Mercurial > repos > xuebing > sharplabtool
comparison tools/filters/ucsc_gene_table_to_intervals.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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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> | |
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> |