Repository: DataBiosphere/toil

Issue:
toil status --help doesn't work
```
(venv)ubuntu@ip-172-31-22-39:~$ toil status --help
Traceback (most recent call last):
  File "/home/ubuntu/venv/bin/toil", line 11, in <module>
    sys.exit(main())
  File "/home/ubuntu/venv/local/lib/python2.7/site-packages/toil/utils/toilMain.py", line 25, in main
    module.main()
  File "/home/ubuntu/venv/local/lib/python2.7/site-packages/toil/utils/toilStatus.py", line 59, in main
    options = parseBasicOptions(parser)
  File "/home/ubuntu/venv/local/lib/python2.7/site-packages/toil/lib/bioio.py", line 262, in parseBasicOptions
    options = parser.parse_args()
  File "/usr/lib/python2.7/argparse.py", line 1690, in parse_args
    args, argv = self.parse_known_args(args, namespace)
  File "/usr/lib/python2.7/argparse.py", line 1722, in parse_known_args
    namespace, args = self._parse_known_args(args, namespace)
  File "/usr/lib/python2.7/argparse.py", line 1928, in _parse_known_args
    start_index = consume_optional(start_index)
  File "/usr/lib/python2.7/argparse.py", line 1868, in consume_optional
    take_action(action, args, option_string)
  File "/usr/lib/python2.7/argparse.py", line 1796, in take_action
    action(self, namespace, argument_values, option_string)
  File "/usr/lib/python2.7/argparse.py", line 996, in __call__
    parser.print_help()
  File "/usr/lib/python2.7/argparse.py", line 2329, in print_help
    self._print_message(self.format_help(), file)
  File "/usr/lib/python2.7/argparse.py", line 2303, in format_help
    return formatter.format_help()
  File "/usr/lib/python2.7/argparse.py", line 281, in format_help
    help = self._root_section.format_help()
  File "/usr/lib/python2.7/argparse.py", line 211, in format_help
    func(*args)
  File "/usr/lib/python2.7/argparse.py", line 211, in format_help
    func(*args)
  File "/usr/lib/python2.7/argparse.py", line 517, in _format_action
    help_text = self._expand_help(action)
  File "/usr/lib/python2.7/argparse.py", line 603, in _expand_help
    return self._get_help_string(action) % params
TypeError: %d format: a number is required, not dict
```



Discussion:

Resolving patch:
diff --git a/src/toil/utils/toilStats.py b/src/toil/utils/toilStats.py
--- a/src/toil/utils/toilStats.py
+++ b/src/toil/utils/toilStats.py
@@ -13,7 +13,7 @@
 # limitations under the License.
 
 
-""" Reports the state of your given jobtree.
+""" Reports data about the given toil run.
 """
 from __future__ import absolute_import
 import logging
diff --git a/src/toil/utils/toilStatus.py b/src/toil/utils/toilStatus.py
--- a/src/toil/utils/toilStatus.py
+++ b/src/toil/utils/toilStatus.py
@@ -49,11 +49,11 @@ def main():
     
     parser.add_argument("--verbose", dest="verbose", action="store_true",
                       help="Print loads of information, particularly all the log files of \
-                      jobs that failed. default=%default",
+                      jobs that failed. default=%(default)s",
                       default=False)
     
     parser.add_argument("--failIfNotComplete", dest="failIfNotComplete", action="store_true",
-                      help="Return exit value of 1 if toil jobs not all completed. default=%default",
+                      help="Return exit value of 1 if toil jobs not all completed. default=%(default)s",
                       default=False)
     parser.add_argument("--version", action='version', version=version)
     options = parseBasicOptions(parser)


Test patch: