While Galaxy tools can be run line-command, we do not recommend running this particular tool with this option outside of Galaxy. Doing so will likely not produce the desired results.
Instead, run the tool within Galaxy. You can always download the output and use it locally.
If you program, the API could be one way to accomplish the task without needing to go through the GUI. Bioblend is a very popular choice: https://galaxyproject.org/develop/api/
Thanks! Jen, Galaxy team