--- a/search.xml	Wed Aug 26 13:34:22 2015 -0400
+++ b/search.xml	Thu Dec 17 12:53:39 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="vsearch_search" name="VSearch search" version="@VERSION@.0">
+<tool id="vsearch_search" name="VSearch search" version="@VERSION@.1">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -11,139 +11,139 @@
     vsearch
 
         @GENERAL@
-        --db $dbfile
-        --dbmask $dbmask
+        --db "$dbfile"
+        #if $dbmask:
+            --dbmask "$dbmask"
+        #end if
 
         ##--fulldp                    full dynamic programming alignment (always on)
         ##--gapext STRING             penalties for gap extension (2I/1E)
         ##--gapopen STRING            penalties for gap opening (20I/2E)
         $hardmask
-        --id $id
-        --iddef $iddef
+        --id "$id"
+        --iddef "$iddef"
 
-        #if $qmask != 'no':
-            --qmask $qmask
+        #if str( $qmask ) != 'no':
+            --qmask "$qmask"
         #end if
 
         ## --rowlen INT                width of alignment lines in alnout output (64)
 
         $self_param
         $selfid_param
-        #if $sizeout:
-            --sizeout $sizeout
-        #end if
-        --strand $strand
-        --usearch_global $queryfile
+        $sizeout
+        --strand "$strand"
+        --usearch_global "$queryfile"
 
-        #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 "$blast6out"
         #end if
-        #if '--dbmatched' in str($outputs):
-            --dbmatched $dbmatched
+        #if '--dbmatched' in str($outputs).split( "," ):
+            --dbmatched "$dbmatched"
         #end if
-        #if '--dbnotmatched' in str($outputs):
-            --dbnotmatched $dbnotmatched
+        #if '--dbnotmatched' in str($outputs).split( "," ):
+            --dbnotmatched "$dbnotmatched"
         #end if
-        #if '--fastapairs' in str($outputs):
-            --fastapairs $fastapairs
+        #if '--fastapairs' in str($outputs).split( "," ):
+            --fastapairs "$fastapairs"
         #end if
-        #if '--notmatched' in str($outputs):
-            --notmatched $notmatched
+        #if '--notmatched' in str($outputs).split( "," ):
+            --notmatched "$notmatched"
         #end if
-        #if '--matched' in str($outputs):
-            --matched $matched
+        #if '--matched' in str($outputs).split( "," ):
+            --matched "$matched"
         #end if
 
         #if $adv_opts.adv_opts_selector == "advanced":
             $adv_opts.top_hits_only
             $adv_opts.rightjust
             $adv_opts.leftjust
-            --target_cov $adv_opts.target_cov
-            --query_cov $adv_opts.query_cov
+            --target_cov "$adv_opts.target_cov"
+            --query_cov "$adv_opts.query_cov"
 
 
-            #if $adv_opts.maxid:
-                --maxid $adv_opts.maxid
+            #if str( $adv_opts.maxid ):
+                --maxid "$adv_opts.maxid"
             #end if
-            #if $adv_opts.maxqt:
-                --maxqt $adv_opts.maxqsize
+            #if str( $adv_opts.maxqt ):
+                --maxqt "$adv_opts.maxqsize"
             #end if
-            #if $adv_opts.maxsizeratio:
-                --maxsizeratio $adv_opts.maxsizeratio
+            #if str( $adv_opts.maxsizeratio ):
+                --maxsizeratio "$adv_opts.maxsizeratio"
             #end if
-            #if $adv_opts.maxsl:
-                --maxsl $adv_opts.maxsl
+            #if str( $adv_opts.maxsl ):
+                --maxsl "$adv_opts.maxsl"
             #end if
-            #if $adv_opts.mid:
-                --mid $adv_opts.mid
+            #if str( $adv_opts.mid ):
+                --mid "$adv_opts.mid"
             #end if
-            #if $adv_opts.minqt:
-                --minqt $adv_opts.minqt
+            #if str( $adv_opts.minqt ):
+                --minqt "$adv_opts.minqt"
             #end if
-            #if $adv_opts.minsizeratio:
-                --minsizeratio $adv_opts.minseqlength
+            #if str( $adv_opts.minsizeratio ):
+                --minsizeratio "$adv_opts.minseqlength"
             #end if
-            #if $adv_opts.minsl:
-                --minsl $adv_opts.minsl
+            #if str( $adv_opts.minsl ):
+                --minsl "$adv_opts.minsl"
             #end if
 
