Update: I see the problem. There are two versions of the tool – and one is older and should be avoided.
Tool panel
Use the first one, named: Remove counterions and fragments from a library of compounds(Galaxy Version 3.1.1+galaxy2)
We keep both because we keep everything (for reproducibility reasons) however we should probably hide the older version in the searches. I’ll work with our administrators to do this.
So – you can continue to work at UseGalaxy.org for this! 