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annotate galaxy-conf/FindOutlierRegions.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 eb53be9a09f4
children
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3e477c7e0e73 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.
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1 <tool id="WigFindOutliers" name="Find outlier regions" version="1.1.0">
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2 <description>such as CNVs</description>
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eb53be9a09f4 Uploaded
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3 <command interpreter="sh">galaxyToolRunner.sh ngs.FindOutlierRegions -i $input -w $window -t $threshold $below -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 name="window" type="integer" value="150" label="Window size" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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7 <param name="threshold" type="float" value="3" label="Threshold (fold times the mean)" />
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eb53be9a09f4 Uploaded
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8 <param name="below" type="boolean" checked="false" truevalue="-b" falsevalue="" label="Search for outliers below the threshold" />
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9 </inputs>
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10 <outputs>
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11 <data format="bed" name="output" metadata_source="input" />
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12 </outputs>
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14 <help>
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16 This tool identifies regions of the genome that may be repetitive elements or CNVs by scanning for windows that have an exceptionally high mean relative to the genome-wide mean.
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18 -----
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20 .. class:: infomark
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22 **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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24 -----
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26 **Syntax**
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28 - **Input data** is Wig or BigWig formatted data from a high-throughput sequencing experiment.
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29 - **Window size** is the size of the moving average to use.
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30 - **Threshold** is the fold times the genome-wide mean that a window's mean must be in order to be considered an outlier region.
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32 </help>
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33 </tool>