Fix #12: support CWL v1.0 simplified syntax

cwl2argparse/cwl_classes.py

@@ -27,13 +27,15 @@ class InputParam(Param):
     def __init__(self, param):
         self.id = param['id']
         self.type = param.get('type', None)
-        if type(self.type) is list and self.type[0] == 'null':
+        if type(self.type) is str and self.type[-2:] == '[]': # v.1.0 syntax simplification ('<type>[]' == array of <type> )
+            self.type = "array"
+        if (type(self.type) is list and self.type[0] == 'null'):
+            self.optional = True
+        elif type(self.type) is str and self.type[-1] == '?':  # v.1.0 ('<type>?' == ['null', '<type>'])
             self.optional = True
+            self.type = self.type[:-1]
         else:
             self.optional = False
-        items_type = param.get('items_type', None)
-        if items_type:
-            self.items_type = items_type
         self.description = param.get('doc', param.get('description', None))
         self.default = param.get('default', None)
         input_binding = param.get('inputBinding', None)
@@ -98,5 +100,5 @@ def __init__(self, filename):
                     param_dict['id'] = id
                     param = OutputParam(param_dict)
                     self.outputs[id] = param
-        self.description = tool.get('description', '')
+        self.description = tool.get('doc', tool.get('description', None))
         self.cwl_version = tool.get('cwlVersion', '')

example/inp.cwl

@@ -0,0 +1,29 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+doc: prints a string a to standard output
+inputs:
+  example_flag:
+    type: boolean
+    inputBinding:
+      position: 1
+      prefix: -f
+  example_string:
+    type: string
+    inputBinding:
+      position: 3
+      prefix: --example-string
+  example_int:
+    type: int[]
+    inputBinding:
+      position: 2
+      prefix: -i
+      separate: false
+  example_file:
+    type: File?
+    inputBinding:
+      prefix: --file=
+      separate: false
+      position: 4
+
+outputs: []

example/inp.py

@@ -0,0 +1,18 @@
+import argparse
+
+
+def parser():
+    description="""
+        prints a string to a standard output
+    """
+    parser = argparse.ArgumentParser(description=description)
+    example_flag = parser.add_argument("example_flag",
+       type=bool,)
+    example_file = parser.add_argument("--file",
+       type=argparse.FileType(),)
+    example_string = parser.add_argument("example_string",
+       type=str,)
+    example_int = parser.add_argument("example_int",
+       type=list,       nargs="+",)
+
+    return parser

setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup
 
 setup(name="cwl2argparse",
-      version="0.1.6",
+      version="0.1.7",
       description='Generating Python code from CWL tool descriptions with CWL inputs/outputs as argparse arguments',
       author='Anton Khodak',
       author_email='anton.khodak@ukr.net',