# HG changeset patch
# User iuc
# Date 1613583577 0
# Node ID e674066930b245b2e8d7ce96a0699d99788805b3
# Parent  4a9da2b6c2e3269ef48f5a5b3fd3cfe073e2a508
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 055a83d01b077101110272c44ef0ff2a04d5d1d4"

diff -r 4a9da2b6c2e3 -r e674066930b2 kraken2.xml
--- a/kraken2.xml	Mon Nov 23 20:50:12 2020 +0000
+++ b/kraken2.xml	Wed Feb 17 17:39:37 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy0">
+<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy1">
     <description>
         assign taxonomic labels to sequencing reads
     </description>
@@ -68,8 +68,8 @@
             #if $report.create_report:
                 --report '${report_output}'
                 $report.use_mpa_style
-                $report.report_zero_counts:
-                $report.report_minimizer_data:
+                $report.report_zero_counts
+                $report.report_minimizer_data
             #end if
 
             > '${output}'
@@ -132,16 +132,16 @@
             <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="Unclassified forward" 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="Unclassified reverse" 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="Classified forward" 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="Classified reverse" from_work_dir="cl_out_2.*">
             <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>
         </data>
 
@@ -155,7 +155,6 @@
             <param name="split_reads" value="false"/>
             <param name="quick" value="no"/>
             <param name="confidence" value=".2"/>
-            <param name="only-classified-output" value="false"/>
             <param name="kraken2_database" value="test_entry"/>
             <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
         </test>
@@ -166,13 +165,25 @@
             <param name="split_reads" value="true"/>
             <param name="quick" value="no"/>
             <param name="confidence" value="0"/>
-            <param name="only-classified-output" value="false"/>
             <param name="kraken2_database" value="test_entry"/>
             <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/>
             <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/>
             <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>
+            <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"/>
+            <param name="use-names" value="true"/>
+            <section name="report">
+                <param name="create_report" value="true"/>
+                <param name="report_minimizer_data" value="true"/>
+            </section>
+            <param name="kraken2_database" value="test_entry"/>
+            <output name="report_output" file="kraken_test2_report.tab" ftype="tabular"/>
         </test>
     </tests>
     <help>
diff -r 4a9da2b6c2e3 -r e674066930b2 test-data/kraken_test2_report.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken_test2_report.tab	Wed Feb 17 17:39:37 2021 +0000
@@ -0,0 +1,1 @@
+100.00	240	240	0	0	U	0	unclassified