--- a/multigps.xml	Wed Apr 05 08:35:10 2017 -0400
+++ b/multigps.xml	Wed Apr 05 10:06:47 2017 -0400
@@ -10,10 +10,9 @@
         <![CDATA[
             #set output_dir = $output_html.files_path
             mkdir -p $output_dir &&
-            python '$build_design_file' '$inputs' &&
             multigps
             ## General options
-            --design 'design.tabular'
+            --design '$build_design_file'
             ## Append .txt extensions to events hrefs
             ## in output dataset so files will render
             ## in the browser.
@@ -154,45 +153,31 @@
         ]]>
     </command>
     <configfiles>
-        <inputs name="inputs"/>
         <configfile name="build_design_file">
 <![CDATA[
-import json
-import sys
-
-inputs_path = sys.argv[1]
-params = json.load(open(inputs_path, 'r'))
-condition_repeat = params['condition_repeat']
-fh = open('design.tabular', 'w')
-fh.write('%s\n' % str(params))
-for condition_items in condition_repeat:
-    for signal_items in condition_items['signal_repeat']:
-        signal = signal_items['signal']
-        condition_name = signal_items['condition_name']
-        replicate_name = signal_items['replicate_name']
-        experiment_type = signal['experiment_type']
-        line_items = [signal.file_name, 'Signal', signal.ext.upper(), condition_name, replicate_name, experiment_type]
-        fixedreadcount_cond = signal_items['fixedreadcount_cond']
-        fixedreadcount_select = fixedreadcount_cond['fixedreadcount_select']
-        if fixedreadcount_select == 'yes':
-            line_items.append(fixedreadcount_cond['fixedreadcount'])
-        fh.write('%s\n' % '\t'.join(line_items))
-    for control_items in condition_items['control_repeat']:
-        control = control_items['control']
-        experiment_type = control_items['experiment_type']
-        condition_name = control_items['condition_name']
-        line_items = [control.file_name, 'Control', control.ext.upper(), condition_name]
-        specify_replicate_name_cond = control_items['specify_replicate_name_cond']
-        specify_replicate_name = specify_replicate_name_cond['specify_replicate_name']
-        if specify_replicate_name == 'yes':
-            line_items.append(specify_replicate_name_cond['replicate_name'])
-        line_items.append(experiment_type)
-        fixedreadcount_cond = control_items['fixedreadcount_cond']
-        fixedreadcount_select = fixedreadcount_cond['fixedreadcount_select']
-        if fixedreadcount_select == 'yes':
-            line_items.append(fixedreadcount_cond['fixedreadcount'])
-        fh.write('%s\n' % '\t'.join(line_items))
-fh.close()
+#for $condition_items in $condition_repeat:
+    #for $signal_items in $condition_items.signal_repeat:
+        #if str($signal_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
+            #set $frc =  $signal_items.fixedreadcount_cond.fixedreadcount
+        #else
+            #set $frc = ''
+        #end if
+${signal_items.signal}	Signal	${signal_items.signal.ext.upper()}	${signal_items.condition_name}	${signal_items.replicate_name}	${signal_items.experiment_type}	${frc}
+    #end for
+    #for $control_items in $condition_items.control_repeat:
+        #if str($control_items.specify_replicate_name_cond.specify_replicate_name) == 'yes':
+            #set $rn = $control_items.specify_replicate_name_cond.replicate_name
+        #else:
+            #set $rn = ''
+        #end if
+        #if str($control_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
+            #set $frc = $control_items.fixedreadcount_cond.fixedreadcount
+        #else:
+            #set $frc = ''
+        #end if
+${control_items.control}	Control	${control_items.control.ext.upper()}	${control_items.condition_name}	${rn}	${control_items.experiment_type}	${frc}
+    #end for
+#end for
 ]]>
         </configfile>
     </configfiles>