comparison snpEff_download.xml @ 7:7adfd0589f49 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1

6:20f0429a4bfe

        <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>

                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

@EXTERNAL_DOCUMENTATION@

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

7:7adfd0589f49

        <import>snpEff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
snpEff download -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. GRCh38.86, GRCh37.75, hg38, or GRCm38.86)">
            <help>@SNPEFF_DATABASE_URL@</help>
            <validator type="regex" message="A genome version name is required">\S+</validator>
        </param>
    </inputs>
    <outputs>

                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@EXTERNAL_DOCUMENTATION@
    ]]></help>
    <expand macro="citations" />
</tool>