Referencing files in cron jobs versus format when running from URL

I have a file that works from the URL like: www.mysite.com/cronjob.php and this file includes references to uploaded files like this: /home/mysite/public_html/dir/subdir/filename.xml and this is used in functions like filemtime(). The uploaded files are found on the server using the above path in the code of the php file. However, when I cron the php file from the server using: /ramdisk/bin/php4 -q /home/mysite/public_html/cronjob.php (using the server cPanel Cron Manager Linux command type set up page), the php file does not find the uploaded files, presumably because the above format of /home/mysite/public_html/dir/subdir/filename.xml needs to be a different path. This must be familiar to many, can you help in suggesting change in path required? John