Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/GreedyCaller.xml @ 17:ace7855c1017 draft

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Add back tool_data_table_conf.xml.sample since apparently it's still needed.
author timpalpant
date Sat, 09 Jun 2012 16:10:42 -0400
parents 3e477c7e0e73
children
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3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
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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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13 <help>
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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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20
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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23 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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25 **Syntax**
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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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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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31 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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33 **Output**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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>