# HG changeset patch
# User iuc
# Date 1765107060 0
# Node ID cbe396d9773e29c66d6caabfdc38e1ef2419a321
# Parent  e150ae9302353f0ac76bc45348d473249bbc2d42
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c

diff -r e150ae930235 -r cbe396d9773e kraken2.xml
--- a/kraken2.xml	Tue Aug 19 19:58:36 2025 +0000
+++ b/kraken2.xml	Sun Dec 07 11:31:00 2025 +0000
@@ -43,7 +43,7 @@
 
             $use_names
 
-            #if $report.create_report:
+            #if $report.create_report == "true":
                 --report '${report_output}'
                 $report.use_mpa_style
                 $report.report_zero_counts
@@ -97,32 +97,35 @@
         <param argument="--minimum-hit-groups" type="integer" label="Minimum hit groups" value="2" help="Number of overlapping k-mers sharing the same minimizer needed to make a call" />
         <param argument="--quick" type="boolean" truevalue="--quick" falsevalue="" label="Enable quick operation" help="Quick operation (use first hit)"/>
         <param name="split_reads" type="boolean" label="Split classified and unclassified outputs?" help="Sets --unclassified-out and --classified-out"/>
-
-        <section name="report" title="Create Report" expanded="false">
-            <param name="create_report" type="boolean"  label="Print a report with aggregrate counts/clade to file" help="--report" />
-            <param argument="--use-mpa-style" type="boolean" truevalue="--use-mpa-style" falsevalue="" label="Format report output like Kraken 1's kraken-mpa-report" />
-            <param argument="--report-zero-counts" type="boolean" truevalue="--report-zero-counts" falsevalue="" label="Report counts for ALL taxa, even if counts are zero" />
-            <param argument="--report-minimizer-data" type="boolean" truevalue="--report-minimizer-data" falsevalue="" label="Report minimizer data" help="Report minimizer and distinct minimizer count information in addition to normal Kraken report" />
-        </section>
-
+        <conditional name="report">
+            <param argument="--report" name="create_report" type="select" label="Print a report with aggregrate counts/clade to file" help="Can be used as input for bracken">
+                <option value="true">Yes</option>
+                <option value="false" selected="true">No</option>
+            </param>
+            <when value="true">
+                <param argument="--use-mpa-style" type="boolean" truevalue="--use-mpa-style" falsevalue="" label="Format report output like Kraken 1's kraken-mpa-report" />
+                <param argument="--report-zero-counts" type="boolean" truevalue="--report-zero-counts" falsevalue="" label="Report counts for ALL taxa, even if counts are zero" />
+                <param argument="--report-minimizer-data" type="boolean" truevalue="--report-minimizer-data" falsevalue="" label="Report minimizer data" help="Report minimizer and distinct minimizer count information in addition to normal Kraken report" />
+            </when>
+            <when value="false"/>
+        </conditional>
         <expand macro="input_database"/>  
     </inputs>
     <outputs>
         <data name="classified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads">
-            <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter>   
+            <filter>split_reads and single_paired['single_paired_selector'] == "no"</filter>   
         </data>
         <data name="unclassified_out_s" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">
-            <filter>(split_reads and ('no' in single_paired['single_paired_selector']))</filter>	
+            <filter>split_reads and single_paired['single_paired_selector'] == "no"</filter>	
         </data>
         <data name="report_output" format="tabular" label="${tool.name} on ${on_string}: Report">
-            <filter>(report['create_report'])</filter>
+            <filter>report['create_report'] == "true"</filter>
         </data>
-
         <collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs">
-            <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>	
+            <filter>split_reads and single_paired['single_paired_selector'] == "collection"</filter>	
         </collection>
         <collection name="out_classified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Classified read pairs">
-            <filter>(split_reads and ("collection" in single_paired['single_paired_selector']))</filter>	
+            <filter>split_reads and "collection" in single_paired['single_paired_selector'] == "collection"</filter>	
         </collection>
 
         <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
@@ -195,10 +198,10 @@
                 </param>
             </conditional>
             <param name="use_names" value="true"/>
-            <section name="report">
+            <conditional name="report">
                 <param name="create_report" value="true"/>
                 <param name="report_minimizer_data" value="true"/>
-            </section>
+            </conditional>
             <param name="kraken2_database" value="test_entry"/>
             <output name="report_output" file="kraken_test2_report.tab" ftype="tabular"/>
         </test>
diff -r e150ae930235 -r cbe396d9773e macros.xml
--- a/macros.xml	Tue Aug 19 19:58:36 2025 +0000
+++ b/macros.xml	Sun Dec 07 11:31:00 2025 +0000
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">2.1.3</token>
-    <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@PROFILE@">24.0</token>
+    <token name="@TOOL_VERSION@">2.17.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">24.2</token>
     <token name="@INTYPES@">fasta,fasta.gz,fasta.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
     <xml name="input_database">
         <param label="Select a Kraken2 database" name="kraken2_database" type="select">
diff -r e150ae930235 -r cbe396d9773e test-data/cl_test2_output_1.fastq
Binary file test-data/cl_test2_output_1.fastq has changed
diff -r e150ae930235 -r cbe396d9773e test-data/un_test2_output_1.fastq
Binary file test-data/un_test2_output_1.fastq has changed
diff -r e150ae930235 -r cbe396d9773e test-data/un_test2_output_2.fastq
Binary file test-data/un_test2_output_2.fastq has changed