diff galaxy-conf/GreedyCaller.xml @ 20:9d56b5b85740 draft

Reuploaded to see if tools get loaded correctly this time.

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+++ b/galaxy-conf/GreedyCaller.xml	Fri Jun 15 15:10:26 2012 -0400
@@ -0,0 +1,49 @@
+<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>