When setting external metadata using _handle_metadata_externally (e.g. local and lwr runners) use the requirments of the set metadata tool to determine dependencies. Resolves issue seen with missing samtools command when samtools is not in the path, but has been installed with the dependency system.
Use null object pattern to simplify logic related to no dependency manager being set.
Fixes bug introduced in 4241eff related to dependency_manager being None if tool_dependency_dir is not set.
Use toolbox.get_tool instead of toolbox.tools_by_id.get in tools api show().
Add missing requirement tags to converters, fixes Trello #1349.
Merge stable.