<tool id="bed_clean" name="bed_clean">
  <description>clean up BED files</description>
  <command interpreter="python">bed_clean.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 chromsome size file" >
                <options from_file="chrsize.loc">
                    <column name="name" index="0"/>
                    <column name="value" index="1"/>
                </options>
            </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

5. convert strand * to + 


  </help>
</tool>