Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/RollingReadLength.xml @ 15:3e477c7e0e73 draft

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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.
author timpalpant
date Sat, 09 Jun 2012 16:03:59 -0400
parents 81d5b81fb3c2
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="RollingReadLength" name="Compute mean fragment length" version="1.1.0">
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2 <description>over each locus</description>
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3 <command interpreter="sh">galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output</command>
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4 <inputs>
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5 <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" />
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6 </inputs>
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7 <outputs>
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8 <data format="wig" name="output" />
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9 </outputs>
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10
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11 <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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13 This tool will compute the mean length of all fragments overlapping a given locus, and can be used to identify sites with exceptionally long or short reads.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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15 .. 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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17 This tool requires paired-end SAM, BAM, Bed, or BedGraph formatted data. Using single-end data will result in a constant read length.
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19 </help>
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20 </tool>