<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">snippy</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command><![CDATA[snippy --version]]></version_command>
    </xml>

    <token name="@REFERENCE_SOURCE_FILE@">
        <![CDATA[
        #if $reference_source.reference_source_selector == 'history'
            #if $reference_source.ref_file.is_of_type("fasta")
                ln -sf '$reference_source.ref_file' 'ref.fna' &&
            #elif $reference_source.ref_file.is_of_type("genbank")
                ln -sf '$reference_source.ref_file' 'ref.gbk' &&
            #end if
        #elif $reference_source.reference_source_selector == 'cached'
            ln -sf '$reference_source.ref_file.fields.path' 'ref.fna' &&
        #end if]]>
    </token>

    <token name="@REFERENCE_COMMAND@">
        <![CDATA[
        #if $reference_source.reference_source_selector == 'history'
            #if $reference_source.ref_file.is_of_type("fasta")
                --ref 'ref.fna'
            #elif $reference_source.ref_file.is_of_type("genbank")
                --ref 'ref.gbk'
            #end if
        #elif $reference_source.reference_source_selector == 'cached'
            --ref 'ref.fna'
        #end if
        ]]>
    </token>

    <xml name="reference_selector">
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
                <option value="cached">Use a built-in genome index</option>
                <option value="history">Use a genome from history and build index</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
                    <options from_data_table="all_fasta">
                        <validator type="no_options" message="No reference genomes are available" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta,genbank" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
            </when>
        </conditional>
    </xml>

    <token name="@VERSION@">4.4.3</token>

    <xml name="citations">
      <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",
              url = "https://github.com/tseemann/snippy"}</citation>
      </citations>
    </xml>
</macros>
