<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.jl'
  call
  -o '$output_file'
  -s '$sample_name'
  --db '$kmer_db'
  #if $discard_threshold
  -t '$discard_threshold'
  #end if
  #if $quick_filter
  '$quick_filter'
  #end if
  #if $external_counter
  '$external_counter'
  #end if
  #if $skip_length
  -j '$skip_length'
  #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="data" format="h5"
	   label="Kmer DB" help="Kmer database" />
    <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="quick_filter" type="boolean"
	   label="Quick Filter" help="Quick filter; if the first, middle and last kmers of a read are not in the kmer DB, the read is discarded. Disabled by default."
	   truevalue="-q" falsevalue="" optional="true" />
    <param name="external_counter" type="boolean"
	   label="External Kmer Counter" help="Use external kmc kmer counter. Disabled by default."
	   truevalue="-e" falsevalue="" optional="true" />
    <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[
  usage: MentaLiST.jl call -o O -s S --db DB [-t T] [-q] [-e] [-j J] [-h] files...

  positional arguments:
  files       FastQ input files

  optional arguments:
  -o O        Output file with MLST call
  -s S        Sample name
  --db DB     Kmer database
  -t T        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 <= t <= 1 (type: Float64,
	      default: 0.3
  -q          Quick filter; if the first, middle and last kmers of a
              read are not in the kmer DB, the read is discarded.
	      Disabled by default.
  -e          Use external kmc kmer counter. Disabled by default.
  -j J        Skip length between consecutive k-mers. Defaults to 1.
  -h, --help  show this help message and exit
  ]]></help>
  <citations>
    <citation type="doi">10.1101/172858</citation>
  </citations>
</tool>