Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/IntervalStats.xml @ 14:f58706d4d421 draft

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author timpalpant
date Sat, 19 May 2012 10:40:16 -0400
parents 81d5b81fb3c2
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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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1 <tool id="IntervalStats" name="Compute mean/min/max of intervals" version="1.0.0">
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2 <description>of data in a Wiggle file</description>
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3 <command interpreter="sh">
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4 galaxyToolRunner.sh ngs.IntervalStats -l $windows -s $stat -o $output
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5 #for $input in $inputs
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6 ${input.file}
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7 #end for
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8 </command>
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9 <inputs>
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10 <repeat name="inputs" title="BigWig file">
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11 <param name="file" type="data" format="bigwig,wig" />
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12 </repeat>
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13 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
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14 <param name="stat" type="select" optional="true" label="For each interval, compute the">
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15 <option value="mean">Mean</option>
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16 <!-- TODO <option value="median">Median</option> -->
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17 <option value="max">Max</option>
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18 <option value="min">Min</option>
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" name="output" />
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23 </outputs>
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24
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25 <help>
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27 This tool calculates the arithmetic mean, maximum, or minimum value for the Wig data in each interval. For each Wig file provided, an additional column is added to the output file in the order that they are added above.
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29 .. class:: infomark
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31 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in Wig or BigWig format. Use "edit attributes" to set the correct format if it was not detected correctly.
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33 -----
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34
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35 **Example**
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37 Calculate the mean change in nucleosome occupancy for each gene in the yeast genome:
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39 - 1. Create a "change in occupancy" dataset by subtracting the normalized occupancy Wig files from your two conditions using the WigMath -> Subtract tool.
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40 - 2. Upload a list of intervals corresponding to the genes in the yeast genome, or pull the data from UCSC using Get Data -> UCSC Main.
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41 - 3. Calculate the mean change in occupancy for each gene using this tool and the datasets from (1) and (2).
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42
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43 </help>
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44 </tool>