If you want to test automatically you can use the Unit testing module, see the appstore: https://appstore.home.mendix.com/link/app/390/Mendix/UnitTesting
You can use SoapUI for integration tests, and UI testing with Selenium, see this webinar: http://ww2.mendix.com/expert-webinar-quality-assurance.html
The question is what are your high risk functionalities that needs to be tested? Based on that answer you can make a better selection for which tools you need.
In addition the cordova webapp is also available on a browser, but you cannot test or use the native widgets i.e. camera widget. To my knowledge these functionalities cannot be automatically tested on phonegap.
Wilfried already provided good advice in his answer.
To test your microflow logic, use the Unit Testing module from Mendix.
For functional acceptance testing you won't get along with Selenium IDE. Selenium itself only supports web components. It does not support the native components of your Cordova/Phonegap app.
The Application Test Suite (ATS) will soon support mobile test automation. We're building on top of Appium to support both web and native elements of your hybrid apps. You will be able to test your apps on real devices or on emulators. We're hiding the complexity of Selenium/Appium behind a set of intuitive actions with built-in Mendix support.
Disclaimer: I'm working for Mansystems where I'm responsible for the development of the Application Test Suite