Mercurial > repos > iuc > clair3
changeset 1:63e02ef6e153 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
| author | iuc |
|---|---|
| date | Fri, 28 Oct 2022 20:58:30 +0000 |
| parents | 44f6ec903688 |
| children | |
| files | clair3.xml test-data/full_alignment_1.vcf test-data/full_alignment_1.vcf.gz test-data/merge_output_1.vcf test-data/merge_output_1.vcf.gz test-data/output_cram_test.vcf.gz test-data/pileup_1.vcf test-data/pileup_1.vcf.gz test-data/test1.cram |
| diffstat | 9 files changed, 81 insertions(+), 82 deletions(-) [+] |
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--- a/clair3.xml Wed Jun 15 09:45:05 2022 +0000 +++ b/clair3.xml Fri Oct 28 20:58:30 2022 +0000 @@ -1,8 +1,12 @@ <tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> + <description>germline small variant caller for long-reads</description> <macros> - <token name="@TOOL_VERSION@">0.1.11</token> + <token name="@TOOL_VERSION@">0.1.12</token> <token name="@VERSION_SUFFIX@">0</token> </macros> + <xrefs> + <xref type='bio.tools'>clair3</xref> + </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">clair3</requirement> </requirements> @@ -18,9 +22,13 @@ #if $model_source.source == "datatable" #set model_path = $model_source.model.fields.path #end if - - ln -s '${$bam_input}' input_reads.bam && - ln -s '${$bam_input.metadata.bam_index}' input_reads.bai && + #set $extension = $bam_input.ext + ln -s '${$bam_input}' input_reads.$extension && + #if $extension == 'bam' + ln -s '${$bam_input.metadata.bam_index}' input_reads.bai && + #else + ln -s '${$bam_input.metadata.cram_index}' input_reads.crai && + #end if #if $bed_or_vcf.bed_or_vcf_selector == 'bed' ln -s '$bed_or_vcf.bed_fn' input.bed && @@ -29,7 +37,7 @@ #end if run_clair3.sh - --bam_fn=input_reads.bam + --bam_fn=input_reads.$extension --ref_fn=reference.fasta #if $model_source.source == "datatable" --platform='${model_source.model.fields.platform}' @@ -43,7 +51,7 @@ --model_path=\$(dirname \$(which run_clair3.sh))/models/$model_source.select_built_in #end if --output='.' - --threads=\${GALAXY_SLOTS:-1} + --threads=\${GALAXY_SLOTS:-2} #if $bed_or_vcf.bed_or_vcf_selector == 'bed' --bed_fn=input.bed #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf' @@ -51,9 +59,7 @@ #else $bed_or_vcf.include_all_ctgs #end if - #if $output_options.selection_mode == 'advanced' - $output_options.gvcf - #end if + $gvcf #if $adv.qual --qual=$adv.qual #end if @@ -73,13 +79,14 @@ ]]></command> <inputs> + <param type="data" name="bam_input" argument="--bam_fn" format="bam,cram" label="BAM/CRAM file input" /> <conditional name="ref_source"> <param type="select" label="Reference genome source" name="source"> <option value="history" selected="true">History</option> <option value="builtin">Built-in</option> </param> <when value="history"> - <param type="data" format="fasta" name="ref_fasta" label="Reference genome" /> + <param type="data" format="fasta" name="ref_fasta" argument="--ref_fn" label="Reference genome" /> </when> <when value="builtin"> <param type="select" name="ref_fasta_builtin" label="Reference genome"> @@ -88,12 +95,12 @@ </when> </conditional> <conditional name="model_source"> - <param type="select" label="Select if you want to use built-in models or your own via datatable." name="source"> + <param name="source" type="select" label="Clair3 model" help="Select if you want to use a built-in model shipping with the tool or a model cached on this Galaxy server."> <option value="built-in">Built-in</option> - <option value="datatable">Datatable</option> + <option value="datatable">Cached</option> </param> <when value="built-in"> - <param type="select" name="select_built_in" label="Select built-in model."