--- a/multigps.xml	Tue Apr 04 10:02:01 2017 -0400
+++ b/multigps.xml	Tue Apr 04 10:29:15 2017 -0400
@@ -10,6 +10,7 @@
         <![CDATA[
             #set output_dir = $output_html.files_path
             mkdir -p $output_dir &&
+            python '$design_file_script' '$inputs' &&
             multigps
             ## General options
             #set single_or_multi_expt = $single_or_multi_expt_cond.single_or_multi_expt
@@ -182,6 +183,36 @@
             && mv $output_dir/*.table.txt '$all_events_table'
         ]]>
     </command>
+    <configfiles>
+        <inputs name="inputs"/>
+        <configfile name="design_file_script">
+<![CDATA[
+import sys
+import json
+
+input_json_path = sys.argv[1]
+params = json.load(open(input_json_path, "r"))
+
+if params['single_or_multi_expt_cond']['single_or_multi_expt'] == 'multi':
+    input_items = params['single_or_multi_expt_cond']['input_items']
+    design_file = open('design.tabular', 'w')
+    for item in input_items:
+        experiment_file_name, control_file_name, label, file_format, condition_name, replicate_name, experiment_type, fixed_read_count = item
+        if control_file_name not in ['None', None, '']:
+            control_file_names.append(control_file_name)
+        file_format = file_format.upper()
+        items = [experiment_file_name, label, file_format, condition_name]
+        if replicate_name not in ['None', None, '']:
+            items.append(replicate_name)
+        if experiment_type not in ['None', None, '']:
+            items.append(experiment_type)
+        if fixed_read_count not in ['None', None, '']:
+            items.append(fixed_read_count)
+        design_file.write('%s\n' % '\t'.join(items))
+    design_file.close()
+]]>
+        </configfile>
+    </configfiles>
     <inputs>
         <conditional name="single_or_multi_expt_cond">
             <param name="single_or_multi_expt" type="select" label="Run MultiGPS on single or multiple inputs?">