macs2 rule should handle PE better

[daler]

Currently, in order for macs2 to run in PE mode this line in the wrapper needs to be changed to BEDPE. This is awkward!

Some options:

• expose a paired-end: parameter in the chipseq config section; this would be passed to the peak caller wrapper and handled by the wrapper. It should raise an error if the peak-caller does not support PE reads.
• auto-detect from the BAM whether or not it's PE. I suppose this can be done by inspecting BAM flags, but I feel like specifying a parameter would be more explicit.