<tool id="MapDyads" name="Map dyads" version="1.1.0">
  <description>from sequencing reads</description>
  <command interpreter="bash">
    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="sam,bam,bed,bedGraph" 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>
  
This tool produces a Wig file with the number of dyads at each base pair. For paired-end MNase data, dyads are approximated using the center of the fragment. For Bed/BedGraph formatted input, this means the center of the interval; for SAM/BAM formatted input, this means the middle between the 5' end of mate 1 and the 5' end of mate 2. For single-end data, the estimated mononucleosome fragment length (N) must be specified, which will be used to offset reads from the + and - strands by +/- N/2.
  
.. class:: warningmark

This tool requires sequencing reads in SAM, BAM, Bed, or BedGraph format.

.. class:: warningmark

Since BedGraph format does not contain strand information, all reads in BedGraph format are considered to be on the 5' strand.

</help>
</tool>