def add_arguments(self, parser):
RunCommand.add_arguments(self, parser)
parser.add_argument("files", nargs="+",
help="Variants files")
parser.add_argument("-p", "--id", dest="project_id", metavar="NAME",
help="Define the project identifier. Required.")
parser.add_argument("-a", "--assembly", dest="assembly", metavar="ASSEMBLY",
choices=["hg18", "hg19"], default="hg19",
help="Define the assembly [hg18, hg19]. Default is hg19.")
parser.add_argument("--single-tumor", dest="single_tumor", action="store_true", default=False,
help="Run a single tumor analysis instead of the regular cohort analysis.")
def add_arguments(self, parser):
RunCommand.add_arguments(self, parser)
parser.add_argument("paths", nargs="+",
help="Projects paths")
parser.add_argument("-i", "--include", dest = "include", metavar = "ID", action="append",
help = "Include project which id=ID")
parser.add_argument("-I", "--include-regex", dest = "include_regex", metavar = "REGEX", action="append",
help = "Include project which id matches REGEX")
parser.add_argument("--include-from", dest = "include_from", metavar = "FILE", action="append",
help = "Include project which id found in file FILE")
parser.add_argument("-e", "--exclude", dest = "exclude", metavar = "ID", action="append",
help = "Exclude project which id=ID")
parser.add_argument("-E", "--exclude-regex", dest = "exclude_regex", metavar = "REGEX", action="append",
help = "Exclude project which id matches REGEX")
parser.add_argument("--exclude-from", dest = "exclude_from", metavar = "FILE", action="append",
help = "Exclude project which id found in file FILE")
