Database" >
      <option value="t">Test Pouya Subset (hg19)</option>
      <option value="p">Pouya Encode Motifs (hg19)</option>
      <option value="j">Jaspar and Jolma Motifs (hg19)</option>
      <option value="m">Mouse Motifs (mm9)</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_tab" format="tabular" />
  </outputs>

  <help>
    This tool computes the motifs and the number of motifs that intersect
    any region in a input set of regions.
  </help>
 
</tool>