annotate snpEff_databases.xml @ 5:2950d5afa3fe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

<tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0">
    <description></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" databases |  grep -v '^---' | sed 's/^Genome/#Genome/' | sed  's/  *//g' > "$snpeff_dbs"
]]>
    </command>
    <inputs>
    </inputs>
    <outputs>
        <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" />
    </outputs>
    <tests>
        <test>
            <output name="snpeff_dbs">
                <assert_contents>
                    <has_text text="ebola_zaire" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

@EXTERNAL_DOCUMENTATION@

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