Add optional "upload" attribute to tool definitions.

When extracting workflows, such tools are treated as inputs. This eliminates the need for the hack of hardcoding 'upload1' in tools.py and allows multiple upload tools to exist and function properly when extracting workflows.

lib/galaxy/tools/__init__.py

@@ -1085,7 +1085,7 @@ class Tool( object ):
         if requirements_elem:
             self.parse_requirements( requirements_elem )
         # Determine if this tool can be used in workflows
-        self.is_workflow_compatible = self.check_workflow_compatible()
+        self.is_workflow_compatible = self.check_workflow_compatible(root)
         # Trackster configuration.
         trackster_conf = root.find( "trackster_conf" )
         if trackster_conf is not None:
@@ -1653,7 +1653,7 @@ class Tool( object ):
             version = requirement_elem.get( "version", None )
             requirement = ToolRequirement( name=name, type=type, version=version )
             self.requirements.append( requirement )
-    def check_workflow_compatible( self ):
+    def check_workflow_compatible( self, root ):
         """
         Determine if a tool can be used in workflows. External tools and the
         upload tool are currently not supported by workflows.
@@ -1666,9 +1666,7 @@ class Tool( object ):
         # right now
         if self.tool_type.startswith( 'data_source' ):
             return False
-        # HACK: upload is (as always) a special case becuase file parameters
-        #       can't be persisted.
-        if self.id == "upload1":
+        if util.string_as_bool( root.get( "upload", "False" ) ):
             return False
         # TODO: Anyway to capture tools that dynamically change their own
         #       outputs?

tools/data_source/upload.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 
-<tool name="Upload File" id="upload1" version="1.1.3">
+<tool name="Upload File" id="upload1" version="1.1.3" upload="true">
   <description>
     from your computer  
   </description>