Shell Programming and Scripting

Status quo is, within a web application, which is coded completely in php (not by me, I dont know php), I have to fill out several fields, and execute it manually by clicking the "go" button in my browser, several times a day.

Thats because:
The script itself pulls data (textfiles) from a folder, and works them off one by one. As PHP has limitations regarding execution timings (server restrictions aswell), it can be, that not all the data (textfiles) are executed, so the php-script has to be restartet again and again, where it continues, where it has stopped its work.

My idea is, to run that php-script somehow, as a cron job where I have to set the maximum data to be executet, (maybe 50 textfiles), and run the script every 5 minutes, with these parameters.

What would be the wisest approach for this task? Is it generally possible?

edit:
I could find out, that I can run php from shell and also am able to give it the parameters it need, for example like this:

php functions.php -r '$_GET[parameterX]="whattever";'

Is there something like a "debug mode" which I could switch on, in order to see what parameters go to what variables or what functions are called and so on, when I call the script from the web interface.

$dbg=1; does not seem to help me in any way....

Preferebally debug information should be written into a text file.

edit 2:
So far, I am digging through the code of the php-file corrosponding to the dialog screen, and collecting & writing down the variables of the settings I need to make.

Someone please stop me, if I am on the wrong way and wasting my time.. 8-)