<tool id="correct_stag_database" name="Correct stag database" version="1.0.0">
    <description>with corrected values</description>
    <command detect_errors="exit_code"><![CDATA[
#set input_dir = "input_dir"
python '$__tool_directory__/correct_stag_database.py'
--config_file $__tool_directory__/csd_config.ini
--database_connection_string '$__app__.config.corals_database_connection'
--input '$input'
--output '$output'
]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Tabular file containing corrected values"/>
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} (process log) on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <!--Testing this tool is a bit difficult at the current time.-->
        </test>
    </tests>
    <help>
**What it does**

Accepts a tabular dataset containing corrected values and updates specified column values in the colony,
experiment, genotype, person, phenotype, reef and sample tables in the stag database.  The database must
be Postgres, and this tool exports the database into a file stored in a specified directory on disk before
the database is updated.

The first line of the tabular file must be the header, and the file must have the following columns in order.
 1.  affymetrix id
 2.  sample id
 3.  user specimen id
 4.  field call
 5.  sample depth
 6.  percent missing data coral
 7.  percent heterozygous coral
 8.  percent acerv coral
 9.  percent apalm coral
 10. bcoral genet id
 11. registry id
 12. dna extraction method
 13. dna concentration
 14. colony location
 15. colony latitude
 16. colony longitude
 17. colony depth
 18. reef name
 19. region
 20. reef latitude
 21. reef longitude
 22. geographic origin
 23. coral mlg clonal id
 24. coral mlg rep sample id
 25. genetic coral species call
 26. spawning
 27. sperm motility
 28. tle
 29. disease resist
 30. bleach resist
 31. mortality
 32. healing time
 33. sequence facility
 34. array version
 35. plate barcode
 36. collector last name
 37. collector first name
 38. organization
 39. collector email
 40. collection date
    </help>
    <citations>
        <citation type="doi">https://doi.org/10.1038/s41598-020-69101-z</citation>
    </citations>
</tool>