diff chimera.vsearch.xml @ 7:de3cfb122105 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"

--- a/chimera.vsearch.xml	Tue Dec 08 14:17:28 2020 +0000
+++ b/chimera.vsearch.xml	Fri Jan 22 01:09:52 2021 +0000
@@ -1,4 +1,4 @@
-<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.1">
+<tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.2">
     <description>find potential chimeric sequences using vsearch</description>
     <macros>
         <import>macros.xml</import>
@@ -101,11 +101,11 @@
         <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>
+            <filter>template['source'] == 'self' and template['count'] and template['count'].metadata.groups != []</filter>
         </data>
     </outputs>
     <tests>
-        <test><!-- de novo test with name file -->
+        <test expect_num_outputs="3"><!-- de novo test with name file -->
             <param name="fasta" value="stool_small.unique.fasta"/>
             <param name="source" value="names"/>
             <param name="name" value="stool_small.names"/>
@@ -114,18 +114,29 @@
             <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
-        <test><!-- de novo test with count table-->
+        <test expect_num_outputs="4"><!-- de novo test with count table-->
             <param name="fasta" value="chimera.fasta"/>
             <param name="source" value="self"/>
-            <param name="count" value="chimera.count_table"/>
+            <param name="count" value="chimera.count_table" ftype="mothur.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_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/>
             <output name="out_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/>
             <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
-        <test><!-- test with reference file -->
+        <test expect_num_outputs="3"><!-- de novo test with count table (missing group info)-->
+            <param name="fasta" value="chimera.fasta"/>
+            <param name="source" value="self"/>
+            <param name="count" value="chimera.count_table_wogroups" ftype="mothur.count_table"/>
+            <param name="dereplicate" value="true"/>
+            <!-- for some reason only for count tables wo group info header is printed -->
+            <output name="vsearch.chimeras" file="chimera.vsearch.chimeras_wogroups" ftype="txt"/>
+            <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test expect_num_outputs="3"><!-- test with reference file -->
             <param name="fasta" value="stool_small.unique.fasta"/>
             <param name="source" value="hist"/>
             <param name="reference" value="stool_small.unique.fasta"/>