--- a/deseq2.xml	Wed Dec 02 17:40:45 2015 -0500
+++ b/deseq2.xml	Tue Apr 19 18:10:31 2016 -0400
@@ -59,7 +59,7 @@
     </command>
     <inputs>
         <repeat name="rep_factorName" title="Factor" min="1">
-            <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 
+            <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
                 help="Only letters, numbers and underscores will be retained in this field">
                 <sanitizer>
                     <valid initial="string.letters,string.digits"><add value="_" /></valid>
@@ -105,7 +105,7 @@
         </data>
         <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
             <filter>many_contrasts is True</filter>
-            <discover_datasets pattern="vs" visible="true"/>
+            <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
         </collection>
         <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
             <filter>pdf == True</filter>
@@ -133,7 +133,7 @@
 <![CDATA[
 .. class:: infomark
 
-**What it does** 
+**What it does**
 
 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution
 
@@ -145,7 +145,7 @@
 The following table gives some examples of factors and their levels:
 
 ========= ============== ===============
-Factor    Factor level 1 Factor level 2 
+Factor    Factor level 1 Factor level 2
 --------- -------------- ---------------
 Treatment Treated        Untreated
 --------- -------------- ---------------