Fixed typo
Don't yet have an ACE format datatype in Galaxy
Remove old non-functional example command line
Look at miraconvert return code, not stderr
Actually invoke miraconvert (SAM/BAM pending)
Apply miraconvert filters; fix version switch
Handle empty/missing FASTA file from miraconvert
Support for miraconvert's cstats output

TODO: Handle missing output when there are no contigs better
Remove SAM output option, BAM is enough
Refactor mira4_make_bam.py and use it from mira4_convert.py
Use optparse for version switch
Clearer error message in corner case