--- a/multigps.xml	Wed Apr 05 13:45:19 2017 -0400
+++ b/multigps.xml	Thu Apr 06 09:32:38 2017 -0400
@@ -160,7 +160,7 @@
         #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}	${frc}
+${signal_items.signal}	Signal	${signal_items.signal.ext.upper()}	${condition_items.condition_name}	${signal_items.replicate_name}	${condition_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':
@@ -173,18 +173,18 @@
         #else:
             #set $frc = ''
         #end if
-${control_items.control}	Control	${control_items.control.ext.upper()}	${control_items.condition_name}	${rn}	${control_items.experiment_type}	${frc}
+${control_items.control}	Control	${control_items.control.ext.upper()}	${condition_items.condition_name}	${rn}	${condition_items.experiment_type}	${frc}
     #end for
 #end for ]]></configfile>
     </configfiles>
     <inputs>
         <repeat name="condition_repeat" title="Condition" min="1">
+            <param name="condition_name" type="text" value="cond" label="Condition name" />
+            <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>
-                <expand macro="param_experiment_type" />
-                <param name="condition_name" type="text" value="cond" label="Condition name" />
                 <param name="replicate_name" type="text" value="rep" label="Replicate name" />
                 <expand macro="cond_fixedreadcount" />
             </repeat>
@@ -192,8 +192,6 @@
                 <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx">
                     <validator type="unspecified_build" />
                 </param>
-                <expand macro="param_experiment_type" />
-                <param name="condition_name" type="text" value="cond" label="Condition name" />
                 <conditional name="specify_replicate_name_cond">
                     <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>
@@ -410,8 +408,11 @@
     </outputs>
     <tests>
         <test>
-            <param name="single_or_multi_expt" value="single" />
-            <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
+            <repeat name="condition_repeat">
+                <repeat name="signal_repeat">
+                    <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
+                </repeat>
+            </repeat>
             <param name="advanced_options" value="hide" />
             <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>
             <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/>
@@ -419,9 +420,14 @@
             <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
         </test>
         <test>
-            <param name="single_or_multi_expt" value="single" />
-            <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
-            <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />
+            <repeat name="condition_repeat">
+                <repeat name="signal_repeat">
+                    <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
+                </repeat>
+                <repeat name="control_repeat">
+                    <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />
+                </repeat>
+            </repeat>
             <param name="advanced_options" value="display" />
             <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>
             <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/>