Hi Peter, We edited the ncbi_blastn_wrapper.xml (attachment) a little bit as you can see and created a taxid_name.loc file for testing by our own. This is what we were thinking of in a very simple way. But if the list spreads out we would like to have textbox for pre-selection above the drop-down-menu like it is in the "edit Attributes" menu if it is possible...
Regards, Thomas -----Ursprüngliche Nachricht----- Von: Peter Cock [mailto:p.j.a.c...@googlemail.com] Gesendet: Donnerstag, 13. Juni 2013 11:59 An: Berner, Thomas Cc: firstname.lastname@example.org Betreff: Re: [galaxy-dev] Blast+: new feature filter/mask... by taxid before job in one task On Wed, Jun 12, 2013 at 11:45 AM, Berner, Thomas <thomas.ber...@jki.bund.de> wrote: > Hi guys, > > We recently installed NCBI BLAST + to our local Galaxy instance and > now we need to provide the possibility to filter/mask . by taxon id > (taxid) using the command line option (-window_masker_taxid) of BLAST (cf. > http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the job will be > performed in one task. > > However searching in the documentation and the mailing list, I did not > find anything about this. > So it would be great to provide the possibility to subselect by taxid (e.g. > NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing > the BLAST integration. > > We believe this could be of common interest. It would be great if > anybody could comment on this. > > > Thanks a lot, Thomas Hi Thomas, Full support allowing making your own database with taxid support will be more complicated - but using databases setup via the *.loc file (e.g. a downloaded copy of the NR database) ought not to be too complicated. I think we just need to add another integer parameter under the advanced options to set the -window_masker_taxid value. Would that be enough for your needs? I wrote the NCBI BLAST+ wrappers but this is starting to turn into a team effort. There is a lot of other work in progress on extending the Galaxy BLAST+ wrappers further - I'm setting up a meeting with the other people already working on this during the GCC2013 - perhaps this should be a listed BoF session? http://wiki.galaxyproject.org/Events/GCC2013/BoF Regards, Peter
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/