<tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1">
  
  <description>on a BED file</description>

  <command interpreter="python">
    genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x
  </command>
    
  <inputs>
    
    <param format="bed6" name="input" type="data" help="Input data">
      <label>Select input bed file</label>
    </param>
    
    <param name="shift" size="4" type="integer" value="0" help="distance in basepairs">
        <label>Shift at 5' end</label>
    </param>

    <!-- this parameter is currently not used, may not be feasible to use it
    <param name="coverage" type="select" label="Full coverage">
      <option value="no">NO</option>
      <option value="yes">YES</option>
    </param>
    -->
  
  </inputs>

  <outputs>  
    <data format="genetrack" name="output" />
  </outputs>
   
<help>
**Help**

This tool will create a visualization of the bed file that is selected. 

**Parameters**

- **Shift at 5' end** should be used when the location of interest is at a fixed distance from
  the 5' end for **all sequenced fragments**! 
  
  For example if the sequenced sample consists
  mono-nucleosomal DNA (146bp) we should expect that 
  each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. 
  Therefore we would enter 73 as the shift parameter. Once corrected the reads 
  on each strand will coincide and indicate the actual midpoints 
  of the nucleosomes.
  
  When shifting the averaging process in GeneTrack is able correct for longer or shorter
  than expected fragment sizes as long as the errors are reasonably random.

</help>

</tool>