Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/IntervalAverager.xml @ 22:727fbba02ef7 draft

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Fix a bug in GeneTrackToWig where +/- strands were not merged correctly. Add option to vary the chunk size of tools that process chromosomes in chunks.
author timpalpant
date Tue, 19 Jun 2012 22:09:23 -0400
parents 9d56b5b85740
children b43c420a6135
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1 <tool id="IntervalAverager" name="Average intervals" version="2.1.0">
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2 <description>that have been aligned</description>
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3 <command interpreter="sh">
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4 galaxyToolRunner.sh visualization.IntervalAverager -l $loci -o $output $file1
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5 #for $input in $inputs
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6 ${input.file}
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7 #end for
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8 </command>
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9 <inputs>
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10 <param name="file1" label="Sequencing data" type="data" format="bigwig,wig" />
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11 <repeat name="inputs" title="Additional sequencing data">
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12 <param name="file" type="data" format="bigwig,wig" />
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13 </repeat>
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14 <param format="bed" name="loci" type="data" label="List of intervals (with alignment points)" />
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15 </inputs>
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16 <outputs>
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17 <data format="tabular" name="output" />
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18 </outputs>
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19
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20 <help>
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22 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.
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24 Intervals with alignment points must be provided in the following extended Bed format ::
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26 chr low high id alignment strand
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28 .. class:: infomark
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29
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30 **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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32 -----
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33
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34 **Syntax**
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36 - **Sequencing data** is the genomic data used to create the average
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37 - **List of intervals** is a list of intervals in Bed format with alignment points
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39 </help>
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40 </tool>