Expose element_identifier as a workflow parameter variable.

@lparsons and I had a heated debated in IRC as to whether tools should consume this or workflow authors should be setting these up (revolving around Tophat which doesn't have the enhanced read group handling of the bwa/bowtie wrappers (xref https://github.com/galaxyproject/tools-devteam/pull/103/files)). Regardless about what the "best practice" in general should be - there are always going to be cases where it would be good at the workflow level to be able to consume collection metadata.

Start by reviewing the referenced tools-devteam pull request 103 and the Tophat, bwa, and bowtie wrapper context. No Galaxy files or tests are named, so first locate workflow parameter handling and determine how collection metadata such as element_identifier should be exposed; done means a decided workflow-level behavior with corresponding implementation and tests.

Written by the indexing model from the issue text.