properly include create_bam_output_index type parameters

[crutching]

create_output_bam_index
create_output_bam_md5
create_variant_bam_index
create_variant_bam_md5

If these parameters are specifed (booleans), the output files will need to be properly captured (probably from "from_work_dir") and provided in Galaxy. This may be a case where we would add these alongside other macros, though there are many different optional output files that might be BAM or VCF, so might need a template built in Python.

[crutching]

Note: These are currently being ignored, will not be written to output XMLs.