<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[
        #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

        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
                #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:-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
            #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>
        <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="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>
            <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=""/>
            </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>
            <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" />
                <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>
            <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"/>
            </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>
    </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>