Mercurial > repos > iuc > bwa_mem2
changeset 4:d3e88507ee64 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit e953b3b7dac6cbe9509fdc673907a7c2c7183180
| author | iuc |
|---|---|
| date | Wed, 19 Mar 2025 17:25:56 +0000 |
| parents | bfaa0d22c2e4 |
| children | |
| files | bwa-mem2-idx.xml bwa-mem2.xml macros.xml test-data/bwa_mem2_index.loc test-data/test-cache/bwa-mem-mt-genome.fa.0123 test-data/test-cache/bwa-mem-mt-genome.fa.amb test-data/test-cache/bwa-mem-mt-genome.fa.ann test-data/test-cache/bwa-mem-mt-genome.fa.bwt.2bit.64 test-data/test-cache/bwa-mem-mt-genome.fa.pac test-data/test-cache/reference.0123 test-data/test-cache/reference.amb test-data/test-cache/reference.ann test-data/test-cache/reference.bwt.2bit.64 test-data/test-cache/reference.pac |
| diffstat | 14 files changed, 71 insertions(+), 21 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa-mem2-idx.xml Wed Mar 19 17:25:56 2025 +0000 @@ -0,0 +1,36 @@ +<tool id="bwa_mem2_idx" name="BWA-MEM2 indexer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@"> + <description>Build BWA-MEM2 reference index</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command><![CDATA[ +mkdir '$index.extra_files_path' && +cd '$index.extra_files_path' && +bwa-mem2 index -p 'reference' '${reference}' + ]]></command> + <inputs> + <param name="reference" type="data" format="fasta,fasta.gz" label="Select a genome to index" help="Build an index for this FASTA sequence."/> + </inputs> + <outputs> + <data name="index" format="bwa_mem2_index"/> + </outputs> + <tests> + <test> + <param name="reference" ftype="fasta" value="bwa-mem-mt-genome.fa"/> + <output name="index" ftype="bwa_mem2_index"> + <extra_files name="reference.0123" type="file" value="test-cache/reference.0123"></extra_files> + </output> + </test> + </tests> + <help><![CDATA[ +**What is does** +BWA-MEM2 is the new version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. +The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases. + +This tools build a reference index for the bwa-mem2 galaxy tool. + +@info@ + ]]></help> + <expand macro="citations" /> +</tool>
--- a/bwa-mem2.xml Wed Jul 26 20:02:13 2023 +0000 +++ b/bwa-mem2.xml Wed Mar 19 17:25:56 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="bwa_mem2" name="BWA-MEM2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> +<tool id="bwa_mem2" name="BWA-MEM2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2"> <description>- map medium and long reads (> 100 bp) against reference genome</description> <macros> <import>read_group_macros.xml</import> @@ -283,12 +283,21 @@ <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"/> + <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"/> - <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" /> + <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" /> </test> <test> <param name="reference_source_selector" value="history" /> @@ -296,7 +305,7 @@ <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"/> - <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="4" /> + <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="6" /> </test> <test> <param name="reference_source_selector" value="history" /> @@ -305,7 +314,7 @@ <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"/> - <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" /> + <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" /> </test> <test> <param name="reference_source_selector" value="history" /> @@ -318,7 +327,7 @@ <param name="PL" value="CAPILLARY"/> <param name="LB" value="AARDVARK-1" /> <param name="analysis_type_selector" value="illumina"/> - <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="4" /> + <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="6" /> </test> <test> <param name="reference_source_selector" value="history" /> @@ -328,7 +337,7 @@ <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> <param name="analysis_type_selector" value="illumina"/> <param name="output_sort" value="unsorted"/> - <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="4" /> + <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" /> @@ -338,7 +347,7 @@ <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> <param name="analysis_type_selector" value="illumina"/> <param name="output_sort" value="name"/> - <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="4" /> + <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" /> @@ -347,7 +356,7 @@ <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"/> - <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" /> + <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" /> </test> </tests> <help><![CDATA[
--- a/macros.xml Wed Jul 26 20:02:13 2023 +0000 +++ b/macros.xml Wed Mar 19 17:25:56 2025 +0000 @@ -3,6 +3,7 @@ <token name="@TOOL_VERSION@">2.2.1</token> <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE_VERSION@">20.01</token> <xml name="xrefs"> <xrefs> @@ -29,10 +30,14 @@ <token name="@set_reference_fasta_filename@"><![CDATA[ #if str( $reference_source.reference_source_selector ) == "history": - #set $reference_fasta_filename = "localref.fa" - ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && - bwa-mem2 index - '${reference_fasta_filename}' && + #if $reference_source.ref_file.is_of_type("bwa_mem2_index"): + #set $reference_fasta_filename = $reference_source.ref_file.extra_files_path + "/reference" + #else + #set $reference_fasta_filename = "localref." + $reference_source.ref_file.extension + ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' && + bwa-mem2 index + '${reference_fasta_filename}' && + #end if #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if @@ -41,7 +46,7 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement> - <requirement type="package" version="1.13">samtools</requirement> + <yield></yield> </requirements> </xml> @@ -59,7 +64,7 @@ <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> <option value="cached">Use a built-in genome index</option> - <option value="history">Use a genome from history and build index</option> + <option value="history">Use a reference from history and build index if necessary</option> </param> <when value="cached"> <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> @@ -71,7 +76,7 @@ </param> </when> <when value="history"> - <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" /> + <param name="ref_file" type="data" format="fasta,fasta.gz,bwa_mem2_index" label="Use the following dataset as the reference" help="You can upload a FASTA sequence to the history and use it as reference. For better performance build a reference index separately." /> </when> </conditional> </macro>
--- a/test-data/bwa_mem2_index.loc Wed Jul 26 20:02:13 2023 +0000 +++ b/test-data/bwa_mem2_index.loc Wed Mar 19 17:25:56 2025 +0000 @@ -1,1 +1,1 @@ -mtgenome mtGenome Mitochondiral genome ${__HERE__}/test-cache/bwa-mem-mt-genome.fa \ No newline at end of file +mtgenome mtGenome Mitochondiral genome ${__HERE__}/test-cache/reference
--- a/test-data/test-cache/bwa-mem-mt-genome.fa.amb Wed Jul 26 20:02:13 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -16569 1 1 -3106 1 N
--- a/test-data/test-cache/bwa-mem-mt-genome.fa.ann Wed Jul 26 20:02:13 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -16569 1 11 -0 gi|251831106|ref|NC_012920.1| (null) -0 16569 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/reference.amb Wed Mar 19 17:25:56 2025 +0000 @@ -0,0 +1,2 @@ +16569 1 1 +3106 1 N