Merge pull request #1903 from satra/fix/clirun

fix: store undefined by default so that xor checks don't trip

Author: chrisgorgo

nipype/scripts/utils.py

@@ -60,9 +60,12 @@ def add_args_options(arg_parser, interface):
     inputs = interface.input_spec()
     for name, spec in sorted(interface.inputs.traits(transient=None).items()):
         desc = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name) + 2:]
+        # Escape any % signs with a %
+        desc = desc.replace('%', '%%')
         args = {}
 
         if spec.is_trait_type(traits.Bool):
+            args["default"] = getattr(inputs, name)
             args["action"] = 'store_true'
 
         if hasattr(spec, "mandatory") and spec.mandatory: