Fix some things / add complicated argument parsing that doesn't really work right
Fix some things / add complicated argument parsing that doesn't really work right

SciLifeLab/scilifelab,senthil10/scilifelab,SciLifeLab/scilifelab,senthil10/scilifelab,jun-wan/scilifelab,SciLifeLab/scilifelab,senthil10/scilifelab,kate-v-stepanova/scilifelab,jun-wan/scilifelab,kate-v-stepanova/scilifelab,jun-wan/scilifelab,kate-v-stepanova/scilifelab,jun-wan/scilifelab,kate-v-stepanova/scilifelab,SciLifeLab/scilifelab,senthil10/scilifelab