diff dereplication.xml @ 2:f29e21388219 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2

--- 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>