Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/Autocorrelation.xml @ 13:eb53be9a09f4 draft

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author timpalpant
date Sat, 19 May 2012 10:36:45 -0400
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1 <tool id="Autocovariance" name="Compute the autocovariance" version="2.0.0">
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2 <description>of data in a Wiggle file</description>
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3 <command interpreter="sh">galaxyToolRunner.sh ngs.Autocorrelation -i $input -l $windows -m $max -o $output</command>
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4 <inputs>
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5 <param format="bigwig,wig" name="input" type="data" label="Input data" />
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6 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
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7 <param name="max" type="integer" value="200" label="Maximum shift" />
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8 </inputs>
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9 <outputs>
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10 <data format="tabular" name="output" />
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11 </outputs>
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13 <help>
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15 This tool computes the unnormalized autocovariance_ of intervals of data in a Wig file.
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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 .. _autocovariance: http://en.wikipedia.org/wiki/Autocorrelation
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19 -----
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20
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21 **Syntax**
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23 - **Input data** is the genomic data on which to compute the autocorrelation.
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24 - **List of intervals:** The autocorrelation will be computed for each genomic interval specified in this list.
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25 - **Maximum shift:** In computing the autocorrelation, the data will be phase-shifted up to this limit.
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27 -----
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29 .. class:: infomark
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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
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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 .. class:: infomark
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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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38
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39 </help>
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40 </tool>