--- a/multigps.xml	Thu Apr 06 09:32:38 2017 -0400
+++ b/multigps.xml	Thu Apr 06 10:54:38 2017 -0400
@@ -146,6 +146,9 @@
             #end if
             2>&1
             --out '$output_html.files_path'
+            #if str($output_design_file) == 'yes':
+                && mv '$build_design_file' '$output_design_file'
+            #end if
             && mv $output_dir/*.counts '$replicates_counts'
             && mv $output_dir/*.bed '$output_bed'
             && mv $output_dir/*.html '$output_html'
@@ -179,13 +182,17 @@
     </configfiles>
     <inputs>
         <repeat name="condition_repeat" title="Condition" min="1">
-            <param name="condition_name" type="text" value="cond" label="Condition name" />
+            <param name="condition_name" type="text" value="cond" label="Condition name">
+                <validator type="empty_field" />
+            </param>
             <expand macro="param_experiment_type" />
             <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>
-                <param name="replicate_name" type="text" value="rep" label="Replicate name" />
+                <param name="replicate_name" type="text" value="1" label="Replicate name">
+                    <validator type="empty_field" />
+                </param>
                 <expand macro="cond_fixedreadcount" />
             </repeat>
             <repeat name="control_repeat" title="Control" min="0">
@@ -205,6 +212,10 @@
                 <expand macro="cond_fixedreadcount" />
             </repeat>
         </repeat>
+        <param name="output_design_file" type="select" display="radio" label="Output design file?">
+            <option value="no" selected="true">No</option>
+            <option value="yes">Yes</option>
+        </param>
         <!-- Advanced options -->
         <conditional name="advanced_options_cond">
             <param name="advanced_options" type="select" label="Advanced options">
@@ -401,6 +412,9 @@
         </conditional>
     </inputs>
     <outputs>
+        <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}">
+            <filter>output_design_file == 'yes'</filter>
+        </data>
         <data name="output_bed" format="bed" label="${tool.name} (bed) on ${on_string}"/>
         <data name="output_html" format="html" label="${tool.name} (html) on ${on_string}"/>
         <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/>