Want to implement in PHP form

I love the feel of this plugin, and it looks like it will solve my max upload file size problem with Fatcow. I love the file extension filter the most. Great work. My issue is that I would like to implement this plugin within my PHP front-end uploader. The shortcode generates fine within the admin, but it will not read the shortcode within a PHP file.

Is there a way for me to implement this plugin via PHP?

http://ww.wp.xz.cn/plugins/wp-file-upload/