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comparison galaxy-conf/IntervalStats.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 4b32ed5d4a1b
children
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11:b1952a90d4bf 12:81d5b81fb3c2
1 <tool id="IntervalStats" name="Compute window statistics" version="1.0.0"> 1 <tool id="IntervalStats" name="Compute mean/min/max of intervals" version="1.0.0">
2 <description>on data in a Wiggle file</description> 2 <description>of data in a Wiggle file</description>
3 <command interpreter="sh"> 3 <command interpreter="sh">
4 galaxyToolRunner.sh ngs.IntervalStats -l $windows -o $output 4 galaxyToolRunner.sh ngs.IntervalStats -l $windows -s $stat -o $output
5 #for $input in $inputs 5 #for $input in $inputs
6 ${input.file} 6 ${input.file}
7 #end for 7 #end for
8 </command> 8 </command>
9 <inputs> 9 <inputs>
10 <repeat name="inputs" title="BigWig file"> 10 <repeat name="inputs" title="BigWig file">
11 <param name="file" type="data" format="bigwig,wig" /> 11 <param name="file" type="data" format="bigwig,wig" />
12 </repeat> 12 </repeat>
13 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" /> 13 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
14 <!-- TODO: Implement other statistics 14 <param name="stat" type="select" optional="true" label="For each interval, compute the">
15 <param name="stat" type="select" optional="true" label="For each window, compute the">
16 <option value="mean">Mean</option> 15 <option value="mean">Mean</option>
17 <option value="median">Median</option> 16 <!-- TODO <option value="median">Median</option> -->
18 <option value="max">Max</option> 17 <option value="max">Max</option>
19 <option value="min">Min</option> 18 <option value="min">Min</option>
20 </param> --> 19 </param>
21 </inputs> 20 </inputs>
22 <outputs> 21 <outputs>
23 <data format="tabular" name="output" /> 22 <data format="tabular" name="output" />
24 </outputs> 23 </outputs>
25 24
26 <help> 25 <help>
27 .. class:: warningmark 26
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.
28
29 .. class:: infomark
28 30
29 This tool requires Wiggle/BigWig input data. 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.
32
33 -----
34
35 **Example**
36
37 Calculate the mean change in nucleosome occupancy for each gene in the yeast genome:
38
39 - 1. Create a "change in occupancy" dataset by subtracting the normalized occupancy Wig files from your two conditions using the WigMath -> Subtract tool.
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.
41 - 3. Calculate the mean change in occupancy for each gene using this tool and the datasets from (1) and (2).
42
30 </help> 43 </help>
31 </tool> 44 </tool>