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changeset 2:90759bd72d2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
author iuc
date Sun, 28 Jun 2015 22:49:34 -0400
parents 1b15a6e2b51e
children ebd03dc31ed4
files dereplication.xml test-data/dereplication_result2.fasta test-data/dereplication_uc_result3.fasta
diffstat 3 files changed, 36 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/dereplication.xml	Sun Jun 07 22:48:32 2015 -0400
+++ b/dereplication.xml	Sun Jun 28 22:49:34 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dereplication_result2.fasta	Sun Jun 28 22:49:34 2015 -0400
@@ -0,0 +1,3 @@
+>97485665bcded44c4d86c131ca714848;size=4;
+gtcgctcctaccgattgaatacgttggtgattgaattggataaagagatatcatcttaaatgatagcaaagcggtaaaca
+tttgtaaactagattatttagaggaaggagaagtcgtaacaaggtttcc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dereplication_uc_result3.fasta	Sun Jun 28 22:49:34 2015 -0400
@@ -0,0 +1,5 @@
+S	0	129	*	*	*	*	*	97485665bcded44c4d86c131ca714848	*
+H	0	129	100.0	*	0	0	*	97485665bcded44c4d86c131ca714848	97485665bcded44c4d86c131ca714848
+H	0	129	100.0	*	0	0	*	97485665bcded44c4d86c131ca714848	97485665bcded44c4d86c131ca714848
+H	0	129	100.0	*	0	0	*	97485665bcded44c4d86c131ca714848	97485665bcded44c4d86c131ca714848
+C	0	4	*	*	*	*	*	97485665bcded44c4d86c131ca714848	*