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Tableau Server Published Data Sources are essentially read-only. What you would need to do is open the original workbook or data source that was published and then write Custom SQL on that, then extract it, and publish the new extract (either overwriting your original published source or creating a new one, depending on your need).
Thanks for the information Jonathan.
With this approach will I be able to schedule the data source refresh? will it retain the original data base connection details to refresh the data on the newly created/published data source (using the custom SQL)?