<tool id="ucsc_gene_table_to_intervals1" name="Gene Table To BED">

<description>Parse a UCSC Gene Table dump</description>

  <command interpreter="python">ucsc_gene_table_to_intervals.py --input=$input1 --output=$out_file1 --region=$region $exon</command>

  <inputs>

    <param name="input1" type="data" format="inverval" label="UCSC Gene Table"/>

    <param name="region" type="select">

      <label>Feature Type</label>

      <option value="transcribed">Transcribed</option>

      <option value="coding">Coding</option>

      <option value="utr3">3' UTR</option>

      <option value="utr5">5' UTR</option>

    </param>

    <param name="exon" type="select">

      <label>Only print intervals overlapping an exon</label>

      <option value="">False</option>

      <option value="--exons">True</option>

    </param>

  </inputs>

  <outputs>

    <data name="out_file1" format="bed"/>

  </outputs>

<help>

Read a table dump in the UCSC gene table format and create a BED file corresponding to the requested feature of each gene.

</help>

</tool>