Selective downloading of output files
- Workflow: added automatic download getter and setter.
- BaseWorkflow: added automaticDownload field (with getter and setter).
- GalaxyWorkflow: added reference to workflow engine and overridden version of the getOutput method for delayed downloading.
- GalaxyWorkflowEngine: store history ID in field (saves lots of parameters), added the outputNameToIdsMap field and getOutputIdForOutputName method, created separate downloadOutputFile method, handle automatic downloading.
- GalaxyWorkflowTest and GalaxyWorkflowEngineTest: pass workflow engine to Galaxy workflow constructor.
- ConcatenateExample, HistogramExample, and RandomLinesExample: use the workflow.getOutput() method instead of the workflow.getOutputMap().get() methods.