Short codes are not intended to be used in .php files; they're intended to be used in the content editor. With that said, you can still use the do_shortcode() function and pass it the short code to execute.
What I would do is just write the code I needed in your .php (template) file instead. You're going to have to do that anyway if you were to create a short code.
If you're looking for a short code you can try searching with your editor for "add_shortcode" in the plugin's folder. If there are no results than that plugin has no short codes.