Update BWA and BWA-MEM on main

[jennaj]

Might address this usage enhancement already: galaxyproject/tools-iuc#1785

MTS: https://toolshed.g2.bx.psu.edu/view/devteam/bwa/4f774c1e6049

The version on main (both): 0.7.15.1

MTS versions: BWA 0.7.17.4, BWA-MEM 0.7.17.1

[martenson]

updated on Main in 34a4dd4

[jennaj]

Tool version (BWA 0.7.17.4, BWA-MEM 0.7.17.1). Initial tests pass. More tests, with a variety of inputs, are in progress. Includes using a custom genome and inputting interleaved/BAM.

I'll close this out once all complete, to make sure basic functionality in place.

Test history: https://usegalaxy.org/u/jen/h/test-history-bwa-mem-paired-interleaved-interlaced (includes other tests -- ignore those -- updated tool tests are in datasets 13-17.

For reference, enhancements for these tools have been submitted to the IUC to address the differences between the two tools and accepted inputs. Graphics in 1785 show what is going on.

• Enhancement: Add "Paired Interleaved" as an input option to BWA (exists for BWA-MEM) tools-iuc#1785
• Enhancement: Add BAM input as choice for BWA-MEM (is included for BWA) tools-iuc#1799

[jennaj]

Tests pass, closing, thanks!

BWA included with PR 34a4dd4