From 92cebe7f52229b1cbf1dd8496e7c0640365d4bc8 Mon Sep 17 00:00:00 2001
From: Alejandro Barrera <alejandro.barrera@duke.edu>
Date: Thu, 5 May 2016 16:02:20 -0400
Subject: [PATCH 1/2] Avoid type argument when adding boolean arguments

---
 cwltool/main.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/cwltool/main.py b/cwltool/main.py
index 1c502c508..79107306c 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -285,8 +285,10 @@ def generate_parser(toolparser, tool, namemap):
             _logger.debug(u"Can't make command line argument from %s", inptype)
             return None
 
-        toolparser.add_argument(flag + name, required=required,
-                help=ahelp, action=action, type=atype, default=default)
+        argument_kwargs = {'required': required, 'help': ahelp, 'action': action, 'default': default}
+        if inptype != "boolean":
+            argument_kwargs['type'] = atype
+        toolparser.add_argument(flag + name, **argument_kwargs)
 
     return toolparser
 

From 6fa9a2b5680a9b304aa78a40141405d475e67d60 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <crusoe@ucdavis.edu>
Date: Thu, 5 May 2016 13:47:00 -0700
Subject: [PATCH 2/2] add test for boolean type error

---
 cwltool/main.py            |  9 ++++++---
 tests/test_toolargparse.py | 27 +++++++++++++++++++++++++++
 2 files changed, 33 insertions(+), 3 deletions(-)

diff --git a/cwltool/main.py b/cwltool/main.py
index 79107306c..9ea819598 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -285,10 +285,13 @@ def generate_parser(toolparser, tool, namemap):
             _logger.debug(u"Can't make command line argument from %s", inptype)
             return None
 
-        argument_kwargs = {'required': required, 'help': ahelp, 'action': action, 'default': default}
         if inptype != "boolean":
-            argument_kwargs['type'] = atype
-        toolparser.add_argument(flag + name, **argument_kwargs)
+            typekw = { 'type': atype }
+        else:
+            typekw = {}
+
+        toolparser.add_argument(flag + name, required=required,
+                help=ahelp, action=action, default=default, **typekw)
 
     return toolparser
 
diff --git a/tests/test_toolargparse.py b/tests/test_toolargparse.py
index 7504280ed..29bfeb34c 100644
--- a/tests/test_toolargparse.py
+++ b/tests/test_toolargparse.py
@@ -24,6 +24,24 @@ class ToolArgparse(unittest.TestCase):
       glob: test.txt
 stdout: test.txt
 baseCommand: [cat]
+'''
+
+    script2='''
+#!/usr/bin/env cwl-runner
+cwlVersion: 'cwl:draft-3'
+class: CommandLineTool
+inputs:
+  - id: bdg
+    type: "boolean"
+outputs:
+  - id: output
+    type: File
+    outputBinding:
+      glob: foo
+baseCommand:
+  - echo
+  - "ff"
+stdout: foo
 '''
 
     def test_help(self):
@@ -31,3 +49,12 @@ def test_help(self):
             f.write(self.script)
             f.flush()
             self.assertEquals(main([f.name, '--input', 'README.rst']), 0)
+
+    def test_bool(self):
+        with NamedTemporaryFile() as f:
+            f.write(self.script2)
+            f.flush()
+            try:
+                self.assertEquals(main([f.name, '--help']), 0)
+            except SystemExit as e:
+                self.assertEquals(e.code, 0)