<tool id="cpo_mlst" name="cpo_mlst" version="2.11">
  <description>Modified MLST v2.11 to support for the cpo_prediction workflow</description>
  <requirements>
        <requirement type="package" version="2.11">mlst</requirement>
    </requirements>

    <version_command>mlst --version</version_command>

    <command detect_errors="exit_code"><![CDATA[
        mlst "$input_file" --nopath > "$report"
    ]]></command>

    <inputs>
        <param type="data" name="input_file" format="fasta,genbank" />
        <conditional name="settings">
            <param name="advanced" type="select" label="Specify advanced parameters">
                <option value="simple" selected="true">No, use program defaults.</option>
                <option value="advanced">Yes, see full parameter list.</option>
            </param>
            <when value="simple">
            </when>
            <when value="advanced">
                <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
                <param name="min_dna_cov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" />
                <param name="scheme" type="text" area="false" label="PubMLST Scheme" help="Turn off auto-detection and only use this scheme" optional="true" />
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="report" format="tabular" />
    </outputs>

    <tests>
        <!-- Basic test - will produce no results. -->
        <test>
            <param name="input_file" value="Acetobacter.fna"/>
            <param name="advanced" value="simple"/>
            <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/>
        </test>

        <!-- Basic test - will produce results. -->
        <test>
            <param name="input_file" value="MRSA0252_trimmed.fna"/>
            <param name="advanced" value="simple"/>
            <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
        </test>

        <!-- Advanced test - Min DNA Coverage 100 -->
        <test>
            <param name="input_file" value="MRSA0252_trimmed.fna"/>
            <param name="advanced" value="advanced"/>
            <param name="min_dna_cov" value="100"/>
            <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
        </test>

        <!-- Advanced test - Min DNA ID 100 -->
        <test>
            <param name="input_file" value="MRSA0252_trimmed.fna"/>
            <param name="advanced" value="advanced"/>
            <param name="min_dna_id" value="100"/>
            <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
        </test>
    </tests>

    <help>performs mlst</help>

    <citations>
        <citation type="bibtex">
            @UNPUBLISHED{Seemann2016,
            author = "Seemann T",
            title = "MLST: Scan contig files against PubMLST typing schemes",
            year = "2016",
            note = "https://github.com/tseemann/mlst"}
        </citation>
    </citations>
</tool>