Usage problem in align subcommand

[elhossary]

Problem description:
The (--crossalign_cleaning) argument in align subcommand takes a string containing 3 types of separators (comma, colon, and semicolon), one of these separators (semicolon) was used to split the string by organism. Here the problem occurs, the semicolon can be parsed as statement termination in some CL like bash. The will cause to parse the first part only which will throgh an error in READemption.

Quick fix suggestion:
Use the argument ( nargs="+" ) in the argparse, and change the help message to instruct user to use spaces as a separator instead of semicolon. This arguent will automatically split by space and produce a list of organisms with associated seqids to be splitted by colon and commas as coded.
this will require to fix the parsing function (_string_to_species_and_sequence_ids) in reademptionlib/controller.py too, just directly iterate over the list if it contains more than one item.