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1 <tool id="convertens" name="convert ensembl">
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2 <description>to ucsc</description>
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3 <command interpreter="python">convertEnsembl.py $input $output $skip </command>
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4 <inputs>
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5 <param name="input" format="interval" type="data" label="Original file"/>
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6 <param name="skip" size="10" type="integer" value="0" label="Number of beginning lines to skip"/>
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7 </inputs>
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8 <outputs>
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9 <data format="input" name="output" />
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10 </outputs>
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11 <help>
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12
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13 **What it does**
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14
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15 This tool convert ensembl based interval file to ucsc format: add 'chr' to chromosome number (column 1), and replace '1' and '-1' with '+' and '-' in column 6, respectively.
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16
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17 </help>
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18 </tool>
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