I have a web app calling a native app on android via an iframe intent which does not work in chrome 25 according to the following....
https://developers.google.com/c
You can no longer use an iframe and custom protocol to open a native app.
You can however use the existing intent:// syntax to launch and intent and pass it data, it has the added benefit of taking the user to the Play store if it is not installed.
You either encode the data in the "path" part of the syntax as documented so you could have intent://play/?a=1#Intent;......;end; or you could encode it as an Extra.