--- a/multigps.xml	Tue Apr 04 15:03:10 2017 -0400
+++ b/multigps.xml	Tue Apr 04 15:17:46 2017 -0400
@@ -10,9 +10,9 @@
         <![CDATA[
             #set output_dir = $output_html.files_path
             mkdir -p $output_dir &&
-            '$design_file' &&
             multigps
             ## General options
+            --design '$design_file'
             ## Append .txt extensions to events hrefs
             ## in output dataset so files will render
             ## in the browser.
@@ -157,32 +157,32 @@
         <configfile name="design_file">
 <![CDATA[
 #for cond_i, condition_items in enumerate($condition_repeat):
-    #for experiment_items in condition_items['experiment_repeat']:
-        #set experiment = $experiment_items['experiment']
-        #set replicate_name = $experiment_items['replicate_name']
-        #set experiment_type = $experiment_items['experiment_type']
-        #set line = str($experiment) + 'Signal' + str($experiment.ext.upper()) + str($cond_i) + str($replicate_name) + str($experiment_type)
-        #set fixedreadcount_cond = $experiment_items['fixedreadcount_cond']
+    #for signal_items in condition_items['signal_repeat']:
+        #set signal = $signal_items['signal']
+        #set replicate_name = $signal_items['replicate_name']
+        #set experiment_type = $signal['experiment_type']
+        #set line = str($signal) + '\t' + 'Signal' + '\t' + str($signal.ext.upper()) + '\t' + str($cond_i) + '\t' + str($replicate_name) + '\t' + str($experiment_type)
+        #set fixedreadcount_cond = $signal_items['fixedreadcount_cond']
         #set fixedreadcount_select = $fixedreadcount_cond['fixedreadcount_select']
         #if str($fixedreadcount_select) == 'yes':
-            #set $line += str($fixedreadcount_cond['fixedreadcount'])
+            #set $line += + '\t' + str($fixedreadcount_cond['fixedreadcount'])
         #end if
         '%s\n' % $line
     #end for
     #for control_items in condition_items['control_repeat']:
         #set control = $control_items['control']
         #set experiment_type = $control_items['experiment_type']
-        #set line = str($control_items) + 'Control' + str($control.ext.upper()) + str($cond_i)
+        #set line = str($control_items) + '\t' + 'Control' + '\t' + str($control.ext.upper()) + '\t' + str($cond_i)
         #set specify_replicate_name_cond = $control_items['specify_replicate_name_cond']
         #set specify_replicate_name = $specify_replicate_name_cond.specify_replicate_name
         #if str($specify_replicate_name) == 'yes':
-            #set $line += str($specify_replicate_name_cond['replicate_name'])
+            #set $line += '\t' + str($specify_replicate_name_cond['replicate_name'])
         #end if
-        #set $line += str($experiment_type)
-        #set fixedreadcount_cond = $experiment_items['fixedreadcount_cond']
+        #set $line += '\t' + str($experiment_type)
+        #set fixedreadcount_cond = $control_items['fixedreadcount_cond']
         #set fixedreadcount_select = $fixedreadcount_cond['fixedreadcount_select']
         #if str($fixedreadcount_select) == 'yes':
-            #set $line += str($fixedreadcount_cond['fixedreadcount'])
+            #set $line += '\t' + str($fixedreadcount_cond['fixedreadcount'])
         #end if
         '%s\n' % $line
     #end for
@@ -192,8 +192,8 @@
     </configfiles>
     <inputs>
         <repeat name="condition_repeat" title="Condition" min="1">
-            <repeat name="experiment_repeat" title="Experiment" min="1">
-                <param name="experiment" type="data" format="bam,bed,scidx" label="Select experiment" help="Supported formats are bam, bed and scidx">
+            <repeat name="signal_repeat" title="Signal" min="1">
+                <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx">
                     <validator type="unspecified_build" />
                 </param>
                 <expand macro="param_experiment_type" />
@@ -206,7 +206,7 @@
                 </param>
                 <expand macro="param_experiment_type" />
                 <conditional name="specify_replicate_name_cond">
-                    <param  name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control experiments.  If used, the control will only be used for the corresponding named signal replicate">
+                    <param  name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control.  If used, the control will only be used for the corresponding named signal replicate">
                         <option value="no" selected="True">No</option>
                         <option value="yes">Yes</option>
                     </param>
@@ -248,7 +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 regression on the set of signal/control ratios in 10Kbp windows.">
+                    <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 & Ketes, BMC Bioinformatics 2012.">
                         <option value="no" selected="True">No</option>
                         <option value="yes">Yes</option>
                     </param>