Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/IntervalAverager.xml @ 16:35031c567ece draft

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Add sam_fa_indices.loc.sample to enable DNAProperty and FindNMer tools that require samtools indices to be installed.
author timpalpant
date Sat, 09 Jun 2012 16:06:25 -0400
parents 3e477c7e0e73
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="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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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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 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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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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24 Intervals with alignment points must be provided in the following extended Bed format ::
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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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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26 chr low high id alignment strand
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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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28 .. 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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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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81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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32 -----
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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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34 **Syntax**
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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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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>