Autopano Giga will not have a lot of command line option : you can just provide a folder, some images or a .pano project file in the command line and it will either parse the folder to find picture, put all images in a group or open the .pano. That's all.
If you need command line scripting, it's autopano server only. This product is already available since one year but for the moment it's is reserved for industrial partners to add stitching feature to their product. If you have such a project, don't hesitate to contact us directly.