how to write a JCL which can check the presence of a specific file at a specific time
This cannot be done -- period. JCL does only one thing - execute programs. You can write code and then write JCL to execute that code, if desired.
Furthermore, what you want to do is generally accomplished by the site scheduling software; most of them can identify when a new file is allocated on the system and start up a job based on the presence of that job. This also removes human intervention from the process, allowing you (or whomever) to take a vacation every now and then.