annotate snpEff_download.xml @ 23:74aebe30fb52 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"

<tool id="snpEff_download" name="SnpEff download:" version="@WRAPPER_VERSION@.galaxy2">
    <description> download a pre-built database</description>
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <requirements>
        <expand macro="requirement" />
    </requirements>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
snpEff download -dataDir "\$PWD/temp" -v '$genome_version' &&
mkdir -p '$snpeff_db.files_path' &&
mv temp/'$genome_version' '$snpeff_db.files_path'
    ]]></command>
    <inputs>
        <param name="genome_version" type="text" value="" label="Select the annotation database you want to download (e.g. GRCh38.86, mm10 etc.)" help="The list of available databases can be obtained with 'SnpEff databases' tool">
            <validator type="empty_field" message="A genome version name is required" />
        </param>
    </inputs>
    <outputs>
        <data name="snpeff_db" format="snpeffdb" 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>
        <test>
            <param name="genome_version" value="Bdellovibrio_bacteriovorus_hd100"/>
            <output name="snpeff_db">
                <assert_contents>
                    <has_text text="Bdellovibrio_bacteriovorus_hd100" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool downloads a specified database from @SNPEFF_DATABASE_URL@. It deposits it into the history.

-------

.. class:: infomark

**The usage scenario**

Suppose you want to annoate a VCF file containing variants within mm10 version of the Mouse genome. To do this you can:

    #. Download mm10 snpEff database by typing *mm10* into **Select the annotation database...** text box.
    #. Use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter.

@SNPEFF_IN_GALAXY_INFO@
@EXTERNAL_DOCUMENTATION@
    ]]></help>
    <expand macro="citations" />
</tool>