The problem is that you're mixing up the client (JS) and the server (PHP). PHP is executed on the server and produces some HTML which gets sent to the browser ("the client"). Browsers cannot run PHP because it's a server-side language.
You should evaluate what the desired interaction is between the client and the server here. For example, if you just need to execute some PHP to pass data to JavaScript, you can build up a JavaScript object:
<script type="text/javascript">
<?php // include script that gives you back some data, e.g.: ?>
<?php $somePhpData = array('red', 'yellow', 'blue'); ?>
<?php $jsonData = json_encode($somePhpData); ?>
var dataFromPhpScript = <?php echo $jsonData; ?>
// do something with the data
</script>
Otherwise, if you really need JavaScript to trigger a PHP script running, you're essentially doing AJAX. You'll likely want some sort of REST API. The idea is that you expose a URL from PHP that the JavaScript can call:
<script type="text/javascript">
jQuery(document).ready(function() {
function startScript(scriptName, success) {
$.get('/path/StartScript.php?script-name=' + scriptName)
.done(success)
.fail(fail);
}
startScript('name-of-php-script', function(data) {
// trigger some JavaScript that relies on the output of the PHP script
});
});
</script>