--- a/diffbind.xml	Tue Jan 14 08:13:24 2014 -0500
+++ b/diffbind.xml	Tue Jan 14 18:07:20 2014 -0500
@@ -13,6 +13,8 @@
             -o $outfile
             -p $plots
             -f $format
+        ;
+        cat $infile;
     </command>
     <stdio>
         <regex match="Execution halted" 
@@ -49,12 +51,12 @@
         </param>
     </inputs>
     <configfiles>
-        <configfile name="infile">
+<configfile name="infile">
 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
 #for $sample in $samples:
 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks
 #end for
-        </configfile>
+</configfile>
     </configfiles>
     <outputs>
         <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
@@ -63,7 +65,7 @@
                 <when input="format" value="gff" format="gff" />
             </change_format>
         </data>
-        <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
+        <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
             <filter>pdf == True</filter>
         </data>
     </outputs>