`skip-root-merge` flag used for `skip-hdf5-merge`

[EthanMarx]

The flag for skipping root merge is used for skipping hdf5 merge here.

Separately, is it possible to specify pyomicron only produce h5 files?

[areeda]

Thank you for the bug report, especially for the specific line causing the problem. The fix will be in the release

I do not see anyway [currently] to override the output formats of root, hdf5, xml. I think you could use pyomicron to create the files but add no-submit option then edit parameters.txt but I have not tested it.

I will add that as an enhancement for the next release.