Peter, I have tested the XML parser for blast jobs on a larger set of files. I haven't checked every detail yet but it seems to process it now without problems. Majority tested using blastp on two protein databases with over 2k queries. Another point I already mailed you off list is the ability to capture additional STDOUT and/or STDERR in a log file. Warnings make the galaxy tool run red and you have to view->save->importnew....which is cumbersome and waste of time and resources when files are over 1.5G big. These files processed without any problem though in the xml parser! Thanks and keep up the good work (many people don't realize all hassle you have to go through when wanting/making a tool available via tool_shed to others.. Alex -----Oorspronkelijk bericht----- Van: p.j.a.cock@googlemail.com [mailto:p.j.a.cock@googlemail.com] Namens Peter Verzonden: woensdag 24 november 2010 4:13 Aan: Kanwei Li CC: Bossers, Alex; Galaxy Dev Onderwerp: blastxml to tabular bug fix Hi Kanwei, Could you check and commit the following three changesets from my new branch: http://bitbucket.org/peterjc/galaxy-central/src/blastplus_nov24 i.e. these three changesets: http://bitbucket.org/peterjc/galaxy-central/changeset/8f0e5a169630 http://bitbucket.org/peterjc/galaxy-central/changeset/72fab21f9469 http://bitbucket.org/peterjc/galaxy-central/changeset/72fab21f9469 This address a problem found earlier today by Alex Bossers (CC'd) while testing the BLAST+ wrappers. The problem can occur when when the query sequence is masked (with XXXX characters), this broke my calculation of the identity and mismatch counts (failing an assert statement I'd included as a sanity check). The new unit test is a cut down version of his failing example. Note that in order to run the unit tests, you will need to first re-enable the tool in tools_conf.xml.sample - the converter tests does not depend on the BLAST+ binaries being installed. Thank you, Peter