Julia,

You can control Skyline from the commandline using a program called SkylineRunner.exe which you can download from the same page where you install Skyline:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=SkylineInstall_64_20-1

You can find documentation about the Skyline commandline here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=documentation

You can write commandline scripts that export reports from Skyline.
Is that what you were asking?
-- Nick

Hi Nick,

Thanks for your message. Yes, the documentation you sent me should be enough and will contact you in case I face any troubles.

Best,
Julia

Please note that the PDF is out of date, and you should pay attention to the note on this page telling you how to get the current command-line documentaion.

NOTE: for the most current command-line documentation, run SkylineRunner.exe or SkylineCmd.exe without any command-line arguments. The same information can be found in the Skyline user interface at Help > Documentation > Command Line.