<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[
        #if $ref_source.source == "history"
            ln -s '${ref_source.ref_fasta}' reference.fasta &&
        #elif $ref_source.source == "builtin"
            ln -s '${ref_source.ref_fasta_builtin.fields.path}' reference.fasta &&
        #end if
        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
                #if $model_source.select_built_in == "hifi" or $model_source.select_built_in == "ilmn":
                    --platform='${$model_source.select_built_in}'
                #else
                    --platform='ont'
                #end if
                --model_path=\$(dirname \$(which run_clair3.sh))/models/$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
            #end if
            #if $adv.indel_min_af
                --indel_min_af=$adv.indel_min_af
            #end if
            $adv.enable_phasing
            $adv.no_phasing_for_fa
            $adv.print_ref_calls
            $adv.ploidity_model
            #if $adv.chunk_size
                --chunk_size=$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="source" value="built-in"/>  
                <param name="select_built_in" value="r941_prom_hac_g360+g422"/>
            </conditional>
            <param name="bam_input" value="test1.bam" />
            <conditional name="ref_source">
                <param name="source" value="history" />
                <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=""/>
            </section>
            <assert_stdout>
              <has_text text="[WARNING] No contig intersection found, output header only in" />
            </assert_stdout>
        </test>
        <test expect_num_outputs="4">
            <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.bam" />
            <conditional name="bed_or_vcf">
                <param name="bed_or_vcf_selector" value="unrestricted"/>
                <param name="include_all_ctgs" value="true" />
            </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" />
                <param name="model" value="test_model" />
            </conditional>
            <param name="bam_input" value="test1.bam" />
            <conditional name="bed_or_vcf">
                <param name="bed_or_vcf_selector" value="bed"/>
                <param name="bed_fn" value="test1.bed" />
            </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"/>
            </section>
            <output name="merge_output" ftype="vcf_bgzip">
                <assert_contents>
                    <has_size value="450" delta="50" />
                </assert_contents>
            </output>
            <output name="pileup" ftype="vcf_bgzip">
                <assert_contents>
                    <has_size value="0" />
                </assert_contents>
            </output>
            <output name="full_alignment" ftype="vcf_bgzip">
                <assert_contents>
                    <has_size value="0" />
                </assert_contents>
            </output>
            <output name="phased_bam" ftype="bam">
                <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.
      
      https://github.com/HKU-BAL/Clair3

      LICENSE:

        Copyright 2021 The University of Hong Kong, Department of Computer Science

        Redistribution and use in source and binary forms, with or without modification,
        are permitted provided that the following conditions are met:

        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.

        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.

        3. Neither the name of the copyright holder nor the names of its contributors
           may be used to endorse or promote products derived from this software without
           specific prior written permission.

        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
        ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
        WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
        ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
        (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
        LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
        ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
        (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
        SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
    ]]></help>
    <citations>
        <citation type="doi">10.1101/2021.12.29.474431</citation>
    </citations>
</tool>