Merge pull request #5 from EiffL/master

Adds export of arguments in command line tool

Author: khillion

.gitignore

@@ -1,3 +1,7 @@
 test/__pycache__
 cwlgen/__pycache__
 doc/build/
+.ropeproject/
+build/
+cwlgen.egg*
+dist/

cwlgen/__init__.py

@@ -101,6 +101,10 @@ def export(self, outfile=None):
         # Treat doc for multiline writting
         if self.doc:
             cwl_tool['doc'] = literal(self.doc)
+
+        # Add Arguments
+        cwl_tool['arguments'] = [in_arg.get_dict() for in_arg in self.arguments]
+
         # Add Inputs
         cwl_tool['inputs'] = {}
         for in_param in self.inputs:
@@ -128,7 +132,7 @@ def export(self, outfile=None):
 
         if requirements:
             cwl_tool['requirements'] = requirements
-        
+
         # Write CWL file in YAML
         if outfile is None:
             six.print_(CWL_SHEBANG, "\n", sep='')
@@ -293,8 +297,8 @@ class CommandLineBinding(object):
     Describes how the handle an input or an argument.
     '''
 
-    def __init__(self, load_contents=False, position=None, prefix=None, separate=False,
-                 item_separator=None, value_from=None, shell_quote=False):
+    def __init__(self, load_contents=False, position=None, prefix=None, separate=True,
+                 item_separator=None, value_from=None, shell_quote=True):
         '''
         :param load_contents: Read up to the fist 64 KiB of text from the file and
                               place it in the "contents" field of the file object
@@ -327,7 +331,7 @@ def get_dict(self):
         :return: dictionnary of the object
         :rtype: DICT
         '''
-        dict_binding = {k: v for k, v in vars(self).items() if v is not None and v is not False}
+        dict_binding = {k: v for k, v in vars(self).items() if v is not None}
         return dict_binding
 
 
@@ -427,7 +431,7 @@ def __init__(self, docker_pull=None, docker_load=None, docker_file=None,
 
     def _to_dict(self):
         """
-        Add this requirement to a dictionary description of a 
+        Add this requirement to a dictionary description of a
         tool generated in an export method.
 
         """