comparison clair3.xml @ 1:63e02ef6e153 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41

0:44f6ec903688

<tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <macros>
        <token name="@TOOL_VERSION@">0.1.11</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">clair3</requirement>
    </requirements>
    <version_command><![CDATA[run_clair3.sh --version | cut -f2 -d ' ']]></version_command>
    <command detect_errors="exit_code"><![CDATA[

        samtools faidx reference.fasta &&

        #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 &&

        #if $bed_or_vcf.bed_or_vcf_selector == 'bed'
            ln -s '$bed_or_vcf.bed_fn' input.bed &&
        #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf'
            ln -s '$bed_or_vcf.vcf_fn' input.vcf &&
        #end if

        run_clair3.sh
            --bam_fn=input_reads.bam
            --ref_fn=reference.fasta
            #if $model_source.source == "datatable"
                --platform='${model_source.model.fields.platform}'
                --model_path=${model_source.model.fields.path}
            #else

                    --platform='ont'
                #end if
                --model_path=\$(dirname \$(which run_clair3.sh))/models/$model_source.select_built_in
            #end if
            --output='.'
            --threads=\${GALAXY_SLOTS:-1}
            #if $bed_or_vcf.bed_or_vcf_selector == 'bed'
                  --bed_fn=input.bed
            #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf'
                  --vcf_fn=input.vcf
            #else
                $bed_or_vcf.include_all_ctgs
            #end if
            #if $output_options.selection_mode == 'advanced'
                $output_options.gvcf
            #end if
            #if $adv.qual
            --qual=$adv.qual
            #end if
            #if $adv.snp_min_af
                --snp_min_af=$adv.snp_min_af

                --chunk_size=$adv.chunk_size
            #end if

    ]]></command>
    <inputs>
        <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" />
            </when>
            <when value="builtin">
                <param type="select" name="ref_fasta_builtin" label="Reference genome">
                    <options from_data_table="all_fasta" />
                </param>
            </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">
                <option value="built-in">Built-in</option>
                <option value="datatable">Datatable</option>
            </param>
            <when value="built-in">
                <param type="select" name="select_built_in" label="Select 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>
                    <option value="ilmn">ilmn</option>
                </param>
            </when>
            <when value="datatable">
                <param argument="--model_path" type="select" name="model" label="Select model" >
                    <options from_data_table="clair3_models">
                        <validator type="no_options" message="no modles 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>
        <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>
            <param type="integer" name="chunk_size" value="5000000" min="1" label="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>
        <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>
        <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>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="model_source">

                <param name="ref_fasta" value="test1.fasta" />
            </conditional>
            <conditional name="bed_or_vcf">
                <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"/>
                <param name="ploidity_model" value=""/>

            </conditional>
            <conditional name="ref_source">
                <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>
            <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="phased_bam" file="phased_bam_1.bam" ftype="bam"/>
        </test>
        <test expect_num_outputs="4">
            <conditional name="model_source">
                <param name="source" value="datatable" />

            </conditional>
            <conditional name="ref_source">
                <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>
            <section name="adv">
                <param name="snp_min_af" value="0.5"/>
                <param name="indel_min_af" value="0.12"/>
                <param name="no_phasing_for_fa" value="true" />
                <param name="print_ref_calls" value="true"/>

                <assert_contents>
                    <has_size value="0" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
      Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories:
      pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall.
      Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.

1:63e02ef6e153

<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@">0.1.12</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>
    <version_command><![CDATA[run_clair3.sh --version | cut -f2 -d ' ']]></version_command>
    <command detect_errors="exit_code"><![CDATA[

        samtools faidx reference.fasta &&

        #if $model_source.source == "datatable"
            #set model_path = $model_source.model.fields.path 
        #end if
        #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 &&
        #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf'
            ln -s '$bed_or_vcf.vcf_fn' input.vcf &&
        #end if

        run_clair3.sh
            --bam_fn=input_reads.$extension
            --ref_fn=reference.fasta
            #if $model_source.source == "datatable"
                --platform='${model_source.model.fields.platform}'
                --model_path=${model_source.model.fields.path}
            #else

                    --platform='ont'
                #end if
                --model_path=\$(dirname \$(which run_clair3.sh))/models/$model_source.select_built_in
            #end if
            --output='.'
            --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'
                  --vcf_fn=input.vcf
            #else
                $bed_or_vcf.include_all_ctgs
            #end if
            $gvcf
            #if $adv.qual
            --qual=$adv.qual
            #end if
            #if $adv.snp_min_af
                --snp_min_af=$adv.snp_min_af

                --chunk_size=$adv.chunk_size
            #end if

    ]]></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" argument="--ref_fn" label="Reference genome" />
            </when>
            <when value="builtin">
                <param type="select" name="ref_fasta_builtin" label="Reference genome">
                    <options from_data_table="all_fasta" />
                </param>
            </when>
        </conditional>
        <conditional name="model_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">Cached</option>
            </param>
            <when value="built-in">
                <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>
                    <option value="ilmn">ilmn</option>
                </param>
            </when>
            <when value="datatable">
                <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 cached models available" />
                    </options>
                </param>
            </when>
        </conditional>
        <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>
        <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" 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" label="${tool.name} on ${on_string}: merged output"/>
        <data name="pileup" format="vcf_bgzip" from_work_dir="./pileup.vcf.gz" label="${tool.name} on ${on_string}: pileup">
            <filter>output_files and 'pileup' in output_files</filter>
        </data>
        <data name="full_alignment" format="vcf_bgzip" from_work_dir="./full_alignment.vcf.gz" label="${tool.name} on ${on_string}: full alignment">
            <filter>output_files and 'full_alignment' in output_files</filter>
        </data>
        <data name="phased_bam" format="bam" from_work_dir="./phased_bam.bam" label="${tool.name} on ${on_string}: phased BAM">
            <filter>output_files and 'phased_bam' in output_files</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="model_source">

                <param name="ref_fasta" value="test1.fasta" />
            </conditional>
            <conditional name="bed_or_vcf">
                <param name="bed_or_vcf_selector" value="vcf"/>
                <param name="vcf_fn" value="test1.vcf.gz" />
            </conditional>
            <section name="adv">
                <param name="no_phasing_for_fa" value="true"/>
                <param name="print_ref_calls" value="true"/>
                <param name="ploidity_model" value=""/>

            </conditional>
            <conditional name="ref_source">
                <param name="source" value="builtin" />
                <param name="ref_fasta_builtin" value="test1" />
            </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.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">
            <conditional name="model_source">
                <param name="source" value="datatable" />

            </conditional>
            <conditional name="ref_source">
                <param name="source" value="builtin" />
                <param name="ref_fasta_builtin" value="test1" />
            </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"/>
                <param name="no_phasing_for_fa" value="true" />
                <param name="print_ref_calls" value="true"/>

                <assert_contents>
                    <has_size value="0" />
                </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:
      pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall.
      Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.