<?xml version="1.0"?>
<macros>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="0.5.6">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>

  <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>

  <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>