Update the Dockerfile template to the latest version our Galaxy Docker Container. The new container will be release together with Galaxy next week.
ToolForm: Add drill down element
ToolForm: Fix select2 value selection
ToolForm: Add baseurl, fix dynamic drill down options
Merged in BjoernGruening/galaxy-central-1 (pull request #578)

Update the Dockerfile template to the latest version our Galaxy Docker Container.
Charts: Use most recent select field style
Merge
Merge
Remove debugging statement.
Merge next-stable to default
Add helper for waiting on a job instead of a history.

Used downstream - should try to use this more in API tests.
Allow tools to output collections with static or determinable structure.

By "static" I mean tools such as a FASTQ de-interlacer that would produce a "paired" collection with two datasets everytime. By "determinable" I mean tools that perform N->N operations within the same job - such as a tool that needs to normalize a bunch of datasets all at once and not in separate jobs. (For N->N collection operations that should or can be done in N separate jobs tool authors should just write tools that operate over a dataset and produce a dataset and let the end-user 'map over' that operation.)

There are still large classes of operations where the structure of the output collection cannot be pre-determined - such as splitting files (e.g. bam files by read group) - that are not implemented in this commit.

Model:

The models have been updated to do a more thorough job of tracking collection outputs. 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.

Workflow:

Workflows containing such operations can be executed - but the workflow editor has not been updated to handle this complexity (and it will require a significant overhaul) so such tools are not available in the workflow editor.

Tool Testing:

This commit also introduces a new tool XML syntax for describing tests on output collections. See files test/functional/tools/collection_creates_list.xml and test/functional/tools/collection_creates_pair.xml for examples.

Tests:

Includes two tools to test this - one that uses explicit pair output names and one that iterates over the structure of input list to produce an output list.

Includes several new tools API tests that test the tools described above via the API and implicit mapping over such tools. Includes two new workflow API tests - one that verifies a simple workflow with output collections works and one that verifies mapping over workflow steps in collections works.
Allow tools to output collections with a dynamic number of datasets.

Models:

Track whether dataset collections have been populated yet.

Dataset collections are still effectively immutable once populated - but dynamic output collections require them to be sort of likely `final` fields in Java (analogy courtesy of JJ) - allowing them to be declared before they are initialized or populated. This is tracked by the `populated_state` field.

Tools:

Output collections can now describe `discover_datasets` elements just like datasets - except in this case instead of dynamically populating new datasets in the history - they will comprise the collection. `designation` has been reused to serve as the element_identifier for the collection element corresponding to the dataset.

See Pull Request 356 for more information on the discover_datasets tag https://bitbucket.org/galaxy/galaxy-central/pull-request/356/enhancements-for-runtime-discovered.

Workflows:

Update workflow execution and recovery for dynamic output collections.

Galaxy workflow data flow before collections

* - * - * - * - * - *

Galaxy worfklow data flow after collections (iteration 1)

* - * - * \
           * - * - *
* - * - * /         \
                     * - * - *
* - * - * \         /
           * - * - *
* - * - * /

Galaxy worfklow data flow after this commit

              / * - * \
         * - *         * - *
        /     \ * - * /     \
       /                     \
      /                       \
     /        / * - * \        \
* - * -- * - *         * - * -- * - *
     \        \ * - * /        /
      \                       /
       \                     /
        \     / * - * \     /
         * - *         * - *
              \ * - * /
More configurable format and metadata handling for output collections.

Imporvements to testing code.
A simpler way to configure output pairs (exploiting static structure).

See example and comments in test/functional/tools/collection_creates_pair_from_type.xml.
Update workflow extraction backend for output collections.
WIP: Improved testing revealed not quite done with workflow extraction.
Jobs API order_by.
Workflow extraction of output collections.
Better workflow extraction.