[galaxy-dev] Alignment Extractors - in batch?

Hello, I have multiple sequence alignment files in the *maf format, containing whole genome alignments from 6 species. I'm interested in extracting the sequence surrounding the exons of ~16,000 genes. I was wondering if it would be possible to run the Alignment Extractors tool in batch? Would it be possible for me to run it on the command line? Thanks ins Advance Abhi Ratnakumar By the way I'm a PhD student at Uppsala University, so any executables that you provide will be used for academic purposes only.