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planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 58664d1dbd0725423a50869ecb376f05e59b6449-dirty

<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.8">
    <command detect_errors="exit_code"><![CDATA[
    python $__tool_directory__/shapeit_ref.py
        '${value}'
        '${name}'
        '${path}'
        '${reference_prefix}'
        '${map_prefix}'
        '${sample_prefix}'
        '${output_file}'
    ]]></command>>
    <inputs>
        <param name="value" type="text" label="Short key to identify this reference set (no spaces)" />
        <param name="name" type="text" label="Description of the reference data" />
        <param name="path" type="text" label="Filesystem path to directory containing this reference set" />
        <param name="reference_prefix" type="text" label="Filename prefix for the reference (.hap / .legend / .sample) files" />
        <param name="map_prefix" type="text" label="Filename prefix for map files in this reference set" />
        <param name="sample_prefix" type="text" label="Filename prefix for sample file for this reference set">
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json" />
    </outputs>
    <help><![CDATA[
    This data manager updates the *shapeit_ref* table with information about locally-maintained reference data
    used by the SHAPEIT_ haplotype estimation (i.e. phasing) package. An example for the 1000 Genomes
    dataset is available here_.

    .. _SHAPEIT: http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
    .. _here: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html
    ]]></help>
    <citations>
        <citation type="doi">10.1038/nmeth.1785</citation>
    </citations>
</tool>