Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/BaseAlignCounts.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 9266d807ca85
children eb53be9a09f4
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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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1 <tool id="BaseAlignCounts" name="Calculate coverage" version="1.0.0">
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2 <description>of sequencing reads</description>
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3 <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="sam,bam,bed,bedgraph" label="Sequencing reads" />
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6 <param name="X" type="integer" value="-1" label="In silico extension (-1 for read length)" />
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7 </inputs>
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8 <outputs>
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9 <data name="output" format="wig" />
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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 produces a new Wig file with the number of reads/intervals overlapping each base pair. Reads can be artificially extended to match known fragment lengths. If you wish to count the number of reads starting at each base pair, set the read extension to 1. If you wish to count the number of intervals overlapping each base pair, set the extension to -1.
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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16 -----
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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18 .. class:: warningmark
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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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20 This tool requires sequencing reads in SAM, BAM, Bed, or BedGraph format. If you are artificially extending reads, ensure that the strand is set correctly in SAM, BAM, and Bed files.
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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 .. 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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24 If you would like to convert valued interval data (e.g. BedGraph files from microarrays) to Wig format, use the Converters -> Interval to Wig converter.
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26 .. class:: infomark
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28 **TIP:** If you are going to be using reads in SAM format for multiple analyses, it is often more efficient to first convert it into BAM format using NGS: SAM Tools -> SAM-to-BAM.
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30 -----
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32 **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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34 - **Sequencing reads** are mapped reads from a high-throughput sequencing experiment.
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35 - **In silico extension:** Reads will be artificially extended from their 5' end to be this length.
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37 </help>
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38 </tool>