Creat a bootable ISO file from the command prompt?

I have a bootable flash drive with a WINPE install on it, and I would like to be able to convert said bootable usb to an iso file from a batch or powershell file. I’ve tried using tools like Folder2iso, but it does not support creating an iso file that is bootable. ImgBurn seemed promising but not matter how much I mess with the config, the iso never boots, plus it is not easy to make portable which is something I need for the program I am creating.