Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/GreedyCaller.xml @ 22:727fbba02ef7 draft

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Fix a bug in GeneTrackToWig where +/- strands were not merged correctly. Add option to vary the chunk size of tools that process chromosomes in chunks.
author timpalpant
date Tue, 19 Jun 2012 22:09:23 -0400
parents 9d56b5b85740
children b43c420a6135
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1 <tool id="CallNukes" name="Call Nucleosomes" version="1.1.0">
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2 <description>in an MNase experiment</description>
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3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.GreedyCaller -d $dyads -s $smoothed -n $N -o $output</command>
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4 <inputs>
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5 <param name="dyads" type="data" format="bigwig,wig" label="Dyad counts" />
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6 <param name="smoothed" type="data" format="bigwig,wig" label="Smoothed dyad counts" />
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7 <param name="N" type="integer" value="147" optional="true" label="Assumed nucleosome size" />
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8 </inputs>
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9 <outputs>
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10 <data name="output" format="tabular" />
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11 </outputs>
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12
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13 <help>
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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
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19 .. class:: warningmark
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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.
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23 -----
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25 **Syntax**
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26
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27 - **Dyad counts** is the relative number of nucleosomes positioned at each base pair.
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28 - **Smoothed dyad counts** should correspond to a smoothed version of the **Dyad counts**
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29 - **Assumed nucleosome size** is the window size used while identifying maxima to restrict overlapping calls.
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31 -----
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33 **Output**
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34
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35 The output format has 10 columns defined as follows
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37 - 1. **Chromosome:** the chromosome of this nucleosome call
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38 - 2. **Start:** the lower coordinate of the call window, equal to the dyad position - N/2
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39 - 3. **Stop:** the higher coordinate of the call window, equal to the dyad position + N/2
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40 - 4. **Length:** the window size (N) of the nucleosome call, equal to the value specified when the tool was run
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41 - 5. **Length standard deviation:** the standard deviation of the nucleosome call length (equal to 0 because it is not currently calculated)
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42 - 6. **Dyad:** the location of the peak maximum (p) in the smoothed dyad density data
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43 - 7. **Dyad standard deviation:** the standard deviation of dyad density around the dyad mean in the dyad counts data
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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]
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45 - 9. **Dyad mean:** the mean of the dyad counts in the window [p-N/2, p+N/2]
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46 - 10. **Occupancy:** the sum of the dyad counts in the window [p-N/2, p+N/2]
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48 </help>
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49 </tool>