Mercurial > repos > timpalpant > java_genomics_toolkit

comparison galaxy-conf/BaseAlignCounts.xml @ 6:422ac2bbb274

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author timpalpant
date Tue, 14 Feb 2012 18:40:50 -0500
parents 604c98e58034
children 4fc118372ae7
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5:604c98e58034 6:422ac2bbb274
1 <tool id="BaseAlignCounts" name="Map coverage" version="1.0.0"> 1 <tool id="BaseAlignCounts" name="Map coverage" version="1.0.0">
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="bam,sam,bed,bedgraph" label="Sequencing reads" /> 5 <param name="input" type="data" format="bam" label="Sequencing reads" />
6 <param name="X" type="integer" value="0" label="In silico extension (leave 0 for read length)" /> 6 <param name="X" type="integer" value="0" label="In silico extension (leave 0 for read length)" />
7 </inputs> 7 </inputs>
8 <outputs> 8 <outputs>
9 <data name="output" format="wig" /> 9 <data name="output" format="wig" />
10 </outputs> 10 </outputs>
11 11
12 <help> 12 <help>
13 .. class:: warningmark 13 .. class:: warningmark
14 14
15 This tool requires sequencing reads in SAM/BAM/Bed/BedGraph format. 15 This tool requires sequencing reads in BAM format.
16 </help> 16 </help>
17 </tool> 17 </tool>