annotate mlst_list.xml @ 5:ded48b36f3b7 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 87f484c6332fae818366a188736d7a735a391204"

<tool id="mlst_list" name="MLST List" version="@VERSION@">
    <description>Lists available schemes for the MLST tool.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="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" >
                <assert_contents>
                    <has_text text="saureus" />
                </assert_contents>
            </output>
        </test>

        <!-- Test the list option -->
        <test>
            <param name="list_type" value="false" />
            <output name="report" ftype="txt" >
                <assert_contents>
                    <has_text text="saureus" />
                </assert_contents>
            </output>
        </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>

    <expand macro="citations" />
</tool>