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<tool id="vep" name="Vep" version="0.1.0">
    <requirements>
        <requirement type="package" version="94.5">ensembl-vep</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $output_options.cell_type.strip():
            #set $cell_type = '--cell_type ' + str( $output_options.cell_type )
        #else:
            #set $cell_type = ''
        #end if

        #if str( $output_options.individual.select ) == "all":
            #set $individual = '--individual all'
        #elif str( $output_options.individual.select ) == "ind":
            #set $individual = '--individual ind ' + str($output_options.individual.list)
        #else:
            #set $individual = ''
        #end if 

        #if str( $output_options.vcf_info_field.select ) == "other":
            #set $vcf_info_field = '--vcf_info_field ' + str( $output_options.vcf_info_field.name )
        #else
            #set $vcf_info_field = '--vcf_info_field ' + str( $output_options.vcf_info_field.select )
        #end if

        #if str( $identifier_options.synonyms.select ) == "yes":
            #set $synonyms = '--synonyms ' + str( $identifier_options.synonyms.file )
        #else
            #set $synonyms = ''
        #end if

        #if str( $filtering_qc.transcript_filter.select ) == "yes":
            #set $transcript_filter = '--transcript_filter "' + str( $filtering_qc.transcript_filter.filter ) + '"'
        #else:
            #set $transcript_filter = ''
        #end if

        #if str( $filtering_qc.chr.select ) == "yes":
            #set chr = '--chr ' + str( $filtering_qc.chr.list )
        #else:
            #set chr = ''
        #end if

        #if str( $filtering_qc.pick_order.select ) == "yes":
            #set $pick_order = '--pick_order ' + str( $filtering_qc.pick_order.list )
        #else:
            #set $pick_order = ''
        #end if

        #if str( $filtering_qc.freq.select ) == "yes":
            #set $freq_pop = str( $filtering_qc.freq.freq_pop )
            #set $freq_freq = str( $filtering_qc.freq.freq_freq )
            #set $freq_gt_lt = str( $filtering_qc.freq.freq_gt_lt )
            #set $freq_filter = str( $filtering_qc.freq.freq_filter )
            #set $freq = $freq_pop + ' --freq_freq ' + $freq_freq + ' ' + $freq_gt_lt + ' ' + $freq_filter
        #else:
            #set $freq = ''
        #end if

