Maybe, but it is hard to tell. Would you like to post back a share link to a history with an example? Small is great, so maybe just a slice of the data only run through this tool is fine. How to generate the link is in the banner of this forum, also here → How to get faster help with your question
Let’s start there, thanks! 
Update: to get this started, I am running the tool test at the EU server. I ran it twice – individual files and a collection of files – sometimes that reveals a small issue with a newer tool like this.
One note: the form was really exact about how the files need to be named, since the underlying tool is probably using that as a “sample identifier”. This means that if your input genome files originally have whitespace in the names (maybe from an upstream tool) you can either rename individual files with the pencil icon, or add the files into a list collection (the element identifiers will be used instead, and those never have spaces).
That will take some time to run. And I used some jargon here as you seem to know your way around Galaxy, but please ask about anything not clear!