Command Line Interface¶
User guide¶
The command line interface has built in help. To display the help, please append -h to the program call, for example:
./patapy.py -h
The help option responds to arguments your provide, so you can get details about your method of choice with:
./patapy.py gsea -h
where gsea is the name of a method; likewise, you can display help for any of samples specification options (case/control/data), e.g.:
./patapy.py control -h
Predefined parsers¶
Parsers are defined in command_line.main
module.
Creating custom arguments and parsers¶
Please see declarative_parser module documentation for instructions.