# HG changeset patch
# User iuc
# Date 1450374819 18000
# Node ID f29e21388219f189ce2cc9425059a9b0c4c3a30e
# Parent  8c4e2933a17a520988cb4d8f5908cae2b98e3711
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2

diff -r 8c4e2933a17a -r f29e21388219 alignment.xml
--- a/alignment.xml	Wed Aug 26 13:34:22 2015 -0400
+++ b/alignment.xml	Thu Dec 17 12:53:39 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.0">
+<tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.1">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -11,11 +11,13 @@
     vsearch
         @GENERAL@
         $acceptall
-        --id $id
-        --iddef $iddef
-        --allpairs_global "$infile"
-        --alnout $outfile
-        --query_cov $query_cov
+        --id "${id}"
+        --iddef "${iddef}"
+        --allpairs_global "${infile}"
+        --alnout "${outfile}"
+        #if str( $query_cov ):
+            --query_cov "${query_cov}"
+        #end if
         @USERFIELDS@
 ]]>
     </command>
@@ -55,10 +57,6 @@
 
 @EXTERNAL_DOCUMENTATION@
 
--------
-
-@REFERENCES@
-
 
 ]]>
     </help>
diff -r 8c4e2933a17a -r f29e21388219 chimera.xml
--- 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>
diff -r 8c4e2933a17a -r f29e21388219 clustering.xml
--- 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>
diff -r 8c4e2933a17a -r f29e21388219 dereplication.xml
--- a/dereplication.xml	Wed Aug 26 13:34:22 2015 -0400
+++ b/dereplication.xml	Thu Dec 17 12:53:39 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.1">
+<tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.2">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -10,22 +10,22 @@
 <![CDATA[
     vsearch
         @GENERAL@
-        --derep_fulllength $infile
-        #if $maxuniquesize:
-            --maxuniquesize $maxuniquesize
+        --derep_fulllength "$infile"
+        #if str($maxuniquesize):
+            --maxuniquesize "$maxuniquesize"
         #end if
-        #if $minuniquesize:
-            --minuniquesize $minuniquesize
+        #if str($minuniquesize):
+            --minuniquesize "$minuniquesize"
         #end if
-        --output $outfile
+        --output "$outfile"
         $sizein
-	$sizeout
-        --strand $strand
-        #if $topn:
-            --topn $topn
+        $sizeout
+        --strand "$strand"
+        #if str($topn):
+            --topn "$topn"
         #end if
         #if $uc:
-            --uc $uc_outfile
+            --uc "$uc_outfile"
         #end if
 ]]>
     </command>
@@ -99,10 +99,6 @@
 
 @EXTERNAL_DOCUMENTATION@
 
--------
-
-@REFERENCES@
-
 
 ]]>
     </help>
diff -r 8c4e2933a17a -r f29e21388219 masking.xml
--- a/masking.xml	Wed Aug 26 13:34:22 2015 -0400
+++ b/masking.xml	Thu Dec 17 12:53:39 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.0">
+<tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.1">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -10,12 +10,12 @@
 <![CDATA[
     vsearch
         @GENERAL@
-        #if $qmask != 'no':
-            --qmask $qmask
+        #if str( $qmask ) != 'no':
+            --qmask "$qmask"
         #end if
         $hardmask
         --maskfasta "$infile"
-        --output $outfile
+        --output "$outfile"
 
 ]]>
     </command>
@@ -68,10 +68,6 @@
 
 @EXTERNAL_DOCUMENTATION@
 
--------
-
-@REFERENCES@
-
 
 ]]>
     </help>
diff -r 8c4e2933a17a -r f29e21388219 search.xml
--- 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>
diff -r 8c4e2933a17a -r f29e21388219 shuffling.xml
--- a/shuffling.xml	Wed Aug 26 13:34:22 2015 -0400
+++ b/shuffling.xml	Thu Dec 17 12:53:39 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.0">
+<tool id="vsearch_shuffling" name="VSearch shuffling" version="@VERSION@.1">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -10,10 +10,12 @@
 <![CDATA[
     vsearch
         @GENERAL@
-        --output $outfile
-        --seed $seed
-        --shuffle $infile
-        --topn $topn
+        --output "$outfile"
+        --seed "$seed"
+        --shuffle "$infile"
+        #if str( $topn ):
+            --topn "$topn"
+        #end if
 ]]>
     </command>
     <inputs>
@@ -48,10 +50,6 @@
 
 @EXTERNAL_DOCUMENTATION@
 
--------
-
-@REFERENCES@
-
 
 ]]>
     </help>
diff -r 8c4e2933a17a -r f29e21388219 sorting.xml
--- a/sorting.xml	Wed Aug 26 13:34:22 2015 -0400
+++ b/sorting.xml	Thu Dec 17 12:53:39 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.1">
+<tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.2">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -14,20 +14,20 @@
             --sortbylength "$sorting_mode.infile"
         #else:
             --sortbysize "$sorting_mode.infile"
-            #if $sorting_mode.minsize:
-                --minsize $sorting_mode.minsize
+            #if str( $sorting_mode.minsize ):
+                --minsize "$sorting_mode.minsize"
             #end if
-            #if $sorting_mode.maxsize:
-                --maxsize $sorting_mode.maxsize
+            #if str( $sorting_mode.maxsize ):
+                --maxsize "$sorting_mode.maxsize"
             #end if
         #end if
-        --output $outfile
+        --output "$outfile"
         #if $relabel:
             --relabel "$relabel"
         #end if
         $sizeout
-        #if $topn:
-            --topn $topn
+        #if str( $topn ):
+            --topn "$topn"
         #end if
 
 ]]>
@@ -112,10 +112,6 @@
 
 @EXTERNAL_DOCUMENTATION@
 
--------
-
-@REFERENCES@
-
 
 ]]>
     </help>
diff -r 8c4e2933a17a -r f29e21388219 vsearch_macros.xml
--- a/vsearch_macros.xml	Wed Aug 26 13:34:22 2015 -0400
+++ b/vsearch_macros.xml	Thu Dec 17 12:53:39 2015 -0500
@@ -174,8 +174,6 @@
 
 ]]>
     </token>
-    <token name="@REFERENCES@">
-    </token>
     <token name="@USERFIELDS_HELP@">
 **Available fields in user defined tabular output**