<tool id="MapDyads" name="Map dyads" version="1.0.0">
  <description>from sequencing reads</description>
  <command interpreter="sh">
    galaxyToolRunner.sh nucleosomes.MapDyads -i $input -a ${chromInfo} -o $output
    #if $type.read == 'single'
      -s $type.size
    #end if
  </command>
  <inputs>
      <param name="input" type="data" format="bam" label="Sequencing reads" />
      <conditional name="type">
        <param name="read" type="select" label="Type of reads">
          <option value="paired" selected="true">Paired-End</option>
          <option value="single">Single-End</option>
        </param>
        <when value="single">
          <param name="size" type="integer" value="147" label="Estimated mononucleosome length (used to offset +/- strands)" />
        </when>
        <when value="paired">
          <!-- No values here -->
        </when>
      </conditional>
  </inputs>
  <outputs>
      <data name="output" format="wig" />
  </outputs>
  
<help>
.. class:: warningmark

  This tool requires sequencing reads in BAM format. If your reads are in SAM format, use the SAM-to-BAM tool under NGS: SAMTools.

.. class:: warningmark

For paired-end MNase data, read centers are approximated by using the center of the read. For single-end data, the estimated mononucleosome fragment length must be specified, which will be used to offset reads from the + and - strands.
</help>
</tool>
