Keyboard, Mouse shortcuts and Matlab

Hello. I need to control two different applications: to obtain some data in clipboard in one application, then to process those data in Matlab.

I'd like to use Keyboard, Mouse shortcuts programs for such purposes. For the moment I try several such kind of programs, like Auto Hot Keys (AHK), Mouse Recorder Pro, Mini Mouse Macro. All of these programs record into macro file keyboard and mouse movements into first program, but when I switch focus into Matlab window, such record is blocked. I didn't see records about switch to Matlab window and any records about commands I typed in Matlab window are also absent. It looks like Matlab blocked all attempts of such kind.

Do somebody know about possibility to control Matlab commands from similar keyboard, mouse shortcuts programs? Is it possible to "open" Matlab for such kind of control?

Thanks for constructive information