You can use velocity to have "scriptable" sql templates that you can use to work with the files in a flexible way. You have primitive statements like conditionals and loops to build your sql commands.
But I strongly suggest to use prepared statements and/or stored procedures.
Building your SQL the way you're planning will make you vulnerable to SQL injection, the DB server will not be able to cache the sql queries (which will lead to bad performance).
BTW: You can store the definition of the prepared statements in files too. This is not the best solution but pretty close to it and you get the benefit of SQL-injection protection and performance.
When your SQL schema is not build to work with prepared statements or stored procedures you might want to rethink your schema. Maybe it needs to be refactored.
