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.cock@googlemail.com] Gesendet: Donnerstag, 13. Juni 2013 11:59 An: Berner, Thomas Cc: galaxy-dev@lists.bx.psu.edu 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.berner@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