--- a/chimera.xml	Wed Aug 26 13:34:22 2015 -0400
+++ b/chimera.xml	Thu Dec 17 12:53:39 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.0">
+<tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.1">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -10,30 +10,30 @@
 <![CDATA[
     vsearch
         @GENERAL@
-        --abskew $abskew
-        --chimeras $outfile
-        --dn $dn
-        --mindiffs $mindiffs
-        --mindiv $mindiv
-        --minh $minh
-        --xn $xn
+        --abskew "${abskew}"
+        --chimeras "${outfile}"
+        --dn "${dn}"
+        --mindiffs "${mindiffs}"
+        --mindiv "${mindiv}"
+        --minh "${minh}"
+        --xn "${xn}"
         $self_param
         $selfid_param
         #if $detection_mode.detection_mode_select == 'denovo':
-            --uchime_denovo $detection_mode.infile_denovo
+            --uchime_denovo "${detection_mode.infile_denovo}"
         #else:
             --uchime_ref $detection_mode.infile_reference
-            --db $detection_mode.db
+            --db "${detection_mode.db}"
         #end if
 
-        #if 'nonchimeras' in str($outputs):
-            --nonchimeras $nonchimeras
+        #if 'nonchimeras' in str($outputs).split( "," ):
+            --nonchimeras "${nonchimeras}"
         #end if
-        #if 'uchimealns' in str($outputs):
-            --uchimealns $uchimealns
+        #if 'uchimealns' in str($outputs).split( "," ):
+            --uchimealns "${uchimealns}"
         #end if
-        #if 'uchimeout' in str($outputs):
-            --uchimeout $uchimeout
+        #if 'uchimeout' in str($outputs).split( "," ):
+            --uchimeout "${uchimeout}"
         #end if
 
 ]]>
@@ -79,13 +79,13 @@
     <outputs>
         <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
         <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera">
-            <filter>'nonchimeras' in outputs</filter>
+            <filter>outputs and 'nonchimeras' in outputs</filter>
         </data>
         <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments">
-            <filter>'uchimealns' in outputs</filter>
+            <filter>outputs and 'uchimealns' in outputs</filter>
         </data>
         <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information">
-            <filter>'uchimeout' in outputs</filter>
+            <filter>outputs and 'uchimeout' in outputs</filter>
         </data>
     </outputs>
     <tests>
@@ -124,10 +124,6 @@
 
 @EXTERNAL_DOCUMENTATION@
 
--------
-
-@REFERENCES@
-
 
 ]]>
     </help>