/tools/filters/ucsc_gene_table_to_intervals.xml

 1<tool id="ucsc_gene_table_to_intervals1" name="Gene Table To BED">
 2<description>Parse a UCSC Gene Table dump</description>
 3  <command interpreter="python">ucsc_gene_table_to_intervals.py --input=$input1 --output=$out_file1 --region=$region $exon</command>
 4  <inputs>
 5    <param name="input1" type="data" format="inverval" label="UCSC Gene Table"/>
 6    <param name="region" type="select">
 7      <label>Feature Type</label>
 8      <option value="transcribed">Transcribed</option>
 9      <option value="coding">Coding</option>
10      <option value="utr3">3' UTR</option>
11      <option value="utr5">5' UTR</option>
12    </param>
13    <param name="exon" type="select">
14      <label>Only print intervals overlapping an exon</label>
15      <option value="">False</option>
16      <option value="--exons">True</option>
17    </param>
18  </inputs>
19  <outputs>
20    <data name="out_file1" format="bed"/>
21  </outputs>
22<help>
23Read a table dump in the UCSC gene table format and create a BED file corresponding to the requested feature of each gene.
24</help>
25</tool>