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view data_manager/data_manager_snpEff_databases.xml @ 9:08d7998c3afb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"
author iuc
date Wed, 12 Feb 2020 18:33:53 -0500
parents a6400027d849
children
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<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.3.1t" tool_type="manage_data" profile="18.09">
    <description>Read the list of available SnpEff databases</description>
    <requirements>
        <requirement type="package" version="4.3.1t">snpeff</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/data_manager_snpEff_databases.py' '$out_file'
    ]]></command>
    <inputs>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <output name="out_file">
                <assert_contents>
                    <!-- Check that a genome was added -->
                    <has_text text="GRCh38.86" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This tool updates the list of SnpEff databases for the SnpEff Download data manager.
It should only need to be run once for a SnpEff version, since it populates the SnpEff Download data manager from the SnpEff config file.

For information about SnpEff: http://snpeff.sourceforge.net
    ]]></help>
    <citations>
        <citation type="doi">10.4161/fly.19695</citation>
    </citations>
</tool>