diff dereplication.xml @ 1:8c4e2933a17a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d

--- a/dereplication.xml	Thu May 21 03:58:09 2015 -0400
+++ b/dereplication.xml	Wed Aug 26 13:34:22 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.0">
+<tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.1">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -18,16 +18,14 @@
             --minuniquesize $minuniquesize
         #end if
         --output $outfile
-        #if $sizein:
-            --sizein $sizein
+        $sizein
+	$sizeout
+        --strand $strand
+        #if $topn:
+            --topn $topn
         #end if
-        #if $sizeout:
-            --sizeout $sizeout
-        #end if
-        --strand $strand
-        --topn $topn
         #if $uc:
-            --uc $uc
+            --uc $uc_outfile
         #end if
 ]]>
     </command>
@@ -45,7 +43,7 @@
     </inputs>
     <outputs>
         <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
-        <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">
+        <data name="uc_outfile" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">
             <filter>uc is True</filter>
         </data>
     </outputs>
@@ -55,9 +53,28 @@
             <param name="strand" value="both" />
             <param name="minuniquesize" value="1" />
             <param name="maxuniquesize" value="100000" />
+            <param name="topn" value="10000" />
+            <output name="outfile" file="dereplication_result1.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
+            <param name="strand" value="both" />
+            <param name="minuniquesize" value="1" />
+            <param name="maxuniquesize" value="100000" />
+            <param name="sizeout" value="--sizeout"/>
+            <param name="topn" value="" />
+            <output name="outfile" file="dereplication_result2.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
+            <param name="strand" value="both" />
+            <param name="minuniquesize" value="1" />
+            <param name="maxuniquesize" value="100000" />
             <param name="sizeout" value="--sizeout"/>
             <param name="topn" value="10000" />
-            <output name="outfile" file="dereplication_result1.fasta" ftype="fasta" />
+            <param name="uc" value="--uc" />
+            <output name="outfile" file="dereplication_result2.fasta" ftype="fasta" />
+            <output name="uc_outfile" file="dereplication_uc_result3.fasta" ftype="fasta" />
         </test>
     </tests>
     <help>