annotate snpEff_download.xml @ 6:20f0429a4bfe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit bd4fbe120288bf8452e479cbd82aa1bbf5c4bd31

<tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0">
    <description>Download a new database</description>
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
    @CONDA_SNPEFF_JAR_PATH@ &&
    java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version"
]]>
    </command>
    <inputs>
        <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
            <help>@SNPEFF_DATABASE_URL@</help>
            <validator type="regex" message="A genome version name is required">\S+</validator>
        </param>
    </inputs>
    <outputs>
        <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
    </outputs>
    <tests>
        <test>
            <param name="genome_version" value="ebola_zaire"/>
            <output name="snpeff_db">
                <assert_contents>
                    <has_text text="ebola_zaire" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

@EXTERNAL_DOCUMENTATION@

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