/tools/filters/ucsc_gene_table_to_intervals.xml
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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>