<macros>
  <token name="@VERSION@">2.3</token>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="2.3.1">kat</requirement>
    </requirements>
  </xml>
  <xml name="stdio">
    <stdio>
      <exit_code range="1:" />
      <exit_code range=":-1" />
      <regex match="Error:" />
      <regex match="Exception:" />
    </stdio>
  </xml>
  <xml name="version_command">
    <version_command>kat --version</version_command>
  </xml>
  <xml name="citations">
    <citations>
      <citation type="doi">10.1101/064733</citation>
      <yield />
    </citations>
  </xml>
  <token name="@THREADS@">
    --threads \${GALAXY_SLOTS:-4}
  </token>
  <xml name="macro_input">
    <conditional name="single_or_paired">
      <param name="type" type="select" label="Read type">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
        <option value="collection">Collection Paired-end</option>
      </param>
      <when value="single">
        <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
      </when>
      <when value="paired">
        <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
        <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
      </when>
      <when value="collection">
        <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
      </when>
    </conditional>
  </xml>
  <xml name="macro_kmers"> 
    <param name="kmer" type="integer" value='27' label="Kmer size" help="The kmer length to use in the kmer hashes.  Larger values will provide more discriminating power between kmers but at the expense of additional memory and lower coverage."/>
  </xml>
</macros>