added choices to --tree_builder and other args
#207
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Without choices under `-t`, there is nothing to protect the user from doing e.g., `-t 16`. This would happen if the end-user tried to use `-t` to mean `--threads` (which it doesn't). Without the choices, the error is uninformative (try for example `run_gubbins.py -v -t 2 alignment.fasta`).
andrewjpage
reviewed
Nov 27, 2017
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Gladly |
nickjcroucher
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this pull request
Oct 6, 2021
added choices to `--tree_builder` and other args
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Without
choicesunder-t, there is nothing to protect the user from doing e.g.,-t 16. This would happen if the end-user tried to use-tto mean--threads(which it doesn't). Without the choices, the error from incorrectly using-tis uninformative (try for examplerun_gubbins.py -v -t 2 alignment.fasta).For consistency, have added
choicesto--converge_method, and--raxml_model.