I had figured out that I needed to restart the server after changing config files, and the debug info you sent was helpful.

On Mon, Nov 19, 2012 at 10:38 AM, James Taylor <james@jamestaylor.org> wrote:

On Fri, Nov 16, 2012 at 2:35 PM, Joshua Orvis <jorvis@gmail.com> wrote:
> If I removed that line how is it still part of the call? Is Galaxy caching
> the xml tool files?

Did you restart Galaxy? Tool configuration files are read at startup.
You can also force a tool to be reloaded in the admin interface.

> Also, is there a way to see the precise commands being
> executed by Galaxy for any particular tool?

These are logged at the debug level, either to the console or
paster.log depending on how you start Galaxy.