--- a/multigps.xml	Tue Apr 04 17:08:56 2017 -0400
+++ b/multigps.xml	Tue Apr 04 19:30:00 2017 -0400
@@ -8,6 +8,7 @@
     </requirements>
     <command detect_errors="aggressive">
         <![CDATA[
+            #set design_file = '$build_design_file'
             #set output_dir = $output_html.files_path
             mkdir -p $output_dir &&
             multigps
@@ -153,7 +154,7 @@
         ]]>
     </command>
     <configfiles>
-        <configfile name="design_file">
+        <configfile name="build_design_file">
 <![CDATA[
 #for $cond_i, $condition_items in enumerate($condition_repeat):
     #for $signal_items in $condition_items['signal_repeat']:
@@ -247,7 +248,7 @@
                 </conditional>
                 <!-- Scaling data -->
                 <conditional name="scale_data_cond">
-                    <param  name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using the Normalization of ChIP-seq (NCIS) method described by Liang &amp; Ketes, BMC Bioinformatics 2012.">
+                    <param  name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using the Normalization of ChIP-seq (NCIS) method.[2]">
                         <option value="no" selected="True">No</option>
                         <option value="yes">Yes</option>
                     </param>
@@ -510,6 +511,22 @@
 
     </help>
     <citations>
-        <citation type="doi">10.1371/journal.pcbi.1003501</citation>
+        <citation type="bibtex">
+            @article{Mahony2014,
+            journal = {PLOS Computational Biology},
+            author = {1. Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK},
+            title = {An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding},
+            year = {2014},}
+            volume = {10},
+            number = {3},
+            pages = {e1003501},}
+        </citation>
+        <citation type="bibtex">
+            @article{Liang2012,
+            journal = {BMC Bioinformatics},
+            author = {2. Liang, Ketes},
+            title = {Normalization of ChIP-seq data with control},
+            year = {2012},}
+        </citation>
     </citations>
 </tool>