bactopia-pubmlst-setup
One-time setup for interacting with the PubMLST API
Usage
bactopia-pubmlst-setup [OPTIONS]
Required Options
| Option | Type | Default | Description |
|---|---|---|---|
--client-id, -ci | STRING | The client ID for the site | |
--client-secret, -cs | STRING | The client secret for the site |
API Options
| Option | Type | Default | Description |
|---|---|---|---|
--site, -s | CHOICE (pubmlst, pasteur) | pubmlst | Only print citation matching a given name |
--database, -d | STRING | pubmlst_yersinia_seqdef | The organism database to interact with for setup. Note: the default is available from both PubMLST and Pasteur |
--save-dir, -sd | STRING | /home/rpetit3/.bactopia | The directory to save the token |
--force | BOOL | false | Force overwrite of existing token files |
Additional Options
| Option | Type | Default | Description |
|---|---|---|---|
--verbose | BOOL | false | Print debug related text |
--silent | BOOL | false | Only critical errors will be printed |
--version, -V | BOOL | false | Show the version and exit. |