ok for a laod + a process workflow

src/jflow/workflow.py

@@ -91,7 +91,7 @@ class Workflow(threading.Thread):
         except: self.engine_arguments = None
         try:
             # Add config information
-            self.name, self.description, self.parameters = self._get_from_config()
+            self.name, self.description, self.parameters = self._get_from_config(self.parameters_section)
         except:
             raise IOError(self.__class__.__name__ + " workflow property file not found or invalid.")
         
@@ -123,15 +123,16 @@ class Workflow(threading.Thread):
         del odict['_Thread__stderr']
         return odict
     
-    def get_parameters_per_groups(self):
-        parameters, parameters_order = {}, []
-        for param in self.parameters:
+    def get_parameters_per_groups(self, parameters_section="parameters"):
+        name, description, parameters = self._get_from_config(parameters_section)
+        pgparameters, parameters_order = {}, []
+        for param in parameters:
             if param.group not in parameters_order: parameters_order.append(param.group)
-            if parameters.has_key(param.group):
-                parameters[param.group].append(param)
+            if pgparameters.has_key(param.group):
+                pgparameters[param.group].append(param)
             else:
-                parameters[param.group] = [param]
-        return [parameters, parameters_order]
+                pgparameters[param.group] = [param]
+        return [pgparameters, parameters_order]
     
     def get_exec_path(self, software):
         exec_path = self.jflow_config_reader.get_exec(software)
@@ -330,15 +331,15 @@ class Workflow(threading.Thread):
                     extended_args[param.name] = param.default
         return extended_args
     
-    def _get_from_config(self):
+    def _get_from_config(self, parameters_section):
         reader = ConfigParser()
         reader.read(self._get_property_path())
         parameters, param_order = [], []
         try:
             params, sub_order, excludes, hash_params = {}, {}, [], {}
             # first grab all parameters name
-            for param in reader.items(self.parameters_section):
-                cvalue = reader.get(self.parameters_section, param[0])
+            for param in reader.items(parameters_section):
+                cvalue = reader.get(parameters_section, param[0])
                 cparam = param[0].split(".")[0]
                 ckey = ".".join(param[0].split(".")[1:])
                 if len(ckey.split(".")) > 1: