Mercurial > repos > iuc > kraken2
changeset 9:cbe396d9773e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 commit 39ebbc539c35a194c97c93497849b6136bbc7a8c
| author | iuc |
|---|---|
| date | Sun, 07 Dec 2025 11:31:00 +0000 |
| parents | e150ae930235 |
| children | |
| files | kraken2.xml macros.xml test-data/cl_test2_output_1.fastq test-data/un_test2_output_1.fastq test-data/un_test2_output_2.fastq |
| diffstat | 5 files changed, 23 insertions(+), 20 deletions(-) [+] |
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--- 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>
--- 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">