Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/IntervalAverager.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 eb53be9a09f4
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1 <tool id="IntervalAverager" name="Average intervals" version="1.0.0">
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2 <description>that have been aligned</description>
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3 <command interpreter="sh">galaxyToolRunner.sh visualization.IntervalAverager -i $input -l $loci -o $output</command>
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4 <inputs>
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5 <param format="wig,bigwig" name="input" type="data" label="Sequencing data" />
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6 <param format="bed" name="loci" type="data" label="List of intervals (with alignment points)" />
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7 </inputs>
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8 <outputs>
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9 <data format="tabular" name="output" />
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10 </outputs>
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12 <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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14 This tool calculates the average signal for a set of aligned intervals. Intervals are lined up on their alignment point (column 5 in the Bed file), flipped if on the - strand, and averaged. The output is equivalent to aligning the data in a matrix and then taking the columnwise average of the matrix.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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16 Intervals with alignment points must be provided in the following extended Bed format ::
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18 chr low high id alignment strand
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20 .. class:: infomark
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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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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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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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24 -----
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26 **Syntax**
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28 - **Sequencing data** is the genomic data used to create the average
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29 - **List of intervals** is a list of intervals in Bed format with alignment points
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31 </help>
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32 </tool>