function var_piwik() {
if (!is_admin()) {
wp_register_script( 'piwik', get_template_directory_uri() . '/js/piwik.js','',null,true);
wp_enqueue_script('piwik');
}
}
add_action('init', 'var_piwik');
<script type="text/javascript">
var _paq = _paq || [];
(function(){
var u=(("https:" == document.location.protocol) ? "https://analytics.mysite.com/" : "http://analytics.mysite.com/");
_paq.push(['setSiteId', 1]);
_paq.push(['setTrackerUrl', u+'piwik.php']);
_paq.push(['setVisitorCookieTimeout', '604800']);
_paq.push(['setSessionCookieTimeout', '0']);
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
var d=document,
g=d.createElement('script'),
s=d.getElementsByTagName('script')[0];
g.type='text/javascript';
g.defer=true;
g.async=true;
s.parentNode.insertBefore(g,s);
})();
</script>
then add
wp-content/js/piwik.js to W3 Total Cache Minify