view data_manager/shapeit_ref.xml @ 0:f86c65c60056 draft

planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22

<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.1">
    <command detect_errors="aggressive"><![CDATA[
    python $__tool_directory__/shapeit_ref.py
        '${key}'
        '${description}'
        '${path}'
        '${prefix}'
        '${output_file}'
    ]]></command>>
    <inputs>
        <param name="key" type="text" label="Short key to identify this reference set (no spaces)" />
        <param name="description" type="text" label="Description of the reference data" />
        <param name="path" type="text" label="Filesystem path to directory containing this reference set" />
        <param name="prefix" type="text" label="Filename prefix for files in 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>