0
|
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>
|
|
23 Read 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> |