Update tag latest_2014.10.06 for changeset c9759aa6e40f
open citation url in _blank (prevents browser's insecure content error messages while trying to open in the middle pane - https vs http)
Update tag latest_2014.10.06 for changeset e6de07f8c01f
Fix passing nested parameter replacements to the workflow run API.
Thanks to Nicola for finding the problem https://bitbucket.org/galaxy/galaxy-central/commits/fa92c5497232444ade0e7044184fb8ccf419177c.
Update tag latest_2014.10.06 for changeset 011c8b2118be
ToolForm: Add switch for new tool form to configuration
Merge stable.
Modify Docker set_user option to allow setting a remote user.
Now is disabled by setting this to the empty string instead of false. Add flexibility allows working around the fact that it is not evaluated properly for Pulsar by setting this to be the remote pulsar user :(. Longer term the default option should be the remote user on the worker node instead of the Galaxy user.

I don't believe this feature has been in stable so I am not preserving backward compatiblity.
Fix for ToolParameter.to_dict when the html contains unicode.
Log.debug the name of the galaxy.ini file currently being used.
Bug fix for exception handling of slurm runner's stderr parsing.
Rename variable for clarity after tools can explicitly create collections.

created_collections is ambigious - these are HDCA for implicitly created collections so renaming this field implicit_collections.
Initial work on tool dataset collection outputs from James Johnson.
Allow tools to produce a fixed number of output datasets for a collection.

Valid for tools such as a FASTQ de-interlacer to produce a pair - but not tools that produce a dynamic number of inputs. So far these tools are unusable in workflows and cannot be 'mapped' over - for instance you cannot take a list of interlaced files a produce a list of de-interlaced pairs.

Rename data_collection element to collection to match pattern already formed in tests.
Add paired collection output test.
Prevent tools producing collections from being used in workflows.

Certainly feasible someday but workflow editor logic will require significant overhaul.
WIP: Allow a known variable number of outputs from collections.

Should allow N->N operations without crazy workflow scheduling.
Model changes to track output collection parts...

Jobs just producing HistoryDatasetCollectionAssociations works fine for simple jobs producing collections - but you don't want to map a list over a tool that produces a pair and produce a bunch of pairs HDCAs and a list:pair HDCA- you just want a bunch of pieces and the one list:pair at that the top.  I think anyway... could totally be wrong.
Allow mapping over tools that produce output collections...

... for 'known' output collections (i.e. not dynamically dicovered - not yet implemented) and only for tool execution. None of this currently works for workflows.
WIP: Collection testing.