remove id field from input and output and change order of attributes

Author: khillion

cwlgen/__init__.py

@@ -24,6 +24,7 @@
 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]
+DEF_VERSION = 'v1.0'
 CWL_TYPE = ['null', 'boolean', 'int', 'long', 'float', 'double', 'string', 'File',
             'Directory', None]
 
@@ -37,6 +38,8 @@ class CommandLineTool(object):
     Contain all informations to describe a CWL command line tool.
     '''
 
+    __CLASS__ = 'CommandLineTool'
+
     def __init__(self, tool_id=None, base_command=None, label=None, doc=None,
                  cwl_version=None, stdin=None, stderr=None, stdout=None):
         '''
@@ -63,22 +66,22 @@ def __init__(self, tool_id=None, base_command=None, label=None, doc=None,
         and requirements (:class:`cwlgen.Requirement` objects)
         are stored in lists which are initialized empty.
         '''
-        self.id = tool_id
-        self.baseCommand = base_command
-        self.label = label
-        self.doc = doc
         if cwl_version not in CWL_VERSIONS:
             LOGGER.warning("CWL version is not recognized as a valid version.")
-            cwl_version = None
+            cwl_version = DEF_VERSION
         self.cwlVersion = cwl_version
-        self.stdin = stdin
-        self.stderr = stderr
-        self.stdout = stdout
+        self.id = tool_id
+        self.label = label
+        self.requirements = []  # List of Several object inhereting from [Requirement]
+        self.hints = []
         self.inputs = []  # List of [CommandInputParameter] objects
         self.outputs = []  # List of [CommandOutputParameter] objects
+        self.baseCommand = base_command
         self.arguments = []  # List of [CommandLineBinding] objects
-        self.requirements = []  # List of Several object inhereting from [Requirement]
-        self.hints = []
+        self.doc = doc
+        self.stdin = stdin
+        self.stderr = stderr
+        self.stdout = stdout
         self.successCodes = []
         self.temporaryFailCodes = []
         self.permanentFailCodes = []
@@ -88,7 +91,7 @@ def export(self, outfile=None):
         Export the tool in CWL either on STDOUT or in outfile.
         '''
         cwl_tool = {k: v for k, v in vars(self).items() if v is not None and v != []}
-        cwl_tool['class'] = 'CommandLineTool'
+        cwl_tool['class'] = self.__CLASS__
         # Add Inputs
         if self.inputs:
             cwl_tool['inputs'] = {}
@@ -209,6 +212,7 @@ def get_dict(self):
         :rtype: DICT
         '''
         dict_in = Parameter.get_dict(self)
+        del dict_in['id']
         if self.inputBinding:
             dict_in['inputBinding'] = self.inputBinding.get_dict()
         return dict_in
@@ -253,6 +257,7 @@ def get_dict(self):
         :rtype: DICT
         '''
         dict_out = Parameter.get_dict(self)
+        del dict_out['id']
         if self.outputBinding:
             dict_out['outputBinding'] = self.outputBinding.get_dict()
         return dict_out

examples/example.cwl

@@ -1,27 +1,26 @@
 #!/usr/bin/env cwl-runner
 
-cwlVersion: v1.0
 id: my_tool
 label: my_tool is magic
-baseCommand: run_my_tool
-class: CommandLineTool
-doc: Magic is no magic without secrets...
 inputs:
   config_file:
-    type: File
-    doc: config file
     format: http://edamontology.org/format_2330
+    doc: config file
+    type: File
     inputBinding:
       position: 1
   threads:
-    type: int
     doc: number of threads
+    type: int
     inputBinding:
       prefix: -t
 outputs:
   result_file:
-    type: File
-    doc: magic results
     format: http://edamontology.org/format_2330
+    doc: magic results
+    type: File
     outputBinding:
       glob: counts.txt
+baseCommand: run_my_tool
+doc: Magic is no magic without secrets...
+class: CommandLineTool