-            #if $adv_opts.mintsize:
-                --mintsize $adv_opts.mintsize
+            #if str( $adv_opts.mintsize ):
+                --mintsize "$adv_opts.mintsize"
             #end if
-            #if $adv_opts.mismatch:
-                --mismatch $adv_opts.mismatch
+            #if str( $adv_opts.mismatch ):
+                --mismatch "$adv_opts.mismatch"
             #end if
-            #if $adv_opts.maxqsize:
-                --maxqsize $adv_opts.maxqsize
+            #if str( $adv_opts.maxqsize ):
+                --maxqsize "$adv_opts.maxqsize"
             #end if
-            #if $adv_opts.mincols:
-                --mincols $adv_opts.mincols
+            #if str( $adv_opts.mincols ):
+                --mincols "$adv_opts.mincols"
             #end if
-            #if $adv_opts.maxsubs:
-                --maxsubs $adv_opts.maxsubs
+            #if str( $adv_opts.maxsubs ):
+                --maxsubs "$adv_opts.maxsubs"
             #end if
-            #if $adv_opts.maxrejects:
-                --maxrejects $adv_opts.maxrejects
+            #if str( $adv_opts.maxrejects ):
+                --maxrejects "$adv_opts.maxrejects"
             #end if
-            #if $adv_opts.maxaccepts:
-                --maxaccepts $adv_opts.maxaccepts
+            #if str( $adv_opts.maxaccepts ):
+                --maxaccepts "$adv_opts.maxaccepts"
             #end if
-            #if $adv_opts.maxdiffs:
-                --maxdiffs $adv_opts.maxdiffs
+            #if str( $adv_opts.maxdiffs ):
+                --maxdiffs "$adv_opts.maxdiffs"
             #end if
-            #if $adv_opts.maxgaps:
-                --maxgaps $adv_opts.maxgaps
+            #if str( $adv_opts.maxgaps ):
+                --maxgaps "$adv_opts.maxgaps"
             #end if
-            #if $adv_opts.maxhits:
-                --maxhits $adv_opts.maxhits
+            #if str( $adv_opts.maxhits ):
+                --maxhits "$adv_opts.maxhits"
             #end if
-            #if $adv_opts.match:
-                --match $adv_opts.match
+            #if str( $adv_opts.match ):
+                --match "$adv_opts.match"
             #end if
-            #if $adv_opts.idprefix:
-                --idprefix $adv_opts.idprefix
+            #if str( $adv_opts.idprefix ):
+                --idprefix "$adv_opts.idprefix"
             #end if
-            #if $adv_opts.idsuffix:
-                --idsuffix $adv_opts.idsuffix
+            #if str( $adv_opts.idsuffix ):
+                --idsuffix str( $adv_opts.idsuffix )
             #end if
 
             #if $adv_opts.uclust_output.uclust_output_select == 'yes':
-                --uc
+                --uc "$uc"
                 $adv_opts.uclust_output.uc_allhits
             #end if
 
             #if $adv_opts.userfields_output.userfields_output_select == 'yes':
                 --userfields '#echo '+'.join( str($adv_opts.userfields_output.userfields).split(',') )#'
-                --userout $userout
+                --userout "$userout"
             #end if
 
             ##--weak_id REAL              include aligned hits with >= id; continue search
-            --wordlength $adv_opts.wordlength
+            --wordlength "$adv_opts.wordlength"
 
-            $$adv_opts.output_no_hits
+            $adv_opts.output_no_hits
 
         #end if
 
@@ -260,7 +260,7 @@
     </inputs>
     <outputs>
         <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">
-            <filter>adv_opts.uclust_output.uclust_output_select == 'yes'</filter>
+            <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['uclust_output']['uclust_output_select'] == 'yes'</filter>
         </data>
         <data name="dbnotmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched database sequences">
             <filter>'--dbnotmatchedt' in outputs</filter>
@@ -284,7 +284,7 @@
             <filter>'--fastapairs' in outputs</filter>
         </data>
         <data name="userout" format="tabular" label="${tool.name} on ${on_string}: tabular output">
-            <filter>adv_opts.userfields_output.userfields_output_select == 'yes'</filter>
+            <filter>adv_opts['adv_opts_selector'] == "advanced" and adv_opts['userfields_output']['userfields_output_select'] == 'yes'</filter>
         </data>
     </outputs>
     <tests>
@@ -380,10 +380,6 @@
 
 @EXTERNAL_DOCUMENTATION@
 
--------
-
-@REFERENCES@
-
 
 ]]>
     </help>