--- a/diffbind.xml	Tue Jan 14 18:07:20 2014 -0500
+++ b/diffbind.xml	Thu Jan 16 04:17:16 2014 -0500
@@ -7,14 +7,22 @@
         <requirement type="package" version="1.0.17">deseq2</requirement>
         <requirement type="package" version="1.8.3">diffbind</requirement>
     </requirements>
-    <command interpreter="Rscript">
-        diffbind.R
+    <command>
+        ## seems that diffbind also needs file extensions to work properly
+        #set $counter = 1
+        #for $sample in $samples:
+            ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &amp;&amp;
+            ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &amp;&amp;
+            ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &amp;&amp;
+            ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &amp;&amp;
+            #set $counter = $counter + 1
+        #end for
+
+        Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R
             -i $infile
             -o $outfile
             -p $plots
             -f $format
-        ;
-        cat $infile;
     </command>
     <stdio>
         <regex match="Execution halted" 
@@ -53,8 +61,10 @@
     <configfiles>
 <configfile name="infile">
 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
+#set $counter = 1
 #for $sample in $samples:
-$sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks
+$sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
+#set $counter = $counter + 1
 #end for
 </configfile>
     </configfiles>