I am trying to create a custom keyboard on an iPad application. But each time the input get the focus, the native iPad keyboard pops up. How can I prevent this, in JavaScript.>
I don't think you can prevent the keyboard from appearing on input fields. However you could create an html element that looks just like an input field with CSS and handle the onClick event to show your custom keyboard.
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You should checkout Sencha Touch for developing Web Apps for iOS devices.