Update the Dockerfile template to the latest version our Galaxy Docker Container. The new container will be release together with Galaxy next week.
PEP-8 fixes for lib/galaxy/tools/parameters/output_collect.py
Refactor output_collect for reuse.
Reduces cyclomatic complexity slightly as well.
Refactor small helper out of get_work_dir_outputs for reuse.
Leave comment about not understanding the complexity :).
Rename variable for clarity post output collections.
After tools can explicitly create collections the term created_collections becomes ambigious - these are history collection instances (HDCA) implicitly created by mapping over collections so renaming this field implicit_collections.
Rename variable for clarity.
This method does not just return datasets.
Add file missed with pull request 505.
Refactor dataset collection creation into reusable pieces.
In downstream output collection work this allows creating elements after initial construction - which is useful for output collections composed of dynamically discovered datasets after a job has completed.
Rearrange verify method to make duplication more obvious.
Break up a couple test methods for reuse downstream.
Remove duplication related to verifying a single dataset in tests - allows reuse in downstream when verifying the content of explicitly defined tool output collections.

Refactor out waiting for jobs - seems wrong place to put that logic this should allow easier moving.
Script to build workflows from simpler YAML description.
Split all workflow extraction testing out of test/api/test_workflows.py.
test_workflows.py was pretty unwieldy and the workflow extraction tests were very different than the other tests in that file (e.g. very different helper functions).
Simplify new test_workflow_extraction.py.
Now makes sense to assume all tests consume a history.
Simplify interface to test helper _extract_and_download_workflow.
Makes tests in this file marginally more readable.
Introduce another helper to simplify test_workflow_extraction.py.
Fix for running test_extract_workflow.py stand-alone.
Remove dated TODO from workflow extraction code.
More unit tests for workflow extraction summarize method.
Refactor lib/galaxy/workflow/extract.py to breakup big loop.
Merged in BjoernGruening/galaxy-central-1 (pull request #578)

Update the Dockerfile template to the latest version our Galaxy Docker Container.