--- a/deseq2.xml	Fri Aug 03 17:23:46 2018 -0400
+++ b/deseq2.xml	Wed Sep 05 15:54:03 2018 -0400
@@ -64,6 +64,9 @@
     -f '#echo json.dumps(temp_factor_names)#'
     -l '#echo json.dumps(filename_to_element_identifiers)#'
     -t $fit_type
+    #if $batch_factors
+        --batch_factors '$batch_factors'
+    #end if
     #if $outlier_replace_off:
         -a
     #end if
@@ -105,7 +108,7 @@
                 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
             </repeat>
         </repeat>
-
+        <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/>
         <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" />
 
         <conditional name="tximport">
@@ -206,6 +209,28 @@
                 </assert_contents>
             </output>
         </test>
+        <!--Ensure additional batch factor correction works -->
+        <test expect_num_outputs="2">
+            <repeat name="rep_factorName">
+                <param name="factorName" value="Treatment"/>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Treated"/>
+                    <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Untreated"/>
+                    <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
+                </repeat>
+            </repeat>
+            <param name="batch_factors" value="batch_factors.tab"/>
+            <param name="pdf" value="False"/>
+            <param name="normCounts" value="True"/>
+            <output name="deseq_out">
+                <assert_contents>
+                    <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" />
+                </assert_contents>
+            </output>
+        </test>
         <!--Ensure counts files without header works -->
         <test expect_num_outputs="2">
             <repeat name="rep_factorName">