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comparison galaxy-conf/GreedyCaller.xml @ 12:81d5b81fb3c2 draft

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Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
parents b1952a90d4bf
children 3e477c7e0e73
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11:b1952a90d4bf 12:81d5b81fb3c2
9 <outputs> 9 <outputs>
10 <data name="output" format="tabular" /> 10 <data name="output" format="tabular" />
11 </outputs> 11 </outputs>
12 12
13 <help> 13 <help>
14
15 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.
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17 .. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html
18
14 .. class:: warningmark 19 .. class:: warningmark
15 20
16 This tool requires dyad counts and smoothed dyad counts. 21 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.
22
23 -----
24
25 **Syntax**
26
27 - **Dyad counts** is the relative number of nucleosomes positioned at each base pair.
28 - **Smoothed dyad counts** should correspond to a smoothed version of the **Dyad counts**
29 - **Assumed nucleosome size** is the window size used while identifying maxima to restrict overlapping calls.
30
31 -----
32
33 **Output**
34
35 The output format has 10 columns defined as follows
36
37 - 1. **Chromosome:** the chromosome of this nucleosome call
38 - 2. **Start:** the lower coordinate of the call window, equal to the dyad position - N/2
39 - 3. **Stop:** the higher coordinate of the call window, equal to the dyad position + N/2
40 - 4. **Length:** the window size (N) of the nucleosome call, equal to the value specified when the tool was run
41 - 5. **Length standard deviation:** the standard deviation of the nucleosome call length (equal to 0 because it is not currently calculated)
42 - 6. **Dyad:** the location of the peak maximum (p) in the smoothed dyad density data
43 - 7. **Dyad standard deviation:** the standard deviation of dyad density around the dyad mean in the dyad counts data
44 - 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]
45 - 9. **Dyad mean:** the mean of the dyad counts in the window [p-N/2, p+N/2]
46 - 10. **Occupancy:** the sum of the dyad counts in the window [p-N/2, p+N/2]
47
17 </help> 48 </help>
18 </tool> 49 </tool>