| Previous changeset 4:63b68fe4af85 (2024-03-05) Next changeset 6:1ad55977a040 (2026-02-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 |
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modified:
deepvariant.xml macros.xml |
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added:
test-data/phix174.par_regions.bed |
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| diff -r 63b68fe4af85 -r fd52f65372c9 deepvariant.xml --- a/deepvariant.xml Tue Mar 05 08:10:46 2024 +0000 +++ b/deepvariant.xml Mon Feb 02 12:34:14 2026 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id=\'deepvariant\' name=\'DeepVariant\' version=\'@TOOL_VERSION@+galaxy@SUFFIX_VERSION@\' profile=\'20.01\'>\n+<tool id=\'deepvariant\' name=\'DeepVariant\' version=\'@TOOL_VERSION@+galaxy@SUFFIX_VERSION@\' profile=\'@PROFILE@\'>\n <description>deep learning-based variant caller</description>\n <macros>\n <import>macros.xml</import>\n@@ -11,6 +11,14 @@\n #if $regions_conditional.regions_option == \'bed\'\n && ln -s \'${regions_conditional.bed_file}\' region.bed\n #end if\n+ #if $par_regions_bed\n+ && ln -s \'${par_regions_bed}\' par_regions.bed\n+ #end if\n+ #set $logging_dir_value = None\n+ #if $create_runtime_report\n+ #set $logging_dir_value = \'logging\'\n+ && mkdir -p \'$logging_dir_value\'\n+ #end if\n #if $reference_genome.source == \'history\':\n #set $ref_genome = \'reference.fasta\'\n && ln -s -f \'${reference_genome.history_item}\' $ref_genome\n@@ -21,17 +29,43 @@\n && run_deepvariant\n --model_type=$model_type\n --ref=$ref_genome\n- --reads=reads_alignment.bam\n+ --reads=\'reads_alignment.bam\'\n+ #if $sample_name\n+ --sample_name \'$sample_name\'\n+ #end if\n --output_vcf=\'./output.vcf.gz\'\n #if $output_gvcf\n --output_gvcf=\'./output.g.vcf.gz\'\n #end if\n #if $regions_conditional.regions_option == \'region\'\n- --regions $regions_conditional.region_literal\n+ --regions \'$regions_conditional.region_literal\'\n #else if $regions_conditional.regions_option == \'bed\'\n- --regions region.bed\n+ --regions \'region.bed\'\n+ #end if\n+ --disable_small_model=$disable_small_model\n+ #if $haploid_contigs\n+ --haploid_contigs=\'$haploid_contigs\'\n+ #end if\n+ #if $par_regions_bed\n+ --par_regions_bed=\'par_regions.bed\'\n+ #end if\n+ #if $logging_dir_value\n+ --logging_dir=\'$logging_dir_value\'\n #end if\n- ##--call_variants_extra_args="use_openvino=true" ## Setting this will use OpenVINO on Intel CPUs, which empirically reduces call_variants runtime by 15%-25%.\n+ #if $report_title\n+ --report_title=\'$report_title\'\n+ #end if\n+ --runtime_report=$create_runtime_report\n+ #if $make_examples_extra_args\n+ --make_examples_extra_args=\'$make_examples_extra_args\'\n+ #end if\n+ #if $call_variants_extra_args\n+ --call_variants_extra_args=\'$call_variants_extra_args\'\n+ #end if\n+ #if $postprocess_variants_extra_args\n+ --postprocess_variants_extra_args=\'$postprocess_variants_extra_args\'\n+ #end if\n+ $vcf_stats_report\n --num_shards=\\${GALAXY_SLOTS:-2}\n && gunzip \'./output.vcf.gz\'\n #if $output_gvcf\n@@ -57,6 +91,7 @@\n </when>\n </conditional>\n <param argument="--reads" type="data" format="bam" label="BAM file" help="An aligned reads file in BAM format. The reads must be aligned to the reference genome" />\n+ <param argument="--sample_name" type="text" optional="true" label="Sample name" help="Sample name to use instead of the SM tag in the BAM header. Example: NA12878" />\n <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling">\n <option value="WGS">WGS: Illumina whole genome sequencing</option>\n <option value="WES">WES: Illumina whole exome sequencing</option>\n@@ -88,10 +123,28 @@\n </when>\n </conditional>\n <param argument="--output_gvcf" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Generate genomic VCF (gVCF) output" help="The key difference between a regular VCF and a gVCF is that the gVCF has records for all sites, whether there is a variant call there or not. The goal is to have every site represented in the file '..b'file" ftype="vcf">\n+ <assert_contents>\n+ <has_text text="#CHROM"/>\n+ <has_text text="##fileformat=VCFv4.2"/>\n+ </assert_contents>\n+ </output>\n+ <output name="html_report" ftype="html">\n+ <assert_contents>\n+ <is_valid_xml />\n+ <has_n_lines n="34" delta="10" />\n+ <has_text text="Variant types"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test expert options extra-args-->\n+ <test expect_num_outputs="2">\n+ <conditional name="reference_genome">\n+ <param name="source" value="history"/>\n+ <param name="history_item" value="reference.fasta"/>\n+ </conditional>\n+ <param name="reads" value="reads.bam"/>\n+ <param name="model_type" value="WGS"/>\n+ <conditional name="regions_conditional">\n+ <param name="regions_option" value="disabled"/>\n+ </conditional>\n+ <section name="advanced_options">\n+ <param name="vcf_stats_report" value="True"/>\n+ </section>\n+ <section name="expert_options">\n+ <param name="make_examples_extra_args" value="min_base_quality=10"/>\n+ <param name="call_variants_extra_args" value="allow_empty_examples=true"/>\n+ <param name="postprocess_variants_extra_args" value="cnn_homref_call_min_gq=20.0"/>\n+ </section>\n+ <output name="vcf_file" ftype="vcf">\n+ <assert_contents>\n+ <has_text text="#CHROM"/>\n+ <has_text text="##fileformat=VCFv4.2"/>\n+ </assert_contents>\n+ </output>\n+ <output name="html_report" ftype="html">\n+ <assert_contents>\n+ <is_valid_xml />\n+ <has_n_lines n="34" delta="10" />\n+ <has_text text="Variant types"/>\n </assert_contents>\n </output>\n </test>\n@@ -254,11 +436,13 @@\n \n DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.\n \n+DeepVariant runs a pipeline of three steps: **make_examples**, **call_variants**, and **postprocess_variants**. The **Expert options** section exposes extra-args fields for each step. Use these only with parameters that are accepted by the corresponding DeepVariant binary (see `run_deepvariant --helpfull` and the subcommand help, e.g. `/opt/deepvariant/bin/make_examples --helpfull` in the container).\n+\n DeepVariant supports germline variant-calling in diploid organisms.\n \n-- NGS (Illumina) data for either a `whole genome <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-case-study.md>`_ or `whole exome <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-exome-case-study.md>`_.\n-- PacBio HiFi data, see the `PacBio case study <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-pacbio-model-case-study.md>`_.\n-- Hybrid PacBio HiFi + Illumina WGS, see the `hybrid case study <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-hybrid-case-study.md>`_.\n+- NGS (Illumina) data for either a `whole genome <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-case-study.md>`_ or `whole exome <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-exome-case-study.md>`_.\n+- PacBio HiFi data, see the `PacBio case study <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-pacbio-model-case-study.md>`_.\n+- Hybrid PacBio HiFi + Illumina WGS, see the `hybrid case study <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-hybrid-case-study.md>`_.\n \n Please also note:\n \n' |
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| diff -r 63b68fe4af85 -r fd52f65372c9 macros.xml --- a/macros.xml Tue Mar 05 08:10:46 2024 +0000 +++ b/macros.xml Mon Feb 02 12:34:14 2026 +0000 |
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| @@ -1,6 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">1.5.0</token> - <token name="@SUFFIX_VERSION@">1</token> + <token name="@TOOL_VERSION@">1.9.0</token> + <token name="@SUFFIX_VERSION@">0</token> + <token name="@PROFILE@">23.1</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0199</edam_topic> |
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| diff -r 63b68fe4af85 -r fd52f65372c9 test-data/phix174.par_regions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phix174.par_regions.bed Mon Feb 02 12:34:14 2026 +0000 |
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| @@ -0,0 +1,1 @@ +K03455 0 100 |