For questions about Biobakery specific tools or data, asking them directly at their forum will get definitive answers.
That said, this is what we know about your question:
When using this version of the MetaPhlAn tool, if you are able to load a fasta database into your Galaxy history, you can use it directly by toggling the option Database with clade-specific marker genes to From history.
At the link you shared, those appear to be archives. If they contain just one file, then you can load by URL directly into the Upload tool (use all default settings!).
If those archives contain more than one file, download to somewhere else, uncompressed, then load just the fasta file you want to use into Galaxy by local file browsing.
Since you are administrating your own server, I’ll also share some more options, and complexities!
- The Biobakery server hosts a custom version of many tools.
- Those versions may be in the Main ToolShed but also maybe the Test ToolShed.
- Some of those tool version may not work well in more current Galaxy releases.
- And, some of those tool versions have a Data Manager tool available to index server hosted indexes. Please see Hands-on: Reference Data with Data Managers / Reference Data with Data Managers / Galaxy Server administration.
- You could also probably add indexes manually. There isn’t a step-by-step for this … but I would suggested reviewing the DM tools, and inspecting the files in the source repository, your local server tool-data files, the indexes from Biobakery to figure out the connections needed.
Search here with the tool name as a keyword to review:
- Main ToolShed at https://toolshed.g2.bx.psu.edu/
- Test ToolShed at https://testtoolshed.g2.bx.psu.edu/
Hope this helps, and you can ask follow up questions once oriented. 