# HG changeset patch
# User timpalpant
# Date 1329262850 18000
# Node ID 422ac2bbb274a750a8a319d91249e1fb16728181
# Parent  604c98e58034fffdd956ead962427dbfa3508503
Uploaded

diff -r 604c98e58034 -r 422ac2bbb274 dist/java-genomics-toolkit.jar
Binary file dist/java-genomics-toolkit.jar has changed
diff -r 604c98e58034 -r 422ac2bbb274 galaxy-conf/BaseAlignCounts.xml
--- a/galaxy-conf/BaseAlignCounts.xml	Tue Feb 14 13:04:54 2012 -0500
+++ b/galaxy-conf/BaseAlignCounts.xml	Tue Feb 14 18:40:50 2012 -0500
@@ -2,7 +2,7 @@
   <description>of sequencing reads</description>
   <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
   <inputs>
-    <param name="input" type="data" format="bam,sam,bed,bedgraph" label="Sequencing reads" />
+    <param name="input" type="data" format="bam" label="Sequencing reads" />
     <param name="X" type="integer" value="0" label="In silico extension (leave 0 for read length)" />
   </inputs>
   <outputs>
@@ -12,6 +12,6 @@
   <help>
     .. class:: warningmark
     
-    This tool requires sequencing reads in SAM/BAM/Bed/BedGraph format.
+    This tool requires sequencing reads in BAM format.
   </help>
 </tool>
diff -r 604c98e58034 -r 422ac2bbb274 lib/java-genomics-io.jar
Binary file lib/java-genomics-io.jar has changed