--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/BaseAlignCounts.xml	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,21 @@
+<tool id="BaseAlignCounts" name="Map coverage" version="1.0.0">
+  <description>of sequencing reads</description>
+  <command>galaxyToolRunner.sh -i $input -g $dbkey -x $X -p 4 -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.
+    
+    .. class:: warningmark
+    
+    This tool was contributed by Timothy Palpant.
+  </help>
+</tool>