--- a/cuff_macros.xml	Wed Nov 11 12:35:18 2015 -0500
+++ b/cuff_macros.xml	Tue Feb 07 18:40:18 2017 -0500
@@ -1,11 +1,13 @@
 <macros>
   <token name="@VERSION@">2.2.1</token>
+
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="2.2.1">cufflinks</requirement>
       <yield />
     </requirements>
   </xml>
+
   <xml name="stdio">
     <stdio>
         <exit_code range="1:" />
@@ -26,21 +28,21 @@
         </param>
         <when value="BAM">
             <repeat name="conditions" title="Condition" min="2">
-                <param name="name" title="Condition name" type="text" label="Name"/>
+                <param name="name" label="Condition name" type="text"/>
                 <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/>
             </repeat>
         </when>
         <when value="CXB">
             <repeat name="conditions" title="Condition" min="2">
-                <param name="name" title="Condition name" type="text" label="Name"/>
+                <param name="name" label="Condition name" type="text"/>
                 <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/>
             </repeat>
         </when>
         <when value="CONDITION_LIST">
-            <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" />
+            <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list" />
         </when>
         <when value="CONDITION_REPLICATE_LIST">
-            <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" />
+            <param name="conditions" label="List of Conditions" type="data_collection" collection_type="list:list" />
         </when>
     </conditional>
   </xml>
@@ -48,16 +50,16 @@
             #if $in_type.set_in_type in ['BAM', 'CXB']
                 #for $condition in $in_type.conditions:
                     #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] )
-                    $samples
+                    '$samples'
                 #end for
             #elif $in_type.set_in_type == 'CONDITION_LIST'
                 #for $sample in $in_type.conditions:
-                    $sample
+                    '$sample'
                 #end for
             #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST'
                 #for $condition_list in $in_type.conditions:
                     #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] )
-                    $samples
+                    '$samples'
                 #end for
             #end if
   </token>
@@ -79,11 +81,11 @@
   <token name="@CUFFLINKS_GTF_INPUTS@">
             ## Inputs.
             #for $input_file in $inputs:
-                "${input_file}"
+                '${input_file}'
             #end for
             #for $additional_input in $additional_inputs:
                 #for $input_file in $additional_input.additional_inputs:
-                  "${input_file}"
+                    '${input_file}'
                 #end for
             #end for
   </token>