add stdout as type for output

Author: khillion

cwlgen/__init__.py

@@ -18,7 +18,7 @@
 from .import_cwl import parse_cwl
 
 logging.basicConfig(level=logging.INFO)
-LOGGER = logging.getLogger(__name__)
+_LOGGER = logging.getLogger(__name__)
 
 
 #  Function(s)  ------------------------------
@@ -60,7 +60,8 @@ def __init__(self, tool_id=None, base_command=None, label=None, doc=None,
         are stored in lists which are initialized empty.
         '''
         if cwl_version not in CWL_VERSIONS:
-            LOGGER.warning("CWL version is not recognized as a valid version.")
+            _LOGGER.warning("CWL version {} is not recognized as a valid version.".format(cwl_version))
+            _LOGGER.warning("CWL version is set up to {}.".format(DEF_VERSION))
             cwl_version = DEF_VERSION
         self.cwlVersion = cwl_version
         self.id = tool_id

cwlgen/elements.py

@@ -8,10 +8,11 @@
 CWL_SHEBANG = "#!/usr/bin/env cwl-runner"
 CWL_VERSIONS = ['draft-2', 'draft-3.dev1', 'draft-3.dev2', 'draft-3.dev3',
                 'draft-3.dev4', 'draft-3.dev5', 'draft-3', 'draft-4.dev1',
-                'draft-4.dev2', 'draft-4.dev3', 'v1.0.dev4', 'v1.0', None]
+                'draft-4.dev2', 'draft-4.dev3', 'v1.0.dev4', 'v1.0']
 DEF_VERSION = 'v1.0'
 CWL_TYPE = ['null', 'boolean', 'int', 'long', 'float', 'double', 'string', 'File',
-            'Directory', None]
+            'Directory', 'stdout', None]
+DEF_TYPE = 'null'
 
 
 class Parameter(object):
@@ -40,8 +41,9 @@ def __init__(self, param_id, label=None, secondary_files=None, param_format=None
         :type param_type: STRING corresponding to CWLType
         '''
         if param_type not in CWL_TYPE:
-            _LOGGER.warning("The type is incorrect for the parameter.")
-            param_type = None
+            _LOGGER.warning("The type {} is incorrect for the parameter.".format(param_type))
+            _LOGGER.warning("type is set to {}.".format(DEF_TYPE))
+            param_type = DEF_TYPE
         self.id = param_id
         self.label = label
         self.secondaryFiles = secondary_files