<tool id="mlst_list" name="MLST List" version="0.1.0">
    <requirements>
        <requirement type="package" version="2.6">mlst</requirement>
    </requirements>

    <version_command>mlst --version</version_command>

    <command detect_errors="exit_code"><![CDATA[
        mlst $list_type > "$report"
    ]]></command>

    <inputs>
        <param name="list_type" type="boolean" label="Output allele information" truevalue="--longlist" falsevalue="--list"
            help="Selecting 'Yes' will provide the alleles for all MLST schemes" optional="false" />
    </inputs>

    <outputs>
        <data format="txt" name="report" label="${tool.name} - list of schemes"/>
    </outputs>

    <tests>
        <!-- Test the longlist option -->
        <test>
            <param name="list_type" value="true" />
            <output name="report" ftype="txt" file="output_longlist.txt" />
        </test>

        <!-- Test the list option -->
        <test>
            <param name="list_type" value="false" />
            <output name="report" ftype="txt" file="output_list.txt" />
        </test>
    </tests>

    <help><![CDATA[
**What it does**

MLST List will list all the scheme names used by MLST. Selecting the long list option will also provide the alleles for all MLST schemes.

    ]]></help>

    <citations>
      <citation type="bibtex">
        @UNPUBLISHED{Seemann2016,
        author = "Seemann T",
        title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
        year = "2016",
        note = "https://github.com/tseemann/abricate"}
      </citation>
    </citations>
</tool>