As a computational reproducibility platform, Code Ocean focuses on publishing reproducible code. In practice, this means that all analyses should be set to run headlessly -- meaning without user input during runtime, and also without any display popping up while code is executing.
Accordingly, any code published on Code Ocean that that requires user input -- such as selecting points on a screen -- will need to be modified to either accept inputs at the outset (via an interface) or to select inputs on a user's behalf.
This has three main implications for your capsule.
First, write a master script that executes all of your code without requiring any user input or selection, and without pausing in the middle.
Second, save your files explicitly to the /results folder rather than expecting results to pop up.
Third, if you wish to allow users to set their own parameters, either clearly indicate how to do so in your master script, or set up an interface to make the process straightforward for them.