> + <param type="select" name="select_built_in" label="Built-in model"> <option value="r941_prom_sup_g5014">r941_prom_sup_g5014</option> <option value="r941_prom_hac_g360+g422">r941_prom_hac_g360+g422</option> <option value="hifi">hifi</option> @@ -101,68 +108,60 @@ </param> </when> <when value="datatable"> - <param argument="--model_path" type="select" name="model" label="Select model" > + <param name="model" argument="--model_path" type="select" label="Cached model from server" > <options from_data_table="clair3_models"> - <validator type="no_options" message="no modles available" /> + <validator type="no_options" message="no cached models available" /> </options> </param> </when> </conditional> - <param type="data" name="bam_input" format="bam" label="BAM file input." /> - <conditional name="bed_or_vcf"> - <param type="select" name="bed_or_vcf_selector" label="Restict variant calling to:"> - <option value="unrestricted" selected="true">Whole reference (unrestricted)</option> - <option value="bed" selected="true">Regions defined in BED dataset</option> - <option value="vcf">Sites defined in VCF dataset</option> - </param> - <when value="bed"> - <param type="data" name="bed_fn" format="bed" label="Call variants only in the provided bed regions."/> - </when> - <when value="vcf"> - <param type="data" name="vcf_fn" format="vcf" label="Candidate sites VCF file input, variants will only be called at the sites in the VCF file if provided."/> - </when> - <when value="unrestricted"> - <param type="boolean" name="include_all_ctgs" truevalue="--include_all_ctgs" falsevalue="" checked="true" label="Call variants on all contigs, otherwise call in chr{1..22,X,Y} and {1..22,X,Y}, default: disable." /> - </when> - </conditional> - <conditional name="output_options"> - <param label="Use advanced output options" name="selection_mode" type="select"> - <option selected="true" value="defaults">Show merged output file only</option> - <option value="advanced">Show intermediate output files</option> - </param> - <when value="defaults"/> - <when value="advanced"> - <param name="full_alignment_check" type="boolean" label="Show full alignment file"/> - <param name="pileup_check" type="boolean" label="Show pileup file"/> - <param name="phased_bam_check" type="boolean" label="Show itermediate phased BAM file"/> - <param type="boolean" name="gvcf" truevalue="--gvcf" falsevalue="" label="Enable GVCF output, default: disable" /> - </when> + <conditional name="bed_or_vcf"> + <param type="select" name="bed_or_vcf_selector" label="Restict variant calling to:"> + <option value="unrestricted" selected="true">Whole reference (unrestricted)</option> + <option value="bed" selected="true">Regions defined in BED dataset</option> + <option value="vcf">Sites defined in VCF dataset</option> + </param> + <when value="bed"> + <param type="data" argument="--bed_fn" format="bed" label="Call variants only in the provided bed regions."/> + </when> + <when value="vcf"> + <param type="data" argument="--vcf_fn" format="vcf" label="Candidate sites VCF file input" help="Variants will only be called at the sites in the VCF file if provided."/> + </when> + <when value="unrestricted"> + <param type="boolean" argument="--include_all_ctgs" truevalue="--include_all_ctgs" falsevalue="" checked="true" label="Call variants on all contigs" help="If disabled, call in chr{1..22,X,Y} and {1..22,X,Y}" /> + </when> </conditional> - <section name="adv" title="Advanced Parameters" expanded="false"> - <param type="integer" name="qual" value="0" min="0" label="If set, variants with >qual will be marked PASS, or LowQual otherwise." /> - <param type="float" name="snp_min_af" value="0.08" min="0" max="1" label="Minimum SNP AF required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy, default: ont:0.08,hifi:0.08,ilmn:0.08." /> - <param type="float" name="indel_min_af" value="0.15" min="0" max="1" label="Minimum INDEL AF required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy, default: ont:0.15,hifi:0.08,ilmn:0.08." /> - <param type="boolean" name="enable_phasing" truevalue="--enable_phasing" falsevalue="" label="Output phased