Mechanism to define site-specific parameters to aid defining job destinations.
This is based on work by Hector del Risco at the University of Florida.

Various tool-style parameters can be defined in job_resource_params_conf.xml (see sample) and these define the pool of all possible resource parameters that can be injected into a tool. These can be groupped together and assigned to tools in job_conf.xml (see documented changes to job_conf.xml.sample_advanced).

A conditional is then injected into each tool that gives the end-user the ability to select these parameters. The values of these parameters (as a dict) can then be obtained by dynamic job destination that define a 'resource_params' argument.

Lots here still needs to be tested/verified - can workflows exported from Galaxies without resource parameters (or different ones, be reused in Galaxies with resource parameters) (I think yes?)? can workflows exported with resource parameters be used in other Galaxies (I think yes?), how best to present UI while running workflows? (maybe nothing needs to be changed), should exported job parameter data be swept clean (say when exporting a workflow for instance).

A great extension to this would be to support conditional when defining parameters.

Finally, the Galaxy team will make a reasonable effort to support this syntax for job_conf.xml, job_resource_params_conf.xml, and internal interface for job parameters for sometime once this changeset has reached -stable but until these interfaces may change.
Fix unit tests for 46a487e.
Fix documentation in the Tool Shed API users controller.
Fix debug typo in the Tool Shed's step handler.
Pes-8 fixes for the Tool Shed's repository_registry module.
Fix for installing tool dependencies with type set_environment.
Merge in set_environment bugfix from stable.
Fix import in the Tool Shed's common_install_util module.
Add change that was lost when resolving a merge conflict.
Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm
Fix for Safari Caching External View application 302 redirect links. See https://trello.com/c/optldnPm
Merge fix from stable.
Stop loading indicator at the end of get_next_chunk regardless of result.
Pack scripts.
Charts: Adding chart subset selection filter, setting zoomable charts as default
Charts: Remove helper function
Charts: Extend boxplot options
Charts: Improve notifications and error handling
Fix the exception handler in the Tool Shed APi submit() function so that an expected dict is returned instead of a string.
Fix for installing from toolshed that uses 307 redirects that are not being handled nicely by urllib2.urlopen when the urllib2.Request has data provided.