Mercurial > repos > timpalpant > java_genomics_toolkit

diff galaxy-conf/BaseAlignCounts.xml @ 4:4b32ed5d4a1b

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author timpalpant
date Tue, 14 Feb 2012 00:59:33 -0500
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children 604c98e58034
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/BaseAlignCounts.xml	Tue Feb 14 00:59:33 2012 -0500
@@ -0,0 +1,17 @@
+<tool id="BaseAlignCounts" name="Map coverage" version="1.0.0">
+  <description>of sequencing reads</description>
+  <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -g ${chromInfo} -x $X -o $output</command>
+  <inputs>
+    <param name="input" type="data" format="bam,sam,bed,bedgraph" label="Sequencing reads" />
+    <param name="X" type="integer" value="0" label="In silico extension (leave 0 for read length)" />
+  </inputs>
+  <outputs>
+    <data name="output" format="wig" />
+  </outputs>
+  
+  <help>
+    .. class:: warningmark
+    
+    This tool requires sequencing reads in SAM/BAM/Bed/BedGraph format.
+  </help>
+</tool>