variants using whatshap, default: disable" /> - <param type="boolean" name="no_phasing_for_fa" truevalue="--no_phasing_for_fa" falsevalue="" label="EXPERIMENTAL: Call variants without whatshap phasing in full alignment calling, default: disable." /> - <param type="boolean" name="print_ref_calls" truevalue="--print_ref_calls" falsevalue="" label="Show reference calls (0/0) in vcf file, default: disable." /> - <param type="select" name="ploidity_model" label="Call with the following ploidy model" help="EXPERIMENTAL: Enable haploid calling mode. Only 1/1 is considered as a variant, default: disable. EXPERIMENTAL: Enable haploid calling mode. 0/1 and 1/1 are considered as a variant, default: disable."> - <option value="" selected="true">diploid</option> - <option value="--haploid_sensitive">haploid (sensitive)</option> - <option value="--haploid_precise">haploid (precise)</option> + <param type="boolean" argument="--gvcf" truevalue="--gvcf" falsevalue="" label="Enable GVCF output" help="GVCF stands for Genomic VCF. A GVCF is a kind of VCF, so the basic format specification is the same as for a regular VCF but contains extra information. Default: disable" /> + <param name="output_files" type="select" display="checkboxes" multiple="true" label="Optional additional output files"> + <option value="full_alignment">Full alignment file</option> + <option value="pileup">Pileup file</option> + <option value="phased_bam">Phased BAM file</option> + </param> + <section name="adv" title="Advanced parameters" expanded="false"> + <param type="integer" argument="--qual" value="0" min="0" label="Qual" help="If set, variants with >qual will be marked PASS, or LowQual otherwise." /> + <param type="float" argument="--snp_min_af" value="0.08" min="0" max="1" label="Minimum SNP AF" help="Minimum SNP AF required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy. Default: ont:0.08,hifi:0.08,ilmn:0.08." /> + <param type="float" argument="--indel_min_af" value="0.15" min="0" max="1" label="Minimum INDEL AF" help="Minimum INDEL AF required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy. Default: ont:0.15,hifi:0.08,ilmn:0.08." /> + <param type="boolean" argument="--enable_phasing" truevalue="--enable_phasing" falsevalue="" label="Enable phasing" help="Output phased variants using whatshap. Default: disable" /> + <param type="boolean" argument="--no_phasing_for_fa" truevalue="--no_phasing_for_fa" falsevalue="" label="Call variants without whatshap phasing" help="EXPERIMENTAL: Call variants without whatshap phasing in full alignment calling. Default: disable" /> + <param type="boolean" argument="--print_ref_calls" truevalue="--print_ref_calls" falsevalue="" label="Print reference calls" help="Show reference calls (0/0) in vcf file. Default: disable." /> + <param type="select" name="ploidity_model" label="Call with the following ploidy model" help="EXPERIMENTAL. When haploid sensitive is enabled only 1/1 is considered as a variant. When haploid precise is enabled only 0/1 and 1/1 are considered as a variant. Default: diploid."> + <option value="" selected="true">Diploid</option> + <option value="--haploid_sensitive">Haploid sensitive (--haploid_sensitive)</option> + <option value="--haploid_precise">haploid precise (--haploid_precise)</option> </param> - <param type="integer" name="chunk_size" value="5000000" min="1" label="The size of each chuck for parallel processing, default: 5Mbp." optional="true" /> + <param type="integer" argument="--chunk_size" value="5000000" min="1" label="Chunk size" help="The size of each chuck for parallel processing. Default: 5Mbp." optional="true" /> </section> </inputs> <outputs> - <data name="merge_output" format="vcf_bgzip" from_work_dir="./merge_output.vcf.gz" /> - <data name="pileup" format="vcf_bgzip" from_work_dir="./pileup.vcf.gz"> - <filter>output_options['selection_mode'] == 'advanced' and output_options['pileup_check']</filter> + <data