Increase consistency in I/Os #159
Description
Increasing consistency in I/Os would be to the benefit of the package: some scripts require a single file at the input, whereas others assume a folder is given (wm_append_clusters.py, or wm_harden_transform.py, the last one ). Due to this inconsistent behavior, the shell scripts (wm_apply_ORG_atlas_to_subject.sh) get more complicated as for each Python script call, further work needs to be done to adapt to the file vs. folder input argument model, adding more code that is specific to the Python script call. It is probably best to use nargs=+ and a file-based approach in Python scripts, so that the behavior is consistent. and the shell script could use a single function that lists all e.g. tractography files, and that can be reused for those Python scripts requiring multiple input files.
Besides, wm_harden_transform.py, at its minimum, requires a single file, so it should accept a single file at its input. There may be other scripts that do such a behavior as well, and could benefit from increased consistency.