view tools/filters/ucsc_gene_table_to_intervals.xml @ 0:9071e359b9a3

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<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>