view region_motif_intersect.xml @ 34:fe8a884363df draft

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<tool id="region_motif_intersect" name="Region Motif Intersect">
  <description>for computing the motifs that lie inside a region set</description>
  <!--<requirements>
    <requirement type="package" version="1.0.0">MOTIF_DATA_MANAGER</requirement>
  </requirements>-->
  <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 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>