view genotype_population_info.xml @ 2:836b90a08eab draft default tip

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<tool id="genotype_population_info" name="Generate genotype population" version="1.0.0">
    <description>information from a partial dataset</description>
    <command detect_errors="exit_code"><![CDATA[
python $__tool_directory__/genotype_population_info.py
--database_connection_string '$__app__.config.corals_database_connection'
--input_partial_info '$input_partial_info'
--output '$output'
]]></command>
    <inputs>
        <param name="input_partial_info" type="data" format="tabular" label="Partial genotype population file"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <!--Testing this tool is a bit difficult at the current time.-->
        </test>
    </tests>
    <help>
**What it does**

Accepts a file that contains Affymetrix identifiers and a subset of the user specimen identifiers and
regions for genotyping.  The corals (stag) database is queried to retrieve the user specimen identifiers
and regions that are missing for each Affymetrix identifier, and a complete set of genotype population
information is produced for use as input to the Coral Multilocus Genotype tool.  This tool must be able
to access the corals (stag) database.
    </help>
    <citations>
        <citation type="doi">https://doi.org/10.1038/s41598-020-69101-z</citation>
    </citations>
</tool>