        vep 
        --format vcf 
        --vcf
        --no_stats
        --dir_plugins $__tool_directory__/dir_plugins
        --cache
        --dir_cache "\$VEP_CACHE_DIR"
        --force_overwrite
        --species ${species}
        --cache_version 99
        --input_file "$input"
        --output_file "$output"
        $offline
        $output_options.variant_class
        $output_options.sift
        $output_options.polyphen
        $output_options.humdiv
        $output_options.nearest
        --distance $output_options.distance
        $output_options.gene_phenotype
        $output_options.regulatory
        $cell_type
        $individual
        $vcf_info_field
        $output_options.phased
        $output_options.total_length
        $output_options.numbers
        $output_options.domains
        $output_options.no_escape
        $output_options.keep_csq
        --terms $output_options.terms
        $output_options.no_headers
        $identifier_options.transcript_version
        $identifier_options.protein
        $identifier_options.symbol
        $identifier_options.ccds
        $identifier_options.tsl
        $identifier_options.appris
        $identifier_options.canonical
        $identifier_options.biotype
        $identifier_options.xref_refseq
        $synonyms
        $co_located_variants_options.check_existing
        $co_located_variants_options.exclude_null_alleles
        $co_located_variants_options.no_check_alleles
        $co_located_variants_options.af
        $co_located_variants_options.max_af
        $co_located_variants_options.af_1kg
        $co_located_variants_options.af_esp
        $co_located_variants_options.af_gnomad
        $co_located_variants_options.af_exac
        $co_located_variants_options.pubmed
        $co_located_variants_options.failed
        $filtering_qc.gencode_basic
        $filtering_qc.all_refseq
        $filtering_qc.exclude_predicted
        $transcript_filter
        $filtering_qc.check_ref
        $filtering_qc.lookup_ref
        $chr
        $filtering_qc.dont_skip
        $filtering_qc.allow_non_variant
        $filtering_qc.coding_only
        $filtering_qc.no_intergenic
        $filtering_qc.pick
        $filtering_qc.pick_allele
        $filtering_qc.pick_allele_gene
        $filtering_qc.per_gene
        $filtering_qc.flag_pick
        $filtering_qc.flag_pick_allele
        $filtering_qc.flag_pick_allele_gene
        $pick_order
        $filtering_qc.most_severe
        $filtering_qc.summary
        $filtering_qc.filter_common
        $freq
        #for $i, $s in enumerate( $other_anotations.plugins )
            --plugin $s.plugin
        #end for
    ]]></command>
    <inputs>
        <param type="data" name="input" format="vcf" />
        <param name="species" type="select">
            <option value="mus_musculus" selected="true">Mus musculus</option>
            <option value="homo_sapiens">Homo sapiens</option>
        </param>
        <param name="cache_type" type="select">
            <option value="" selected="true">ensembl</option>
            <option value="--refseq">refseq</option>
            <option value="--merged">merged</option>
        </param>
        <param name="offline" type="select">
                <option value="--offline">Yes</option>
                <option value="" selected="true">No</option>
            </param>
        <section name="output_options" title="Output options">
            <param name="variant_class" type="select">
                <option value="--variant_class">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="sift" type="select">
                <option value="--sift p">Prediction</option>
                <option value="--sift s">Score</option>
                <option value="--sift b">Both</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="polyphen" type="select">
                <option value="--polyphen p">Prediction</option>
                <option value="--polyphen s">Score</option>
                <option value="--polyphen b">Both</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="humdiv" type="select">
                <option value="--humdiv">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="nearest" type="select">
                <option value="--nearest transcript">Transcript</option>
                <option value="--nearest gene">Gene</option>
                <option value="--nearest symbol">Symbol</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="distance" type="text" value="5000">
                <validator type="regex" message="Has to be a number">\d+(,\d+)?</validator>
            </param>
            <param name="gene_phenotype" type="select">
                <option value="--gene_phenotype">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="regulatory" type="select">
                <option value="--regulatory">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="cell_type" type="text"/>
            <conditional name="individual">
                <param name="select" type="select" label="individual">
                    <option value="all">All</option>
                    <option value="ind">Individual/List</option>
                    <option value="no" selected="true">No</option>
                </param>
                <when value="ind">
                    <param name="list" type="text" />
                </when>
            </conditional>

            <param name="phased" type="select">
                <option value="--phased">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="total_length" type="select">
                <option value="--total_length">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="numbers" type="select">
                <option value="--numbers">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="domains" type="select">
                <option value="--domains">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="no_escape" type="select">
                <option value="--no_escape">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="keep_csq" type="select">
                <option value="--no_escape">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <conditional name="vcf_info_field">
                <param name="select" type="select" label="vcf_info_field">
                    <option value="CSQ" selected="true">CSQ</option>
                    <option value="ANN">ANN</option>
                    <option value="other">Other</option>
                </param>
                <when value="other">
                    <param name="name" type="text" />
                </when>
            </conditional>
            <param name="terms" type="select">
                <option value="SO" selected="true">SO</option>
                <option value="display">display</option>
                <option value="NCBI">NCBI</option>
            </param>
            <param name="no_headers" type="select">
                <option value="--no_headers">Yes</option>
                <option value="" selected="true">No</option>
            </param>
        </section>

        <section name="identifier_options" title="Identifiers options">
            <!-- TODO add hgvs -->
            <!-- TODO add hgvsg -->
            <!-- TODO add shift_hgvs -->
            <param name="transcript_version" type="select">
                <option value="--transcript_version">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="protein" type="select">
                <option value="--protein">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="symbol" type="select">
                <option value="--symbol">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="ccds" type="select">
                <option value="--ccds">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="tsl" type="select">
                <option value="--tsl">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="appris" type="select">
                <option value="--appris">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="canonical" type="select">
                <option value="--canonical">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="biotype" type="select">
                <option value="--biotype">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="xref_refseq" type="select">
                <option value="--xref_refseq">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <conditional name="synonyms">
                <param name="select" type="select" label="synonyms">
                    <option value="yes">Yes</option>
                    <option value="no" selected="true">No</option>
                </param>
                <when value="yes">
                    <param type="data" name="file" format="tabular" />
                </when>
            </conditional>
        </section>

