fix --help on CWL descriptions

Author: mr-c

cwltool/main.py

@@ -255,10 +255,10 @@ def generate_parser(toolparser, tool, namemap):
         default = None # type: Any
 
         if inptype == "File":
-            action = cast(FileAction, argparse.Action)
+            action = cast(argparse.Action, FileAction)
         elif isinstance(inptype, dict) and inptype["type"] == "array":
             if inptype["items"] == "File":
-                action = cast(FileAppendAction, argparse.Action)
+                action = cast(argparse.Action, FileAppendAction)
             else:
                 action = "append"
 

tests/test_toolargparse.py

@@ -0,0 +1,33 @@
+import unittest
+from tempfile import NamedTemporaryFile
+from cwltool.main import main
+
+
+class ToolArgparse(unittest.TestCase):
+
+
+    script='''
+#!/usr/bin/env cwl-runner
+cwlVersion: "cwl:draft-3"
+class: CommandLineTool
+description: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"
+inputs:
+  #Give it a list of input files
+  - id: input
+    type: File
+    inputBinding:
+      position: 0 
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: test.txt
+stdout: test.txt
+baseCommand: [cat]
+'''
+
+    def test_help(self):
+        with NamedTemporaryFile() as f:
+            f.write(self.script)
+            f.flush()
+            self.assertEquals(main([f.name, '--input', 'README.rst']), 0)