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