Hi @matias
Please see this topic for where to make the request to the EU server administrators.
However, this particular tool doesn’t seem to be quite ready to use! There is no development repository and the entire content appears to be just two lines in the Main ToolShed (what you linked) and the same is in the Test ToolShed (here). It might be a placeholder or a test.
The underlying tool does seem to be open source, so this could probably be wrapped for Galaxy, unless there is something special about it that I missed!
And I don’t see that the IUC is working on it. You could make a request to them for a new tool to be wrapped. Add this under Issues and link in the original software and what is currently in the ToolShed for context. You can also link this topic. Please let us know if you would like help with this!
Finally, for strain identification via mapping and variant calls, you might be interested in this 
GTN tutorial. The logic and rules around typing will vary by species, but most if not all of what is applied in El Gato software should be possible in Galaxy, too.
I hope this helps! Follow up questions are welcome and please correct me if I misunderstood anything! 