add display_name option

bin/jflow_server.py

@@ -117,7 +117,8 @@ class JFlowServer (object):
                                    "choices": param.choices,
                                    "action": param.action,
                                    "type": param.get_type(),
-                                   "name": param.name})            
+                                   "name": param.name,
+                                   "display_name": param.display_name})            
             workflows.append({"name": instance.name,
                               "help": instance.description,
                               "class": instance.__class__.__name__,

src/jflow/parameter.py

@@ -72,7 +72,7 @@ class Parameter(object):
     """
     
     def __init__(self, name, help, flag, default=None, type=types.StringType, choices=None, 
-                 required=False, action="store", sub_parameters=[], group="default"):
+                 required=False, action="store", sub_parameters=[], group="default", display_name=None):
 
         self.name = name
         self.flag = flag
@@ -81,6 +81,9 @@ class Parameter(object):
         self.nargs = None
         self.sub_parameters = sub_parameters
         self.group = group
+        if display_name == None:
+            self.display_name = name
+        else: self.display_name = display_name
         
         if len(self.sub_parameters) > 0:
             self.nargs = "+"

src/jflow/workflow.py

@@ -328,6 +328,7 @@ class Workflow(threading.Thread):
                 else:
                     params[cparam][ckey] = cvalue
                 if cparam not in param_order: param_order.append(cparam)
+            
             for param_name in param_order:
                 sub_params, current_params, sub_objs = {}, {}, []
                 for param in params[param_name]:
@@ -338,7 +339,10 @@ class Workflow(threading.Thread):
                         else:
                             sub_params[sub_params_values[0]][sub_params_values[1]] = params[param_name][param]
                     else:
+                        if param == "name": current_params["display_name"] = params[param_name]["name"]
+                        else: current_params[param] = params[param_name][param]
                         current_params[param] = params[param_name][param]
+                current_params["name"] = param_name
                 if sub_order.has_key(param_name):
                     for sub_param in sub_order[param_name]:
                         sub = Parameter(**sub_params[sub_param])
@@ -349,7 +353,8 @@ class Workflow(threading.Thread):
         except:
             pass
         # finally add the metadata parameter
-        metadata = Parameter(name="metadata", flag="--metadata", help="Which metadata should be linked to this workflow", action="append")
+        metadata = Parameter(name="metadata", flag="--metadata", help="Which metadata should be linked to this workflow", 
+                             action="append", display_name="Metadata")
         parameters.append(metadata)
         return [reader.get("global", "name"),
                 reader.get("global", "description"),

src/js/jflow-wfform.js

@@ -208,7 +208,7 @@
 			// it the parameter has ne already been settled
 			'  {{if Object.keys(parameters).indexOf(param.name) == -1 }}',
 			'  <div class="control-group">',
-			'    <label class="control-label">${param.name}</label>',
+			'    <label class="control-label">${param.display_name}</label>',
 			'    <div class="controls">',
 			// if it's a multiple choice parameter, add a select
 			'    {{if param.choices}}',

workflows/alignment/workflow.properties

@@ -31,18 +31,18 @@ description = align reads against a reference genome
 #      .action [store]: the basic type of action to be taken (store|append)
 #
 [parameters]
-read_1.name = read_1
+read_1.name = Read 1
 read_1.flag = --read-1
 read_1.help = Which read1 files should be used
 read_1.required = True
 read_1.action = append
 
-read_2.name = read_2
+read_2.name = Read 2
 read_2.flag = --read-2
 read_2.help = Which read2 files should be used (if single end, leave empty)
 read_2.action = append
 
-reference_genome.name = reference_genome
+reference_genome.name = Reference genome
 reference_genome.flag = --reference-genome
 reference_genome.help = Which genome should the read being align on
 reference_genome.required = True