1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
|
from easydev import SmartFormatter
import argparse
class Options(argparse.ArgumentParser):
def __init__(self, prog="test"):
usage = """standalone test"""
description="""blabla"""
super(Options, self).__init__(usage=usage, prog=prog,
description=description, formatter_class=SmartFormatter)
self.add_argument("--config-params", dest="config_params",
type=str,
help="""FORMAT|Overwrite any field in the config file by using
the following convention. A config file is in YAML format
and has a hierarchy of parametesr. For example:
samples:
file1: R1.fastq.gz
file2: R2.fastq.gz
bwa_mem_phix:
mem:
threads: 2
""")
def test():
options = Options()
try:
options.parse_args(["--help"])
except:
pass
|
