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Tools in a room can be hidden from certain user groups through the "The tool is visible for" customising option.
The purpose of this hiding is usually to keep the left hand side of the room tidy and simple, and provide the pupils with access to the contents through links e.g. from the frontpage of the room.
It is important to notice that this only hides the tool button, while the contents within the tool are still available for all users in the room. This includes the possibility of browsing through the contents of the tool after clicking to view the folder structure in the top right corner.
If you wish to specifically make some contents available only to some users, please use customised folders. See e.g. here. You can also make a folder hidden hence rendering it invisible in the resource tool while still granting access to the folder contents through links.