<tool id="FindNuke" name="Find boundary nucleosomes" version="1.0.0">
  <description>in windows</description>
  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.FindBoundaryNucleosomes -i $input -l $loci -o $output</command>
  <inputs>
    <param name="input" type="data" format="nukes" label="Nucleosome calls" />
    <param name="loci" type="data" format="bed" label="List of intervals" />
  </inputs>
  <outputs>
    <data name="output" format="bed" metadata_source="loci" />
  </outputs>
  
  <help>
    .. class:: warningmark
    
    Use the Greedy Caller tool to create a file of called nucleosomes, then use this tool to identify the first nucleosome's dyad position from the 5' or 3' end.
  </help>
</tool>