Welcome @Andrea_Trigueros
The datatypes with this tool are handled a bit differently from tools with the common shared datatypes. The developer is working to add the custom types to our registry but I think that is still a request as far as I know (no tickets against Galaxy are open yet).
We also have some help at this forum!
Uploading PLINK data → plink and pbed format
Downloading PLINK data → First, download the file from Galaxy. Next, you can adjust the file extensions directly. This will allow tools outside of the Galaxy ecosystem, that would normally use the data, to recognize it. This works for any exotic file type that is not (yet) handled by Galaxy itself.
Example: This is similar to a README.md file you may download from somewhere – it needs to have the .txt extension added in before a word processing tool will understand that it is a “text file”.
Please give this a try and let us know if it works for you! 