Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/GreedyCaller.xml @ 20:9d56b5b85740 draft
Reuploaded to see if tools get loaded correctly this time.
| author | timpalpant |
|---|---|
| date | Fri, 15 Jun 2012 15:10:26 -0400 |
| parents | |
| children | b43c420a6135 |
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| 19:8ad390e82b92 | 20:9d56b5b85740 |
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| 1 <tool id="CallNukes" name="Call Nucleosomes" version="1.1.0"> | |
| 2 <description>in an MNase experiment</description> | |
| 3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.GreedyCaller -d $dyads -s $smoothed -n $N -o $output</command> | |
| 4 <inputs> | |
| 5 <param name="dyads" type="data" format="bigwig,wig" label="Dyad counts" /> | |
| 6 <param name="smoothed" type="data" format="bigwig,wig" label="Smoothed dyad counts" /> | |
| 7 <param name="N" type="integer" value="147" optional="true" label="Assumed nucleosome size" /> | |
| 8 </inputs> | |
| 9 <outputs> | |
| 10 <data name="output" format="tabular" /> | |
| 11 </outputs> | |
| 12 | |
| 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. | |
| 16 | |
| 17 .. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html | |
| 18 | |
| 19 .. class:: warningmark | |
| 20 | |
| 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 | |
| 48 </help> | |
| 49 </tool> |