I assume you are running storm in cluster mode on a remote machine. In this case, storm suggests you to use the storm jar command. It is true, that this by default accepts just a few arguments since it is internally using a python script that is calling java.
But it seems to be possible to start storm with a java command as well and pass command line commands to that - see this link .

Another method to pass some variables to topology is the environment variable substitution in a flux file and run

name: topo${ENV-YOURVAR}

when run in bash looks like:

export YOURVAR=test
storm jar yourtopo.jar org.apache.storm.flux.Flux yourtopo.flux -e

Flag -e tells storm to substitute environment variables in the flux file