diff clustering.xml @ 3:4258854759ba draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty

--- a/clustering.xml	Thu Dec 17 12:53:39 2015 -0500
+++ b/clustering.xml	Tue Mar 01 07:07:03 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.2">
+<tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.0">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -10,13 +10,13 @@
 <![CDATA[
     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
+        ##--clusters STRING output each cluster to a separate FASTA file
 
         #if $maxrejects:
             --maxrejects "$maxrejects"
@@ -59,10 +59,10 @@
         $sizein
         $sizeout
         --strand "$strand"
-	$usersort
-	#if $uc:
+        $usersort
+        #if $uc:
             --uc "$uc_outfile"
-	#end if
+        #end if
 
 ]]>
     </command>
@@ -131,22 +131,6 @@
     <tests>
         <test>
             <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
-            <param name="id" value="0.99"/>
-            <param name="maxaccepts" value="1"/>
-            <param name="maxrejects" value="2"/>
-            <param name="sizeout" value=""/>
-            <param name="outputs" value="--centroids,--alnout,--blast6out,--notmatched" />
-            <output name="centroids" file="clustering_centroids_result1.fasta" ftype="fasta" />
-            <output name="blast6out" file="clustering_blast6out_result1.tab" ftype="tabular" />
-            <output name="notmatched" file="clustering_notmatched_result1.fasta" ftype="fasta" />
-            <!-- The result following result files would be too big -->
-            <!--output name="matched" file="clustering_matched_result1.fasta" ftype="fasta" /-->
-            <!--output name="alnout" file="clustering_alnout_result1.fasta" lines_diff="2" ftype="fasta" /-->
-            <!--output name="fastapairs" file="clustering_fastapairs_result1.fasta" ftype="fasta" /-->
-            <!--output name="msaout" file="clustering_msaout_result1.fasta" ftype="fasta" /-->
-        </test>
-        <test>
-            <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
             <param name="clustering_mode_select" value="cluster_smallmem"/>
             <param name="usersort" value="--usersort"/>
             <param name="id" value="0.99"/>
@@ -158,7 +142,7 @@
             <output name="blast6out" file="clustering_blast6out_result2.tab" ftype="tabular" />
             <output name="notmatched" file="clustering_notmatched_result2.fasta" ftype="fasta" />
         </test>
-	<test>
+        <test>
             <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
             <param name="clustering_mode_select" value="cluster_smallmem"/>
             <param name="usersort" value="--usersort"/>
@@ -171,7 +155,7 @@
             <output name="centroids" file="clustering_centroids_result2.fasta" ftype="fasta" />
             <output name="uc_outfile" file="clustering_uc_result3.uc" ftype="tabular" />
         </test>
-	<test>
+        <test>
             <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
             <param name="clustering_mode_select" value="cluster_smallmem"/>
             <param name="usersort" value="--usersort"/>
@@ -183,7 +167,7 @@
             <param name="iddef" value="0"/>
             <output name="centroids" file="clustering_centroids_result4.fasta" ftype="fasta" />
         </test>
-	<test>
+        <test>
             <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
             <param name="clustering_mode_select" value="cluster_fast"/>
             <param name="usersort" value="--usersort"/>