Mercurial > repos > iuc > bwa_mem2
changeset 5:fea76fc17330 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
| author | iuc |
|---|---|
| date | Fri, 28 Mar 2025 08:29:39 +0000 |
| parents | d3e88507ee64 |
| children | d459a463cb73 |
| files | bwa-mem2.xml macros.xml |
| diffstat | 2 files changed, 109 insertions(+), 53 deletions(-) [+] |
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--- a/bwa-mem2.xml Wed Mar 19 17:25:56 2025 +0000 +++ b/bwa-mem2.xml Fri Mar 28 08:29:39 2025 +0000 @@ -4,8 +4,10 @@ <import>read_group_macros.xml</import> <import>macros.xml</import> </macros> - <expand macro="requirements"/> <expand macro="xrefs"/> + <expand macro="requirements"> + <requirement type="package" version="1.21">samtools</requirement> + </expand> <expand macro="stdio"/> <command><![CDATA[ @pipefail@ @@ -282,80 +284,134 @@ <tests> <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="bwa_mem2_index" class="Directory" value="test-cache"/> - <param name="fastq_input_selector" value="paired"/> - <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> - <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> - <param name="analysis_type_selector" value="illumina"/> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="bwa_mem2_index" class="Directory" value="test-cache"/> + </conditional> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="illumina"/> + </conditional> <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" /> </test> <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> - <param name="fastq_input_selector" value="paired"/> - <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> - <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> - <param name="analysis_type_selector" value="illumina"/> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + </conditional> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="illumina"/> + </conditional> <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" /> </test> <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> - <param name="fastq_input_selector" value="single"/> - <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> - <param name="analysis_type_selector" value="illumina"/> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + </conditional> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="single"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="illumina"/> + </conditional> <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="6" /> </test> <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> - <param name="fastq_input_selector" value="paired"/> - <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> - <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> - <param name="analysis_type_selector" value="illumina"/> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + </conditional> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="illumina"/> + </conditional> <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" /> </test> <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> - <param name="fastq_input_selector" value="paired"/> - <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> - <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> - <param name="rg_selector" value="set"/> - <param name="ID" value="rg1"/> - <param name="PL" value="CAPILLARY"/> - <param name="LB" value="AARDVARK-1" /> - <param name="analysis_type_selector" value="illumina"/> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + </conditional> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + </conditional> + <conditional name="rg"> + <param name="rg_selector" value="set"/> + <conditional name="read_group_id_conditional"> + <param name="ID" value="rg1"/> + </conditional> + <conditional name="read_group_lb_conditional"> + <param name="LB" value="AARDVARK-1" /> + </conditional> + <param name="PL" value="CAPILLARY"/> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="illumina"/> + </conditional> <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="6" /> </test> <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> - <param name="fastq_input_selector" value="paired"/> - <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> - <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> - <param name="analysis_type_selector" value="illumina"/> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + </conditional> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="illumina"/> + </conditional> <param name="output_sort" value="unsorted"/> <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="6" /> </test> <test> - <param name="reference_source_selector" value="history" /> - <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> - <param name="fastq_input_selector" value="paired"/> - <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> - <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> - <param name="analysis_type_selector" value="illumina"/> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + </conditional> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="illumina"/> + </conditional> <param name="output_sort" value="name"/> <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="6" /> </test> <test> - <param name="reference_source_selector" value="cached" /> - <param name="ref_file" value="mtgenome"/> - <param name="fastq_input_selector" value="paired"/> - <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> - <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> - <param name="analysis_type_selector" value="illumina"/> + <conditional name="reference_source"> + <param name="reference_source_selector" value="cached" /> + <param name="ref_file" value="mtgenome"/> + </conditional> + <conditional name="fastq_input"> + <param name="fastq_input_selector" value="paired"/> + <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> + <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> + </conditional> + <conditional name="analysis_type"> + <param name="analysis_type_selector" value="illumina"/> + </conditional> <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" /> </test> </tests>
--- a/macros.xml Wed Mar 19 17:25:56 2025 +0000 +++ b/macros.xml Fri Mar 28 08:29:39 2025 +0000 @@ -2,7 +2,7 @@ <import>read_group_macros.xml</import> <token name="@TOOL_VERSION@">2.2.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE_VERSION@">20.01</token> <xml name="xrefs">