Walking through galaxy job submission.

gistfile1.txt

Galaxy Tool/Job Running:
---------------------

Entry points: 
lib/webapps/galaxy/controllers/tool_runner.py (method: index)
lib/webapps/galaxy/api/tools.py (method: create)

Generate tool from id. 

Setup params:
  API: inputs = payload[ 'inputs' ]; params = util.Params( inputs, sanitize = False )
  Controller: params = util.Params( kwd, sanitize = False )
# Note some sort of per tool parameter translation occurs with controller mode.

Next these controllers pass parameters to tool via handle_input:
template, vars = tool.handle_input( trans, params.__dict__, history=target_history)
template, vars = tool.handle_input( trans, params.__dict__ )

lib/galaxy/tools/__init__.py (~ line 1700)

handle_input:
 - Create or fetch tool state.
 - Page logic, errror and validation logic, ultimately though pass to self.execute(trans, incoming=parmas, history=history)
 -> self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs )

DefaultToolAction runs external command: lib/galaxy/tools/actions/__init__.py