Awesome, I'll take a look. And, if you're able to pull it together easily enough, clean branches are always nice. -Dannon On Feb 22, 2012, at 10:59 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote: Basic BLAST XML merging implemented and apparently working: https://bitbucket.org/peterjc/galaxy-central/changeset/ebf65c0b1e26 This does not currently attempt to remap the iteration numbers or automatically assigned query names, e.g. you can have this kind of thing in the middle of the XML at a merge point: <Iteration_iter-num>1</Iteration_iter-num> <Iteration_query-ID>Query_1</Iteration_query-ID> That isn't a problem for some tools, e.g. my code in Galaxy to convert BLAST XML to tabular, but I suspect it could cause trouble elsewhere. If anyone has specific suggestions for what to test, that would be great. If this is an issue, then the merge code needs a little more work to edit these values. I think the FASTA split code could be reviewed for inclusion though. Dan - do you want to look at that? Would a clean branch help? Peter