gistfile1.txt

function jens($matches)
{ 
    $path = '';
    $parts = explode(',', $matches[1]);
    foreach($parts as $match)
        $path .= '/' . str_replace('\'', '', trim($match));
    
    return $path;
}

$replaced = preg_replace_callback('/<\?php myclass->my_function\((.*?)\); \?>/', 'jens', $str);

echo $replaced;