[2] | 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> |
---|