<tool id="FindNuke" name="Find boundary nucleosomes" version="2.0.0">
  <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="tabular" label="Nucleosome calls" />
    <param name="loci" type="data" format="bed,bedgraph,gff" label="List of intervals" />
  </inputs>
  <outputs>
    <data name="output" format="bed" metadata_source="loci" />
  </outputs>
  
  <help>
    
.. class:: infomark
    
Use the Call Nucleosomes tool to create a file of called nucleosomes, then use this tool to identify the first nucleosome's dyad position (peak maximum) from the 5' and 3' end of the gene.

.. class:: infomark

**TIP:** Nucleosome calls must be in tabular format of the kind produced by the Nucleosomes -> Call nucleosomes tool. Intervals must be in either Bed, BedGraph, or GFF format.

-----

**Syntax**

- **Nucleosome calls** is a list of stereotypic nucleosome position calls.
- **List of intervals:** The 5' and 3' boundary nucleosomes will be found for each interval in this list

  </help>
</tool>