diff chimera.vsearch.xml @ 1:b4e60c1d77ac draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746

--- a/chimera.vsearch.xml	Tue Mar 20 22:09:26 2018 -0400
+++ b/chimera.vsearch.xml	Fri Apr 06 04:13:19 2018 -0400
@@ -1,4 +1,4 @@
-<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.0">
+<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.1">
     <description>find potential chimeric sequences using vsearch</description>
     <macros>
         <import>macros.xml</import>
@@ -98,8 +98,11 @@
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
-        <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: uchime.chimeras"/>
-        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: uchime.accnos"/>
+        <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: vsearch.chimeras"/>
+        <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: vsearch.accnos"/>
+        <data name="out_count" format="mothur.count_table" from_work_dir="template.*vsearch.pick.count_table" label="${tool.name} on ${on_string}: vsearch.count_table">
+            <filter>template['source'] == 'self' and template['count']</filter>
+        </data>
     </outputs>
     <tests>
         <test><!-- de novo test with name file -->
@@ -112,11 +115,13 @@
             <expand macro="logfile-test"/>
         </test>
         <test><!-- de novo test with count table-->
-            <param name="fasta" value="stool_small.unique.fasta"/>
+            <param name="fasta" value="chimera.fasta"/>
             <param name="source" value="self"/>
-            <param name="count" value="stool_small.count_table"/>
-            <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
-            <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
+            <param name="count" value="chimera.count_table"/>
+            <param name="dereplicate" value="true"/>
+            <output name="vsearch.chimeras" file="chimera.vsearch.chimeras" ftype="txt"/>
+            <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos"/>
+            <output name="out_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/>
             <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>