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.berner(a)jki.bund.de&gt; 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

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