If you wish to repackage software for use with Intune (which can only distribute MSI or EXE files), it is helpful to use Inno Setup 5 for this purpose. A script has been authored to work with the directory structure here to repackage software as an EXE for use with Intune.
Download the latest Inno Setup and save it to the \Install.MDT folder. Launch setup from there and install using default values.
There isn't much to configure other than to check the path to the Inno Setup utility in the \Repackage\Repackage.ps1 script.