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Merge pull request #8088 from mvdbeek/fasta_gz_bwa_mem
BWA/BWA-MEM: support gzipped (fasta.gz) reference from history
2 parents 054af73 + 0812241 commit b3e1ffb

4 files changed

Lines changed: 108 additions & 45 deletions

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‎tools/bwa/bwa-mem.xml‎

Lines changed: 105 additions & 43 deletions
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<?xml version="1.0"?>
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<tool id="bwa_mem" name="Map with BWA-MEM" version="@TOOL_VERSION@" profile="22.05">
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<tool id="bwa_mem" name="Map with BWA-MEM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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<description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
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<macros>
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<import>read_group_macros.xml</import>
@@ -284,68 +284,130 @@ bwa mem
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<tests>
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<!-- `samtools sort` in the new update adds PG lines to the output so the lines_diff is changed from "2" to "4" -->
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<test expect_num_outputs="1">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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<param name="analysis_type_selector" value="illumina"/>
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<conditional name="reference_source">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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</conditional>
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<conditional name="fastq_input">
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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</conditional>
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<conditional name="analysis_type">
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<param name="analysis_type_selector" value="illumina"/>
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</conditional>
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<output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
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</test>
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<test expect_num_outputs="1">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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<param name="fastq_input_selector" value="single"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
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<param name="analysis_type_selector" value="illumina"/>
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<!-- gzip-compressed reference from history; bwa reads it transparently, so output matches the plain-fasta test above -->
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<conditional name="reference_source">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta.gz" value="bwa-mem-mt-genome.fa.gz"/>
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</conditional>
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<conditional name="fastq_input">
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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</conditional>
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<conditional name="analysis_type">
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<param name="analysis_type_selector" value="illumina"/>
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</conditional>
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<output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
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</test>
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<test expect_num_outputs="1">
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<conditional name="reference_source">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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</conditional>
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<conditional name="fastq_input">
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<param name="fastq_input_selector" value="single"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
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</conditional>
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<conditional name="analysis_type">
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<param name="analysis_type_selector" value="illumina"/>
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</conditional>
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<output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="4" />
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</test>
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<test expect_num_outputs="1">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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<param name="analysis_type_selector" value="illumina"/>
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<conditional name="reference_source">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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</conditional>
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<conditional name="fastq_input">
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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</conditional>
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<conditional name="analysis_type">
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<param name="analysis_type_selector" value="illumina"/>
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</conditional>
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<output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
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</test>
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<test expect_num_outputs="1">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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<param name="index_a" value="is"/>
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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<param name="rg_selector" value="set"/>
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<param name="ID" value="rg1"/>
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<param name="PL" value="CAPILLARY"/>
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<param name="LB" value="AARDVARK-1" />
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<param name="analysis_type_selector" value="illumina"/>
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<conditional name="reference_source">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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<param name="index_a" value="is"/>
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</conditional>
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<conditional name="fastq_input">
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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</conditional>
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<conditional name="rg">
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<param name="rg_selector" value="set"/>
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<conditional name="read_group_id_conditional">
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<param name="do_auto_name" value="false"/>
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<param name="ID" value="rg1"/>
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</conditional>
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<param name="PL" value="CAPILLARY"/>
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<conditional name="read_group_lb_conditional">
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<param name="do_auto_name" value="false"/>
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<param name="LB" value="AARDVARK-1" />
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</conditional>
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</conditional>
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<conditional name="analysis_type">
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<param name="analysis_type_selector" value="illumina"/>
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</conditional>
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<output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="4" />
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</test>
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<test expect_num_outputs="1">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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<param name="analysis_type_selector" value="illumina"/>
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<conditional name="reference_source">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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</conditional>
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<conditional name="fastq_input">
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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</conditional>
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<conditional name="analysis_type">
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<param name="analysis_type_selector" value="illumina"/>
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</conditional>
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<param name="output_sort" value="unsorted"/>
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<output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="4" />
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</test>
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<test expect_num_outputs="1">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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<param name="analysis_type_selector" value="illumina"/>
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<conditional name="reference_source">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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</conditional>
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<conditional name="fastq_input">
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<param name="fastq_input_selector" value="paired"/>
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<param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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<param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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</conditional>
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<conditional name="analysis_type">
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<param name="analysis_type_selector" value="illumina"/>
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</conditional>
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<param name="output_sort" value="name"/>
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<output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="4" />
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</test>
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<test expect_num_outputs="1">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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<conditional name="reference_source">
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<param name="reference_source_selector" value="history" />
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<param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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</conditional>
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<conditional name="fastq_input">
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<param name="fastq_input_selector" value="paired_collection"/>
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<param name="fastq_input1">

‎tools/bwa/bwa.xml‎

Lines changed: 1 addition & 1 deletion
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@@ -1,5 +1,5 @@
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<?xml version="1.0"?>
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<tool id="bwa" name="Map with BWA" version="@TOOL_VERSION@" profile="22.05">
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<tool id="bwa" name="Map with BWA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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<description>- map short reads (&lt; 100 bp) against reference genome</description>
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<macros>
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<import>read_group_macros.xml</import>

‎tools/bwa/bwa_macros.xml‎

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<import>read_group_macros.xml</import>
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<token name="@TOOL_VERSION@">0.7.19</token>
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<token name="@VERSION_SUFFIX@">1</token>
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<token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
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</param>
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</when>
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<when value="history">
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<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" />
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<param name="ref_file" type="data" format="fasta,fasta.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence (optionally gzip-compressed) to the history and use it as reference" />
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<param name="index_a" type="select" label="Algorithm for constructing the BWT index" help="(-a)">
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<option value="auto">Auto. Let BWA decide the best algorithm to use</option>
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<option value="is">IS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB</option>

‎tools/bwa/test-data/bwa-mem-mt-genome.fa.gz‎

5.25 KB
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