<tool id="snippy-core" name="snippy-core" version="0.2.0">

  <requirements>
      <requirement type="package" version="3.0">snippy</requirement>
  </requirements>
  <stdio>
      <exit_code range="1:" />
  </stdio>

    <command interpreter="perl">
      <![CDATA[

        snippy_core_wrapper.pl
        $is_reference
        --mincov $mincov
        --indirs '${" ".join(map(str, $indirs))}'

    ]]></command>

    <inputs>
      <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" />
      <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." />
      <param name="mincov" type="integer" value="10" min="1" label="Minimum coverage" help="Minimum depth of coverage to consider core (default '10')" />
    </inputs>

    <outputs>
      <data format="fasta" name="alignment_fasta" label="${tool.name} on ${on_string} core alignment fasta" from_work_dir="core.aln" />
      <data format="tabular" name="alignment_table" label="${tool.name} on ${on_string} core alignment table" from_work_dir="core.tab" />
      <data format="txt" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt" />
    </outputs>

    <help><![CDATA[
Synopsis:
  Combine multiple Snippy folders into a core SNP alignment

Usage:
  ../../snippy/bin/snippy-core [options] [--noref] snippyDir1/ snippyDir2/ snippyDir3/ ...

Options:

  --help!         This help.

  --quiet!        No output to stderr (default '0').

  --verbose!      Verbose output (default '0').

  --inprefix=s    Preferred input prefix of Snippy files (default 'snps').

  --prefix=s      Output file prefix (default 'core').

  --noref!        Exclude reference (default '0').

  --mincov=i      Minimum depth of coverage to consider core (default '10').

  --aformat=s     Output alignment format: nexus fasta phylip maf clustalw ... (default 'fasta').

    ]]></help>

  <citations>
    <citation type="bibtex">@UNPUBLISHED{Seemann2013,
      author = "Seemann T",
      title = "snippy: fast bacterial variant calling from NGS reads",
      year = "2015",
      note = "https://github.com/tseemann/snippy"}</citation>
  </citations>

</tool>