<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.2">
  <requirements>
    <requirement type="package" version="0.1.2">mentalist</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    mentalist
    call
    -o '$output_file'
    -s '$sample_name'
    --db '$kmer_db.fields.path'
    #if $discard_threshold
        -t '$discard_threshold'
    #end if
    $input_fastqs.forward $input_fastqs.reverse
  ]]></command>
  <inputs>
    <param name="sample_name" type="text"
	   label="Sample Name" help="Sample Name" />
    <param name="kmer_db" type="select">
      <options from_data_table="mentalist_databases">
	<validator type="no_options" message="No MentaLiST databases are available" />
      </options>
    </param>
    <param name="discard_threshold" type="float"
	   label="Discard Threshold" help="A read of length L is discarded if it has at less than (L - k) * t hits to the same locus in the kmer database, where k is the kmer length. 0 &lt;= t &lt;= 1"
	   value="0.3" min="0" max="1" />
    <param name="skip_length" type="integer"
	   label="Skip Length" help="Skip length between consecutive k-mers."
	   value="1" min="1" max="32" />
    <param name="input_fastqs" type="data_collection" collection_type="paired" format="fastq"
	   label="Input FastQ" help="FastQ input files" />
  </inputs>
  <outputs>
    <data name="output_file" format="tsv"/>
  </outputs>
  <help><![CDATA[
  ]]></help>
  <citations>
    <citation type="doi">10.1101/172858</citation>
  </citations>
</tool>