<tool id="CallNukes" name="Call Nucleosomes" version="1.0.0">
  <description>in an MNase experiment</description>
  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.GreedyCaller -d $dyads -s $smoothed -n $N -o $output</command>
  <inputs>
      <param name="dyads" type="data" format="bigwig,wig" label="Dyad counts" />
      <param name="smoothed" type="data" format="bigwig,wig" label="Smoothed dyad counts" />
      <param name="N" type="integer" value="147" optional="true" label="Assumed nucleosome size" />
  </inputs>
  <outputs>
      <data name="output" format="tabular" />
  </outputs>
  
<help>
.. class:: warningmark

This tool requires dyad counts and smoothed dyad counts.

.. class:: warningmark

This tool was contributed by Timothy Palpant.
</help>
</tool>
