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comparison galaxy-conf/BaseAlignCounts.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 eb53be9a09f4
children
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14:f58706d4d421 15:3e477c7e0e73
1 <tool id="BaseAlignCounts" name="Calculate coverage" version="1.0.0"> 1 <tool id="BaseAlignCounts" name="Calculate coverage" version="2.0.0">
2 <description>of sequencing reads</description> 2 <description>of sequencing reads</description>
3 <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command> 3 <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
4 <inputs> 4 <inputs>
5 <param name="input" type="data" format="sam,bam,bed,bedgraph" label="Sequencing reads" /> 5 <param name="input" type="data" format="sam,bam,bed,bedgraph" label="Sequencing reads" />
6 <param name="X" type="integer" value="-1" label="In silico extension (-1 for fragment length)" /> 6 <param name="X" type="integer" value="-1" label="In silico extension (-1 for fragment length)" />