<?xml version="1.1"?>
<macros>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="0.7.0">mykrobe</requirement>
    </requirements>    
  </xml>
  <token name="@select_inputs@">
    <![CDATA[
         #set $name='sample'
         #set $type='fastq'
         ## Adding sample name, indicate specie and inputs fastq(s) files
          #if $data_type.type == "paired":

            ln -s '$data_type.fastq_input1' sample_1.fastq &&
            ln -s '$data_type.fastq_input2' sample_2.fastq &&


        #elif $data_type.type == "collection":
            #set $name=str($data_type.fastq_input1.name)
            ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq &&
            ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq &&

        #elif $data_type.type == "single":


            #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
              ln -s '$data_type.fastq_input1' sample.fastq &&

            #end if

            #if $data_type.fastq_input1.is_of_type('bam'):
              ln -s '$data_type.fastq_input1' sample.bam &&
              #set $type='bam'
            #end if

        #end if
    ]]>
  </token>

  <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="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/>
      </when>
      <when value="paired">
        <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
        <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
      </when>
      <when value="collection">
        <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" 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>