<tool id="CallNukes" name="Call Nucleosomes" version="1.1.0">
  <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>
  
Stereotypic nucleosome positions are identified from dyad density maps using an approach similar to the previously reported greedy algorithm in GeneTrack_ (Albert, et al. 2008). Nucleosome calls are identified at peak maxima (p) in the smoothed dyad density map, and then excluded in the surrounding window [p–N, p+N], where N is the assumed nucleosome size in base pairs. This process is continued until all possible sterically hindered nucleosome positions are identified.

.. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html

.. class:: warningmark

This tool requires dyad counts and smoothed dyad counts in Wig or BigWig format. Smoothed dyad counts can be generated from dyad counts using the WigMath -> Gaussian smooth tool.

-----

**Syntax**

- **Dyad counts** is the relative number of nucleosomes positioned at each base pair.
- **Smoothed dyad counts** should correspond to a smoothed version of the **Dyad counts**  
- **Assumed nucleosome size** is the window size used while identifying maxima to restrict overlapping calls.  

-----

**Output**

The output format has 10 columns defined as follows

- 1. **Chromosome:** the chromosome of this nucleosome call
- 2. **Start:** the lower coordinate of the call window, equal to the dyad position - N/2
- 3. **Stop:** the higher coordinate of the call window, equal to the dyad position + N/2
- 4. **Length:** the window size (N) of the nucleosome call, equal to the value specified when the tool was run
- 5. **Length standard deviation:** the standard deviation of the nucleosome call length (equal to 0 because it is not currently calculated)
- 6. **Dyad:** the location of the peak maximum (p) in the smoothed dyad density data
- 7. **Dyad standard deviation:** the standard deviation of dyad density around the dyad mean in the dyad counts data
- 8. **Conditional position:** the probability that a nucleosome is at this exact dyad location as opposed to anywhere else in the nucleosome call window [p-N/2, p+N/2]
- 9. **Dyad mean:** the mean of the dyad counts in the window [p-N/2, p+N/2]
- 10. **Occupancy:** the sum of the dyad counts in the window [p-N/2, p+N/2]

</help>
</tool>