<tool id="bedclean" name="clean interval">
  <description>remove off-chromosome lines</description>
  <command interpreter="python">bedclean.py $input $genome $output > $log  </command>
  <inputs>
     <param name="input" type="data" format="interval" label="Original interval file"/>
    <param name="genome" type="select" label="Select genome">
     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
     <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
    </param>
  </inputs>
  <outputs>
    <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/>
    <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/>
  </outputs>
  <help>

**Description**

remove lines that are

1. comment or track name lines

2. on chr*_random

3. or have negative coordinates

4. or the end is larger than chromosome size


  </help>
</tool>