That is a poor way to approach what you want, one of the better methods being something like:
<script src="javascript.js"></script>
<script>Application.init("timer");</script>
But you could do something like this in PHP:
<?php header("Content-type: application/javascript"); ?>
var action = <?php echo $_GET["action"]; ?>;
console.log(action);
With the embed code:
<script src="javascript.php?action=timer"></script>
^^^^ Note we're looking at a PHP file.
If you're determined to have the .js?
extension, you can create a rewrite rule to accommodate that.