# HG changeset patch
# User iuc
# Date 1717664604 0
# Node ID cdee7158adf39654c40de5a290d5dbab64a21b42
# Parent  20e2f64aa1fef66f9838b0d07ce6117f0b86aa45
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 3c6cc780d2d8ea156d167289cc2576fc3e43d2fd

diff -r 20e2f64aa1fe -r cdee7158adf3 kraken2.xml
--- a/kraken2.xml	Fri Feb 09 21:43:22 2024 +0000
+++ b/kraken2.xml	Thu Jun 06 09:03:24 2024 +0000
@@ -135,18 +135,16 @@
             <filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
         </data>
 
-        <data name="out1_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified forward read collection" from_work_dir="un_out_1.*">
+        <collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs">
+            <data name="forward" from_work_dir="un_out_1.*"/>
+            <data name="reverse" from_work_dir="un_out_2.*"/>
             <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>	
-        </data>
-        <data name="out2_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Unclassified reverse read collection" from_work_dir="un_out_2.*">
-            <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
-        </data>
-        <data name="out3_1" format_source="input_pair['forward']" label="${tool.name} on ${on_string}: Classified forward read collection" from_work_dir="cl_out_1.*">
+        </collection>
+        <collection name="out_classified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Classified read pairs">
+            <data name="forward" from_work_dir="cl_out_1.*"/>
+            <data name="reverse" from_work_dir="cl_out_2.*"/>
             <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>	
-        </data>
-        <data name="out4_1" format_source="input_pair['forward']" label="${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>
+        </collection>
 
         <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
         <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
@@ -175,6 +173,29 @@
             <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/>
             <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
         </test>
+        <!-- same test but collection in/output -->
+        <test expect_num_outputs="7">
+            <param name="single_paired_selector" value="collection"/>
+            <param name="input_pair">
+                <collection type="paired">
+                    <element name="forward" value="kraken_test2_R1.fastq" ftype="fastq"/>
+                    <element name="reverse" value="kraken_test2_R2.fastq" ftype="fastq"/>
+                </collection>
+            </param>
+            <param name="split_reads" value="true"/>
+            <param name="quick" value="no"/>
+            <param name="confidence" value="0"/>
+            <param name="kraken2_database" value="test_entry"/>
+            <output_collection name="out_unclassified_paired" type="paired">
+                <element name="forward" file="un_test2_output_1.fastq" ftype="fastq"/>
+                <element name="reverse" file="un_test2_output_2.fastq" ftype="fastq"/>
+            </output_collection>
+            <output_collection name="out_classified_paired" type="paired">
+                <element name="forward" file="cl_test2_output_1.fastq" ftype="fastq"/>
+                <element name="reverse" file="cl_test2_output_2.fastq" ftype="fastq"/>
+            </output_collection>
+            <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
+        </test>
         <test expect_num_outputs="2">
             <param name="single_paired_selector" value="yes"/>
             <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>
diff -r 20e2f64aa1fe -r cdee7158adf3 macros.xml
--- a/macros.xml	Fri Feb 09 21:43:22 2024 +0000
+++ b/macros.xml	Thu Jun 06 09:03:24 2024 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.1.1</token>
+    <token name="@TOOL_VERSION@">2.1.3</token>
     <token name="@INTYPES@">fasta,fastq,fasta.gz,fasta.bz2,fastq.gz,fastq.bz2</token>
     <xml name="input_database">
         <param label="Select a Kraken2 database" name="kraken2_database" type="select">