<tool id="region_motif_intersect" name="Region Motif Intersect">
  <description>for computing the motifs that lie inside a region set</description>
  <command interpreter="Rscript">
    region_motif_intersect.r --args $bgz_file.fields.path $tbi_file.fields.path $in_bed $out_tab
  </command>
  <inputs>
    <param name="in_bed" type="data" format="bed" label="Input BED File" />
    
    <param name="bgz_file" type="select" label="Using motif database BGZ file">
      <options from_data_table="motif_databases"/>
    </param>
    <param name="tbi_file" type="select" label="Using motif database TBI file">
      <options from_data_table="motif_databases"/>
    </param>

    <!--<param name="db_type" type="select" label="Select Motif Database" >
      <option value="t">Test Encode Motifs (hg19)</option>
      <option value="e">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>

  <tests>
    <test>
      <param name="in_bed" value="XXX.bed" />
      <param name="bgz_file" value="XXX" />
      <param name="tbi_file" value="XXX" />
      <output name="output" file="XXX.tab" />     
    </test>
    <test>
      <param name="in_bed" value="XXX.bed" />
      <param name="bgz_file" value="XXX" />
      <param name="tbi_file" value="XXX" />
      <output name="out_tab" file="XXX.tab" />     
    </test>
  </tests>

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