Ok after some further digging it seems that iOS handles this automatically under two conditions:
- you have the app with the custom url scheme installed
- the sms is sent after the installation of the app with custom url scheme
As for Android, it is not supported out of the box even with the above conditions met. Possible solutions are installing 3rd party messaging apps to replace the stock messaging that handle schemes or creating a Cordova plug-in that would read your sms and parse custom url schemes manually (an example of this here).
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