You'll have to add the javascript somewhere, and echo it on a shortcode.
Quick example (I just dropped out of PHP, too much work to write echo)
function slider_func() {
?>
<script>
jQuery(document).ready(function($) {
$('#banner-fade').bjqs({
height: 350,
width: 980,
responsive: true
});
});
</script>
<?php
}
add_shortcode( 'end_slider', 'slider_func' );
Then you'll have to add that somewhere where it's called, a plugin comes to mind, and there you could put this in an external file and use the more proper wp_enqueue_script to add it with jQuery as a depedency