docker tools and -w option

i have a local galaxy instance configured to running tools that support docker.
I’m writing some wrapper for some docker tools.
I want to remove of the -w option that is given by the runner to the docker command because the R scripts that runs inside the docker use the command setwd that cause me to have error Error in setwd("/home") : cannot change working directory.
I can’t edit the R scripts because I didn’t write them.
I can change the job_conf.xml file in order to remove from the docker command the -w option?