You do not need to load data into individual datasets. You’ll probably want to use Data Collections anyway to keep things organized.
Tutorials that cover advanced Upload functions (numerous files organized into data collections). Many tutorials in other topics also include the use of data collections.
That said if you really do need the files, or some set of the files, as individual datasets, use FTP to load the data in batch. Or place the data in a location where it can be retrieved by URL. Multiple URLs can be pasted in at once.
Should you be working at your own Galaxy server, where you are the administrator, data can be loaded in batch into Data Libraries directly from the file system (or other ways). The original FAQ Loading Data posted includes links to
Admin docs that cover the how-to. If you are working with this many datasets, you might need to use your own Galaxy (processing requirements will exceed what is available at public servers).
Note: An uncompressed
.tar archive (no .gz) can be sent through the Upload tool, but only the first dataset is extracted and loads into the Galaxy history. This is noted in the Loading Data FAQ, but is sometimes missed, and is almost always not the desired result anyway.
Hope that helps with some options!