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It's a pipeline - PGAP tool is included as folder instead of Conda package:
https://toolshed.g2.bx.psu.edu/repository?repository_id=b0fc108867dbc651&changeset_revision=e0c913351502
If it works, and we can't offer an alternative (NCBI-ready ouput), I don't see why we shouldn't provide the user with the functionality? PGAP is made by NCBI so it seems reasonable for us to have it on GA.
Ticket: https://support.ehelp.edu.au/a/tickets/107774