Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/Autocorrelation.xml @ 15:3e477c7e0e73 draft

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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.
author timpalpant
date Sat, 09 Jun 2012 16:03:59 -0400
parents 81d5b81fb3c2
children
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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="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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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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>