name="merge_output" format="vcf_bgzip" from_work_dir="./merge_output.vcf.gz" label="${tool.name} on ${on_string}: merged output"/> + <data name="pileup" format="vcf_bgzip" from_work_dir="./pileup.vcf.gz" label="${tool.name} on ${on_string}: pileup"> + <filter>output_files and 'pileup' in output_files</filter> </data> - <data name="full_alignment" format="vcf_bgzip" from_work_dir="./full_alignment.vcf.gz"> - <filter>output_options['selection_mode'] == 'advanced' and output_options['full_alignment_check']</filter> + <data name="full_alignment" format="vcf_bgzip" from_work_dir="./full_alignment.vcf.gz" label="${tool.name} on ${on_string}: full alignment"> + <filter>output_files and 'full_alignment' in output_files</filter> </data> - <data name="phased_bam" format="bam" from_work_dir="./phased_bam.bam"> - <filter>output_options['selection_mode'] == 'advanced' and output_options['phased_bam_check']</filter> + <data name="phased_bam" format="bam" from_work_dir="./phased_bam.bam" label="${tool.name} on ${on_string}: phased BAM"> + <filter>output_files and 'phased_bam' in output_files</filter> </data> </outputs> <tests> @@ -180,10 +179,6 @@ <param name="bed_or_vcf_selector" value="vcf"/> <param name="vcf_fn" value="test1.vcf.gz" /> </conditional> - <conditional name="output_options"> - <param name="selection_mode" value="advanced"/> - <param name="gvcf" value="true" /> - </conditional> <section name="adv"> <param name="no_phasing_for_fa" value="true"/> <param name="print_ref_calls" value="true"/> @@ -207,18 +202,14 @@ <param name="source" value="builtin" /> <param name="ref_fasta_builtin" value="test1" /> </conditional> - <conditional name="output_options"> - <param name="selection_mode" value="advanced"/> - <param name="pileup_check" value="true"/> - <param name="full_alignment_check" value="true"/> - <param name="phased_bam_check" value="true"/> - </conditional> + <param name="gvcf" value="true"/> + <param name="output_files" value="full_alignment,pileup,phased_bam"/> <section name="adv"> <param name="print_ref_calls" value="true"/> </section> - <output name="merge_output" decompress="true" file="merge_output_1.vcf" ftype="vcf_bgzip"/> - <output name="pileup" decompress="true" file="pileup_1.vcf" ftype="vcf_bgzip"/> - <output name="full_alignment" decompress="true" file="full_alignment_1.vcf" ftype="vcf_bgzip"/> + <output name="merge_output" decompress="true" file="merge_output_1.vcf.gz" ftype="vcf_bgzip"/> + <output name="pileup" decompress="true" file="pileup_1.vcf.gz" ftype="vcf_bgzip"/> + <output name="full_alignment" decompress="true" file="full_alignment_1.vcf.gz" ftype="vcf_bgzip"/> <output name="phased_bam" file="phased_bam_1.bam" ftype="bam"/> </test> <test expect_num_outputs="4"> @@ -235,12 +226,7 @@ <param name="source" value="builtin" /> <param name="ref_fasta_builtin" value="test1" /> </conditional> - <conditional name="output_options"> - <param name="selection_mode" value="advanced"/> - <param name="pileup_check" value="true"/> - <param name="full_alignment_check" value="true"/> - <param name="phased_bam_check" value="true"/> - </conditional> + <param name="output_files" value="full_alignment,pileup,phased_bam"/> <section name="adv"> <param name="snp_min_af" value="0.5"/> <param name="indel_min_af" value="0.12"/> @@ -268,6 +254,19 @@ </assert_contents> </output> </test> + <!-- Test input CRAM --> + <test expect_num_outputs="1"> + <conditional name="model_source"> + <param name="source" value="builtin" /> + <param name="select_built_in" value="r941_prom_hac_g360+g422" /> + </conditional> + <param name="bam_input" value="test1.cram" /> + <conditional name="ref_source"> + <param name="source" value="history" /> + <param name="ref_fasta" value="test1.fasta" /> + </conditional> + <output name="merge_output" file="output_cram_test.vcf.gz" ftype="vcf_bgzip"/> + </test> </tests> <help><![CDATA[ Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: