Assuming those are standard Unix timestamps, you can trivially extract/mangle dates any way you want. If your workweek corresponds to a standard calendar week, it's even easier:
SELECT user_id, clock_in-clock_out
FROM yourtable
GROUP BY WEEK(FROM_UNIXTIME(clock_in))
This will just group by single weeks, but this is just to give you a general idea.
MySQL has a very wide variety of date/time functions that can be used for this: http://dev.mysql.com/doc/refman/5.5/en/date-and-time-functions.html#function_week