<tool id="NRLCalculator" name="Compute the NRL" version="1.0.0">
  <description>from nucleosome calls</description>
  <command interpreter="sh">galaxyToolRunner.sh nucleosomes.NRLCalculator -i $input -l $windows -o $output</command>
  <inputs>
      <param format="tabular" name="input" type="data" label="Nucleosome calls" />
      <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals/genes" />
  </inputs>
  <outputs>
      <data format="tabular" name="output" />
  </outputs>
  
<help>
  
This tool calculates the distance between adjacent nucleosome calls (dyads) emanating from the 5' end of an interval. For each interval, the distance is calculated from the +1 to +2 nucleosome, +2 to +3 nucleosome, etc. These distances are appended as additional columns for each interval. ::

  chr  start  stop  id  alignment  strand  +1-to-+2  +2-to-+3  ...
  
Each interval will have a different number of columns based on the number of nucleosome calls that were in that interval.
  
-----
  
.. class:: warningmark

Because the distances are calculated from the 5' end of each gene, as you move into the gene body it becomes more likely that a nucleosome call will be skipped, resulting in an outlier distance (~320bp rather than ~165bp). In addition, nucleosome calls in fuzzy regions tend to be inaccurate, so the NRL distances will not be robust.
  
.. class:: warningmark

This tool requires a set of nucleosome calls as input in the format created by the Nucleosomes -> Call Nucleosomes tool.

.. class:: warningmark

Intervals must be provided in Bed, BedGraph, or GFF format. BedGraph intervals are always considered to be on the + strand.

</help>
</tool>