def parse_args():
class FullPaths(argparse.Action):
"""Expand user- and relative-paths"""
def __call__(self, parser, namespace, values, option_string=None):
setattr(namespace, self.dest, os.path.abspath(os.path.expanduser(values)))
usage = " "
parser = argparse.ArgumentParser(description="STAR-SEQR Parameters:", epilog=usage)
parser.add_argument('-j', '--json', type=str, required=False, action=FullPaths,
default='/data/input/AppSession.json',
help='json input file from basespace app')
parser.add_argument('-s', '--sample_path', type=str, required=False, action=FullPaths,
default='/data/input/samples/',
help='default path for samples')
parser.add_argument('-r', '--results_path', type=str, required=False, action=FullPaths,
default='/data/output/appresults/',
help='default path for results')
parser.add_argument('-t', '--scratch_path', type=str, required=False, action=FullPaths,
default='/data/scratch/',
help='default path for scratch')
args = parser.parse_args()
return args
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