        <section name="co_located_variants_options" title="Co-located variants options">
            <param name="check_existing" type="select">
                <option value="--check_existing">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="exclude_null_alleles" type="select">
                <option value="--exclude_null_alleles">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="no_check_alleles" type="select">
                <option value="--no_check_alleles">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="af" type="select">
                <option value="--af">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="max_af" type="select">
                <option value="--max_af">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="af_1kg" type="select">
                <option value="--af_1kg">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="af_esp" type="select">
                <option value="--af_esp">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="af_gnomad" type="select">
                <option value="--af_gnomad">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="af_exac" type="select">
                <option value="--af_exac">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="pubmed" type="select">
                <option value="--pubmed">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="failed" type="select">
                <option value="--failed 1">Yes</option>
                <option value="--failed 0" selected="true">No</option>
            </param>
        </section>

        <section name="filtering_qc" title="Filtering and QC">
            <param name="gencode_basic" type="select">
                <option value="--gencode_basic">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="all_refseq" type="select">
                <option value="--all_refseq">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="exclude_predicted" type="select">
                <option value="--exclude_predicted">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <conditional name="transcript_filter">
                <param name="select" type="select" label="transcript_filter">
                    <option value="yes">Yes</option>
                    <option value="no" selected="true">No</option>
                </param>
                <when value="yes">
                    <param type="text" name="filter">
                        <sanitizer>
                            <valid initial="string.printable">
                                <remove value="&apos;" />
                            </valid>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <param name="check_ref" type="select">
                <option value="--check_ref">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="lookup_ref" type="select">
                <option value="--lookup_ref">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <conditional name="chr">  <!-- TODO double check, looks correct but doesn't seem to work -->
                <param name="select" type="select" label="chr">
                    <option value="yes">Yes</option>
                    <option value="no" selected="true">No</option>
                </param>
                <when value="yes">
                    <param type="text" name="list" />
                </when>
            </conditional>
            <param name="dont_skip" type="select">
                <option value="" selected="true">Yes</option>
                <option value="--dont_skip">No</option>
            </param>
            <param name="allow_non_variant" type="select">
                <option value="--allow_non_variant">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="coding_only" type="select">
                <option value="--coding_only">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="no_intergenic" type="select">
                <option value="--no_intergenic">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="pick" type="select">
                <option value="--pick">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="pick_allele" type="select">
                <option value="--pick_allele">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="pick_allele_gene" type="select">
                <option value="--pick_allele_gene">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="per_gene" type="select">
                <option value="--per_gene">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="flag_pick" type="select">
                <option value="--flag_pick">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="flag_pick_allele" type="select">
                <option value="--flag_pick_allele">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="flag_pick_allele_gene" type="select">
                <option value="--flag_pick_allele_gene">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <conditional name="pick_order">
                <param name="select" type="select" label="pick_order">
                    <option value="yes">Yes</option>
                    <option value="no" selected="true">No</option>
                </param>
                <when value="yes">
                    <param type="text" name="list" />
                </when>
            </conditional>
            <param name="most_severe" type="select">
                <option value="--most_severe">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="summary" type="select"> <!-- TODO double check, looks correct but doesn't seem to work -->
                <option value="--summary">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <param name="filter_common" type="select">
                <option value="--filter_common">Yes</option>
                <option value="" selected="true">No</option>
            </param>

