Update Tophat for Collection-Aware Read Group Mapping

Last bit of https://github.com/galaxyproject/tools-devteam/issues/92 which was mostly dealt with.

The problem with tophat is that it does not allow arbitrary read groups or at least all of the valid Broad/SAM specification ones. We could pick and choose pieces of the macros to reuse and adapt the conditionals to tophat - or we can try to get tophat to allow the remaining headers to be specifiable.

Tophat source code is at https://github.com/infphilo/tophat.

Current header supported:

```
--rg-id (read group ID)
--rg-sample (sample ID)
--rg-library (library ID)
--rg-description (descriptive string, no tabs allowed)
--rg-platform-unit (e.g Illumina lane ID)
--rg-center (sequencing center name)
--rg-date (ISO 8601 date of the sequencing run)
--rg-platform (Sequencing platform descriptor)
```

Missing options include pi, ks, fo, pg.

See SAM specification for definitions of these options - https://samtools.github.io/hts-specs/SAMv1.pdf.