<tool id="convertens" name="convert ensembl">
  <description>to ucsc</description>
  <command interpreter="python">convertEnsembl.py $input $output $skip  </command>
  <inputs>
    <param name="input" format="interval" type="data" label="Original file"/>
    <param name="skip" size="10" type="integer" value="0" label="Number of beginning lines to skip"/>
  </inputs>
  <outputs>
    <data format="input" name="output" />
  </outputs>
  <help>

**What it does**

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. 

 </help>
</tool>
