| Previous changeset 4:d3e88507ee64 (2025-03-19) Next changeset 6:d459a463cb73 (2025-03-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560 |
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modified:
bwa-mem2.xml macros.xml |
| b |
| diff -r d3e88507ee64 -r fea76fc17330 bwa-mem2.xml --- a/bwa-mem2.xml Wed Mar 19 17:25:56 2025 +0000 +++ b/bwa-mem2.xml Fri Mar 28 08:29:39 2025 +0000 |
| [ |
| b'@@ -4,8 +4,10 @@\n <import>read_group_macros.xml</import>\n <import>macros.xml</import>\n </macros>\n- <expand macro="requirements"/>\n <expand macro="xrefs"/>\n+ <expand macro="requirements">\n+ <requirement type="package" version="1.21">samtools</requirement>\n+ </expand>\n <expand macro="stdio"/>\n <command><![CDATA[\n @pipefail@\n@@ -282,80 +284,134 @@\n \n <tests>\n <test>\n- <param name="reference_source_selector" value="history" />\n- <param name="ref_file" ftype="bwa_mem2_index" class="Directory" value="test-cache"/>\n- <param name="fastq_input_selector" value="paired"/>\n- <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n- <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n- <param name="analysis_type_selector" value="illumina"/>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="bwa_mem2_index" class="Directory" value="test-cache"/>\n+ </conditional>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" value="paired"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n+ <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n+ </conditional>\n+ <conditional name="analysis_type">\n+ <param name="analysis_type_selector" value="illumina"/>\n+ </conditional>\n <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />\n </test>\n <test>\n- <param name="reference_source_selector" value="history" />\n- <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>\n- <param name="fastq_input_selector" value="paired"/>\n- <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n- <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n- <param name="analysis_type_selector" value="illumina"/>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>\n+ </conditional>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" value="paired"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n+ <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n+ </conditional>\n+ <conditional name="analysis_type">\n+ <param name="analysis_type_selector" value="illumina"/>\n+ </conditional>\n <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />\n </test>\n <test>\n- <param name="reference_source_selector" value="history" />\n- <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>\n- <param name="fastq_input_selector" value="single"/>\n- <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>\n- <param name="analysis_type_selector" value="illumina"/>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>\n+ </conditional>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" value="single"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>\n+ </conditional>\n+ <conditional name="analysis_type">\n+ <param name='..b' <param name="reference_source_selector" value="history" />\n- <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>\n- <param name="fastq_input_selector" value="paired"/>\n- <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n- <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n- <param name="analysis_type_selector" value="illumina"/>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>\n+ </conditional>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" value="paired"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n+ <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n+ </conditional>\n+ <conditional name="analysis_type">\n+ <param name="analysis_type_selector" value="illumina"/>\n+ </conditional>\n <param name="output_sort" value="unsorted"/>\n <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="6" />\n </test>\n <test>\n- <param name="reference_source_selector" value="history" />\n- <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>\n- <param name="fastq_input_selector" value="paired"/>\n- <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n- <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n- <param name="analysis_type_selector" value="illumina"/>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>\n+ </conditional>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" value="paired"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n+ <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n+ </conditional>\n+ <conditional name="analysis_type">\n+ <param name="analysis_type_selector" value="illumina"/>\n+ </conditional>\n <param name="output_sort" value="name"/>\n <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="6" />\n </test>\n <test>\n- <param name="reference_source_selector" value="cached" />\n- <param name="ref_file" value="mtgenome"/>\n- <param name="fastq_input_selector" value="paired"/>\n- <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n- <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n- <param name="analysis_type_selector" value="illumina"/>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="cached" />\n+ <param name="ref_file" value="mtgenome"/>\n+ </conditional>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" value="paired"/>\n+ <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>\n+ <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>\n+ </conditional>\n+ <conditional name="analysis_type">\n+ <param name="analysis_type_selector" value="illumina"/>\n+ </conditional>\n <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />\n </test>\n </tests>\n' |
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| diff -r d3e88507ee64 -r fea76fc17330 macros.xml --- a/macros.xml Wed Mar 19 17:25:56 2025 +0000 +++ b/macros.xml Fri Mar 28 08:29:39 2025 +0000 |
| b |
| @@ -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"> |