<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 '$output_file'
    --db '$kmer_db.fields.path'
    #if $discard_threshold
        -t '$discard_threshold'
    #end if
    #if '$fastq_input_selector' == "single"
        -s '$fastq_input1.name'
        '$fastq_input1'
    #end if
    #if '$fastq_input_selector' == "paired"
        -s '$fastq_input1.name'
        '$fastq_input1' '$fastq_input2'
    #end if
    #if '$fastq_input_selector' == "paired_collection"
        -s '$fastq_input.name'
        '$fastq_input.forward' '$fastq_input.reverse'
    #end if
  ]]></command>
  <inputs>
    <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" />
    <conditional name="fastq_input">
      <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
	<option value="paired">Paired</option>
	<option value="single">Single</option>
	<option value="paired_collection">Paired Collection</option>
      </param>
      <when value="paired">
	<param name="fastq_input1" type="data" format="fastq" label="Select first set of reads" help="Specify dataset with forward reads"/>
	<param name="fastq_input2" type="data" format="fastq" label="Select second set of reads" help="Specify dataset with reverse reads"/>
      </when>
      <when value="single">
	<param name="fastq_input1" type="data" format="fastq" label="Select fastq dataset" help="Specify dataset with single reads"/>
      </when>
      <when value="paired_collection">
	<param name="fastq_input" format="fastq" type="data_collection" collection_type="paired" label="Select a paired collection" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data name="output_file" format="tabular"/>
  </outputs>
  <help><![CDATA[
  ]]></help>
  <citations>
    <citation type="doi">10.1101/172858</citation>
  </citations>
</tool>