Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/FindOutlierRegions.xml @ 25:b43c420a6135 draft default tip

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Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author timpalpant
date Sat, 09 Feb 2019 14:02:24 -0500
parents 9d56b5b85740
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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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b43c420a6135 Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
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3 <command interpreter="bash">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" />
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7 <param name="threshold" type="float" value="3" label="Threshold (fold times the mean)" />
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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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13
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14 <help>
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15
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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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27
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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>