comparison data_manager/data_manager_snpEff_download.xml @ 9:08d7998c3afb draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"

8:d107d20dc6bd

<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3r" tool_type="manage_data">
    <description>Download a new database</description>
    <requirements>
        <requirement type="package" version="4.3.1r">snpeff</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/data_manager_snpEff_download.py'
--genome_version '$genome_version'
'$out_file'

    <outputs>
        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="genome_version" value="GRCh38.76"/>
            <output name="out_file">
                <assert_contents>
                    <!-- Check that a genome was added -->
                    <has_text text="GRCh38.76" />
                    <has_text text="snpeffv_regulationdb" />
                </assert_contents>
            </output>
        </test>
    </tests>

9:08d7998c3afb

<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3.1t" tool_type="manage_data" profile="18.09">
    <description>Download a new database</description>
    <requirements>
        <requirement type="package" version="4.3.1t">snpeff</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/data_manager_snpEff_download.py'
--genome_version '$genome_version'
'$out_file'

    <outputs>
        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="genome_version" value="GRCh38.86"/>
            <output name="out_file">
                <assert_contents>
                    <!-- Check that a genome was added -->
                    <has_text text="GRCh38.86" />
                    <has_text text="snpeffv_regulationdb" />
                </assert_contents>
            </output>
        </test>
    </tests>