You can use wpa_supplicant as WPS External Registrar (ER) to configure a device. The command below starts the ER, IP address is optional.
wps_er_start [IP address]
Then use the AP configuration from a locally configured network (e.g., from wps_reg command); this does not change the AP's configuration, but prepares a configuration to be used when adding a new device to the AP's network.
wps_er_set_config <UUID> <network id>
Finally, to configure the device that wants to join the AP
wps_er_pin (use CE PIN)
Here's some more information about these commands.