--- a/clustering.xml	Wed Aug 26 13:34:22 2015 -0400
+++ b/clustering.xml	Thu Dec 17 12:53:39 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.1">
+<tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.2">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -11,54 +11,54 @@
     vsearch
         @GENERAL@
 	
-	#if $clustering_mode.clustering_mode_select == 'cluster_fast':
+	    #if $clustering_mode.clustering_mode_select == 'cluster_fast':
             --cluster_fast "$infile"
-	#else if $clustering_mode.clustering_mode_select == 'cluster_smallmem':
+	    #else if $clustering_mode.clustering_mode_select == 'cluster_smallmem':
             --cluster_smallmem "$infile"
         #end if
         ##--clusters STRING            output each cluster to a separate FASTA file
 
         #if $maxrejects:
-            --maxrejects $maxrejects
+            --maxrejects "$maxrejects"
         #end if
         #if $maxaccepts:
-            --maxaccepts $maxaccepts
+            --maxaccepts "$maxaccepts"
         #end if
 
         $cons_truncate
-        --id $id
-        --iddef $iddef
+        --id "$id"
+        --iddef "$iddef"
 
-        #if '--msaout' in str($outputs):
-            --msaout $msaout
+        #if '--msaout' in str($outputs).split( "," ):
+            --msaout "$msaout"
         #end if
-        #if '--consout' in str($outputs):
-            --consout $consout
+        #if '--consout' in str($outputs).split( "," ):
+            --consout "$consout"
         #end if
-        #if '--centroids' in str($outputs):
-            --centroids $centroids
+        #if '--centroids' in str($outputs).split( "," ):
+            --centroids "$centroids"
         #end if
-        #if '--alnout' in str($outputs):
-            --alnout $alnout
+        #if '--alnout' in str($outputs).split( "," ):
+            --alnout "$alnout"
         #end if
-        #if '--blast6out' in str($outputs):
-            --blast6out $blast6out
+        #if '--blast6out' in str($outputs).split( "," ):
+            --blast6out "$blast6out"
         #end if
-        #if '--notmatched' in str($outputs):
-            --notmatched $notmatched
+        #if '--notmatched' in str($outputs).split( "," ):
+            --notmatched "$notmatched"
         #end if
-        #if '--fastapairs' in str($outputs):
-            --fastapairs $fastapairs
+        #if '--fastapairs' in str($outputs).split( "," ):
+            --fastapairs "$fastapairs"
         #end if
-        #if '--matched' in str($outputs):
-            --matched $matched
+        #if '--matched' in str($outputs).split( "," ):
+            --matched "$matched"
         #end if
-        #if $qmask != 'no':
-            --qmask $qmask
+        #if str( $qmask ) != 'no':
+            --qmask "$qmask"
         #end if
         $sizein
         $sizeout
-        --strand $strand
+        --strand "$strand"
 	$usersort
 	#if $uc:
             --uc "$uc_outfile"
@@ -225,10 +225,6 @@
 
 @EXTERNAL_DOCUMENTATION@
 
--------
-
-@REFERENCES@
-
 
 ]]>
     </help>