Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/IntervalLengthDistribution.xml @ 13:eb53be9a09f4 draft

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author timpalpant
date Sat, 19 May 2012 10:36:45 -0400
parents 81d5b81fb3c2
children 3e477c7e0e73
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1 <tool id="IntervalLengthDistribution" name="Make histogram" version="1.0.0">
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2 <description>of read lengths</description>
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3 <command interpreter="sh">galaxyToolRunner.sh ngs.IntervalLengthDistribution -i $input $freq -o $output</command>
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4 <inputs>
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5 <param name="input" type="data" format="sam,bam,bed,bedgraph,gff" label="Reads/Intervals" />
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6 <param name="freq" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Output normalized frequencies rather than counts" />
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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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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 distribution of interval lengths from a list of intervals or reads in SAM, BAM, Bed, BedGraph, or GFF 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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16 .. 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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18 For paired-end sequencing reads, the length is the length of the fragment (5' end of read 1 to 5' end of read 2)
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20 </help>
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21 </tool>