<macros>
    <token name="@TOOL_VERSION@">0.10.0</token>
    <token name="@PROFILE@">20.09</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement>
      </requirements>
    </xml>

    <token name="@shared_options@">
        <![CDATA[
            #if $kmer:
                --kmer ${kmer}
            #end if
            #if $expected_depth:
                --expected_depth ${expected_depth}
            #end if
            $ont
            $report_all_calls
            #if $expected_error_rate:
                --expected_error_rate ${expected_error_rate}
            #end if
            #if $min_variant_conf:
                --min_variant_conf ${min_variant_conf}
            #end if
            #if $min_gene_conf:
                --min_gene_conf ${min_gene_conf}
            #end if
            #if $min_proportion_expected_depth:
                --min_proportion_expected_depth ${min_proportion_expected_depth}
            #end if
            #if $min_gene_percent_covg_threshold:
                --min_gene_percent_covg_threshold  ${min_gene_percent_covg_threshold}
            #end if
            $guess_sequence_method
            $ignore_minor_calls
            #if $ignore_filtered:
                --ignore_filtered '${ignore_filtered}'
            #end if
            #if $model:
                --model '${model}'
            #end if
            #if $ploidy:
                --ploidy '${ploidy}'
            #end if
        ]]>
    </token>

    <xml name="inputs">
        <conditional name="data_type">
            <param name="type" type="select" label="Specify the read type.">
                <option value="single">Single-end Data</option>
                <option value="paired">Paired-end Data</option>
                <option value="collection">Collection Paired-end Data</option>
            </param>
            <when value="single">
                <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/>
            </when>
            <when value="paired">
                <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/>
                <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/>
            </when>
            <when value="collection">
                <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" />
            </when>
        </conditional>
    </xml>

    <xml name="options">
        <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
        <param argument="--expected_error_rate" optional="True" type="float" label="Expected error rate"  help="Expected sequencing error rate. Set to 0.15 for ONT genotyping"/>
        <param argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth"  help=""/>
        <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data"  help=""/>
        <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping"  help=""/>
        <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping"  help=""/>
        <param argument="--min_gene_percent_covg_threshold" optional="True" type="integer" min="0" label="Minimum gene predict coverage"  help="all genes alleles found above this percent coverage will be reported (default 100 (only best alleles reported))"/>
        <param argument="--min_proportion_expected_depth" optional="True" type="float" label="Minimum depth required on the sum of both alleles" help="Default 0.3 (30%)"/>
        <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>
        <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">
            <option value="diploid">diploid</option>
            <option value="haploid">haploid</option>
        </param>
        <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls"  help=""/>
        <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls"  help="Ignore minor calls when running resistance prediction"/>
        <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/>
        <param argument="--guess_sequence_method" type="boolean" truevalue="--guess_sequence_method" falsevalue="" label="Guess sequence method"  help="Guess if ONT or Illumia based on error rate. If error rate is > 10%, ploidy is set to haploid and a confidence threshold is used"/>
    </xml>

    <token name="@ATTRIBUTION@">
        <![CDATA[
            **MyKrobe predict - Antibiotic resistance predictions**
            Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
            using Bruijn graph.
        ]]>
    </token>

    <xml name="citation">
        <citations>
            <citation type="doi">10.1038/ncomms10063</citation>
        </citations>
    </xml>
</macros>