You can mock opening the app from URL to test your app's deep link handling mechanism.
await device.relaunchApp({url: url});
Example:
describe('relaunchApp', () => {
before(async () => {
await device.relaunchApp({url: 'scheme://some.url'});
});
it('should tap successfully', async () => {
await expect(element(by.label('a label'))).toBeVisible();
});
});
await device.openURL('scheme://some.url');