Updated workflow_job to use internal type values for arguments instead of...

Updated workflow_job to use internal type values for arguments instead of passed ones.  No longer need types included in workflow_module.

chipathlon/workflow_job.py

@@ -445,20 +445,22 @@ class WorkflowJob(object):
                 ...
             }
         """
-        if self._params_are_valid(inputs,outputs):
+        if self._params_are_valid(inputs, outputs):
             job = Job(self.executable)
             for param_name, param_info in inputs.iteritems():
-                if param_info["type"] == "file_list":
+                wj_param = self.get_param_info(param_name)
+                if wj_param["type"] == "file_list":
                     for f in param_info["value"]:
                         job.uses(f["file"], link=Link.INPUT)
-                elif param_info["type"] in chipathlon.conf.argument_types["file"]:
+                elif wj_param["type"] in chipathlon.conf.argument_types["file"]:
                     job.uses(param_info["file"], link=Link.INPUT)
             for output_name, output_info in outputs.iteritems():
+                wj_param = self.get_param_info(output_name)
                 job.uses(output_info["file"], link=Link.OUTPUT, transfer=output_info["transfer"])
                 # Redirect stdout / stderr
-                if output_info["type"] == "stdout":
+                if wj_param["type"] == "stdout":
                     job.setStdout(output_file["name"])
-                elif output_info["type"] == "stderr":
+                elif wj_param["type"] == "stderr":
                     job.setStderr(output_file["name"])
             arg_list = self._create_arg_list(inputs, outputs)
             job.addArguments(*self._create_arg_list(inputs, outputs))
@@ -575,3 +577,12 @@ class WorkflowJob(object):
                 else:
                     arg_list.append(add_value)
         return arg_list
+
+    def get_param_info(self, param_name):
+        """
+        :param param_name: The name of the input/output to get information for.
+        :type param_name: str
+
+        Returns the information associated with a particular input/output.
+        """
+        return self.job_data["inputs"].get(param_name, self.job_data["outputs"].get(param_name))