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comparison galaxy-conf/Autocorrelation.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="Autocorrelation" name="Compute the autocorrelation" version="1.0.0"> 1 <tool id="Autocovariance" name="Compute the autocovariance" version="2.0.0">
2 <description>on data in a Wiggle file</description> 2 <description>of data in a Wiggle file</description>
3 <command interpreter="sh">galaxyToolRunner.sh ngs.Autocorrelation -i $input -l $windows -m $max -o $output</command> 3 <command interpreter="sh">galaxyToolRunner.sh ngs.Autocorrelation -i $input -l $windows -m $max -o $output</command>
4 <inputs> 4 <inputs>
5 <param format="bigwig,wig" name="input" type="data" label="Input data" /> 5 <param format="bigwig,wig" name="input" type="data" label="Input data" />
6 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" /> 6 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
7 <param name="max" type="integer" value="200" label="Maximum shift" /> 7 <param name="max" type="integer" value="200" label="Maximum shift" />
9 <outputs> 9 <outputs>
10 <data format="tabular" name="output" /> 10 <data format="tabular" name="output" />
11 </outputs> 11 </outputs>
12 12
13 <help> 13 <help>
14 .. class:: warningmark 14
15 This tool computes the unnormalized autocovariance_ of intervals of data in a Wig file.
15 16
16 This tool requires Wiggle/BigWig input data. 17 .. _autocovariance: http://en.wikipedia.org/wiki/Autocorrelation
18
19 -----
20
21 **Syntax**
22
23 - **Input data** is the genomic data on which to compute the autocorrelation.
24 - **List of intervals:** The autocorrelation will be computed for each genomic interval specified in this list.
25 - **Maximum shift:** In computing the autocorrelation, the data will be phase-shifted up to this limit.
26
27 -----
28
29 .. class:: infomark
30
31 **TIP:** For more information, see Wikipedia_ (right click to open this link in another window).
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33 .. _Wikipedia: http://en.wikipedia.org/wiki/Autocorrelation
34
35 .. class:: infomark
36
37 **TIP:** If your input data 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. Similarly, the intervals must be in either Bed, BedGraph, or GFF format.
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17 </help> 39 </help>
18 </tool> 40 </tool>