Previously we defaulted to installing tool dependencies and repository dependencies,
and this could be overriden for each repository.
I would like to be able to specify this on the top level of the tool_list.yml and on the commandline,
as well as for each repository separately. So the new aspect here would be the top level parameter in the tool_list.yml (like we are currently handling the api_key and galaxy_url).
Previously we defaulted to installing tool dependencies and repository dependencies, and this could be overriden for each repository. I would like to be able to specify this on the top level of the tool_list.yml and on the commandline, as well as for each repository separately. So the new aspect here would be the top level parameter in the tool_list.yml (like we are currently handling the api_key and galaxy_url).