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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_snpeff commit 225ce35e1c3514cdba7a3637eba9aee964fa85f7
author iuc
date Fri, 13 Mar 2026 13:07:48 +0000
parents 617d95d798fa
children
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<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="5.4.0c" tool_type="manage_data" profile="24.2">
    <description>Read the list of available SnpEff databases</description>
    <requirements>
        <requirement type="package" version="5.4.0c">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="ebola_zaire" />
                </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 and its databases see: https://pcingola.github.io/SnpEff/snpeff/introduction/#databases.
    ]]></help>
    <citations>
        <citation type="doi">10.4161/fly.19695</citation>
    </citations>
</tool>