This is from the tool version included in the Tool Shed repository "mothur_toolsuite"?
If so, the parameter "iters - Number of iterations to try (default 1000):" is a variable and can be modified. Expected impact on performance can be researched in the underlying source tool documentation or by testing. Specific inputs will almost certainly be a factor. Scale up resources as necessary, if possible (when using a CloudMan or local Galaxy), being aware that not all computations scale well (some jobs become exponentially large and unable to run at a satisfactory rate, or at all, under any configuration).
If you are using this tool at a a public Galaxy site (it is not on the Main Galaxy instance at http://usegalaxy.org), then it could be that this has been hard-set by the administrators of the instance. You could contact them about it (contact information is generally on the middle splash page of the browser), but I suspect that moving to your own cloud Galaxy might be necessary in a case such as this.
Hopefully this leads to a solution, Jen, Galaxy team