            <conditional name="freq">
                <param name="select" type="select" label="freq">
                    <option value="yes">Yes</option>
                    <option value="no" selected="true">No</option>
                </param>
                <when value="yes">
                    <param name="freq_pop" type="select">
                        <option value="--freq_pop 1KG_ALL">1000 genomes combined population (global)</option>
                        <option value="--freq_pop 1KG_AFR">1000 genomes combined African population</option>
                        <option value="--freq_pop 1KG_AMR">1000 genomes combined American population</option>
                        <option value="--freq_pop 1KG_EAS">1000 genomes combined East Asian population</option>
                        <option value="--freq_pop 1KG_EUR">1000 genomes combined European population</option>
                        <option value="--freq_pop 1KG_SAS">1000 genomes combined South Asian population</option>
                        <option value="--freq_pop ESP_AA">NHLBI-ESP African American</option>
                        <option value="--freq_pop ESP_EA">NHLBI-ESP European American</option>
                        <option value="--freq_pop gnomAD">gnomAD combined population</option>
                        <option value="--freq_pop gnomAD_AFR">gnomAD African/African American population</option>
                        <option value="--freq_pop gnomAD_AMR">gnomAD Latino population</option>
                        <option value="--freq_pop gnomAD_ASJ">gnomAD Ashkenazi Jewish population</option>
                        <option value="--freq_pop gnomAD_EAS">gnomAD East Asian population</option>
                        <option value="--freq_pop gnomAD_FIN">gnomAD Finnish population</option>
                        <option value="--freq_pop gnomAD_NFE">gnomAD non-Finnish European population</option>
                        <option value="--freq_pop gnomAD_OTH">gnomAD other population</option>
                        <option value="--freq_pop gnomAD_SAS">gnomAD South Asian population</option>
                    </param>
                    <param type="text" name="freq_freq" />
                    <param name="freq_gt_lt" type="select">
                        <option value="--freq_gt_lt gt" selected="true">Greater</option>
                        <option value="--freq_gt_lt lt">Less than</option>
                    </param>
                    <param name="freq_filter" type="select">
                        <option value="--freq_filter include" selected="true">Include</option>
                        <option value="--freq_gt_lt exclude">Exclude</option>
                    </param>
                </when>
            </conditional>
            
            <!-- TODO add check_frequency group -->
        </section>

         <section name="other_anotations" title="Other anotations">
            <repeat name="plugins" title="Plugins" min="0" default="0">
                <param name="plugin" type="select" label="Plugin">
                    <option value="AncestralAllele">AncestralAllele</option>
                    <option value="Blosum62">Blosum62</option>
                    <option value="CADD">CADD</option>
                    <option value="Carol">Carol</option>
                    <option value="CCDSFilter">CCDSFilter</option>
                    <option value="Condel">Condel</option>
                    <option value="Conservation">Conservation</option>
                    <option value="CSN">CSN</option>
                    <option value="DAS">DAS</option>
                    <option value="dbNSFP">dbNSFP</option>
                    <option value="dbscSNV">dbscSNV</option>
                    <option value="Downstream">Downstream</option>
                    <option value="Draw">Draw</option>
                    <option value="ExACpLI">ExACpLI</option>
                    <option value="ExAC">ExAC</option>
                    <option value="FATHMM_MKL">FATHMM_MKL</option>
                    <option value="FATHMM">FATHMM</option>
                    <option value="G2P">G2P</option>
                    <option value="GeneSplicer">GeneSplicer</option>
                    <option value="GO">GO</option>
                    <option value="GXA">GXA</option>
                    <option value="HGVSReferenceBase">HGVSReferenceBase</option>
                    <option value="LD">LD</option>
                    <option value="LocalID">LocalID</option>
                    <option value="LoFtool">LoFtool</option>
                    <option value="LOVD">LOVD</option>
                    <option value="MaxEntScan">MaxEntScan</option>
                    <option value="miRNA">miRNA</option>
                    <option value="MPC">MPC</option>
                    <option value="MTR">MTR</option>
                    <option value="NearestGene">NearestGene</option>
                    <option value="NonSynonymousFilter">NonSynonymousFilter</option>
                    <option value="Phenotypes">Phenotypes</option>
                    <option value="PolyPhen_SIFT">PolyPhen_SIFT</option>
                    <option value="PON_P2">PON_P2</option>
                    <option value="ProteinSeqs">ProteinSeqs</option>
                    <option value="RankFilter">RankFilter</option>
                    <option value="RefSeqHGVS">RefSeqHGVS</option>
                    <option value="REVEL">REVEL</option>
                    <option value="SameCodon">SameCodon</option>
                    <option value="SpliceRegion">SpliceRegion</option>
                    <option value="SubsetVCF">SubsetVCF</option>
                    <option value="TSSDistance">TSSDistance</option>
                    <option value="Wildtype">Wildtype</option>
                </param>
            </repeat>
        </section>
        
        
        
    </inputs>
    <outputs>
        <data name="output" format="vcf" />
    </outputs>
    <help><![CDATA[
        This is a straightforward tool wrapper for VEP, for more information about these parameters visit the VEP documentation: https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html
    ]]></help>
</tool>