# HG changeset patch
# User iuc
# Date 1707515002 0
# Node ID 20e2f64aa1fef66f9838b0d07ce6117f0b86aa45
# Parent  e674066930b245b2e8d7ce96a0699d99788805b3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit b5beeef6c90fe39ce3ace531877d632725839ee4

diff -r e674066930b2 -r 20e2f64aa1fe kraken2.xml
--- a/kraken2.xml	Wed Feb 17 17:39:37 2021 +0000
+++ b/kraken2.xml	Fri Feb 09 21:43:22 2024 +0000
@@ -6,6 +6,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">kraken2</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
     </requirements>
@@ -115,33 +118,33 @@
         <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">
             <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter>	
         </data>
-        <data name="report_output" format="tabular" label="Report: ${tool.name} on ${on_string}">
+        <data name="report_output" format="tabular" label="${tool.name} on ${on_string}: Report">
             <filter>(report['create_report'])</filter>
         </data>
 
-        <data name="out1" format_source="forward_input" label="Unclassified forward" from_work_dir="un_out_1.*">
+        <data name="out1" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified forward reads" from_work_dir="un_out_1.*">
             <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>	
         </data>
-        <data name="out2" format_source="forward_input" label="Unclassified reverse" from_work_dir="un_out_2.*">
+        <data name="out2" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified reverse reads" from_work_dir="un_out_2.*">
             <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
         </data>
-        <data name="out3" format_source="forward_input" label="Classified forward" from_work_dir="cl_out_1.*">
+        <data name="out3" format_source="forward_input" label="${tool.name} on ${on_string}: Classified forward reads" from_work_dir="cl_out_1.*">
             <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>	
         </data>
-        <data name="out4" format_source="forward_input" label="Classified reverse" from_work_dir="cl_out_2.*">
+        <data name="out4" format_source="forward_input" label="${tool.name} on ${on_string}: Classified reverse reads" from_work_dir="cl_out_2.*">
             <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
         </data>
 
-        <data name="out1_1" format_source="input_pair['forward']" label="Unclassified forward" from_work_dir="un_out_1.*">
+        <data name="out1_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified forward read collection" from_work_dir="un_out_1.*">
             <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>	
         </data>
-        <data name="out2_1" format_source="input_pair['forward']" label="Unclassified reverse" from_work_dir="un_out_2.*">
+        <data name="out2_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified reverse read collection" from_work_dir="un_out_2.*">
             <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
         </data>
-        <data name="out3_1" format_source="input_pair['forward']" label="Classified forward" from_work_dir="cl_out_1.*">
+        <data name="out3_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified forward read collection" from_work_dir="cl_out_1.*">
             <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>	
         </data>
-        <data name="out4_1" format_source="input_pair['forward']" label="Classified reverse" from_work_dir="cl_out_2.*">
+        <data name="out4_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified reverse read collection" from_work_dir="cl_out_2.*">
             <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
         </data>
 
@@ -149,7 +152,7 @@
         <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="single_paired_selector" value="no"/>
             <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
             <param name="split_reads" value="false"/>
@@ -158,7 +161,7 @@
             <param name="kraken2_database" value="test_entry"/>
             <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
         </test>
-        <test>
+        <test expect_num_outputs="5">
             <param name="single_paired_selector" value="yes"/>
             <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>
             <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>
@@ -171,9 +174,8 @@
             <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/>
             <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/>
             <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
-
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="single_paired_selector" value="yes"/>
             <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>
             <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>