I have checked the Nios II Software Developer's Handbook and I only found their reference to do it manually (File-->Import-->Nios II Software Build Tools Project-->Project_Location).
Ideally I would like to see in the "explorer tab" all the projects that were previously created with the command line tools without having to import them from the GUI.
The idea to have all projects visible once the eclipse GUI is launched came because when I made a similar (in functionality ) tcl script for the MicroBlaze Xilinx Processor, it was straightforward. I open the eclipse GUI after executing my build script and all the projects I created were already visible in the project explorer tab.
Thank you in advance!
If you create your project in command line environment, you can view it in eclipse GUI explorer unless you import the project to the eclipse explorer. There is no other way to do that.