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
Von: Peter Cock [mailto:firstname.lastname@example.org]
Gesendet: Donnerstag, 13. Juni 2013 11:59
An: Berner, Thomas
Betreff: Re: [galaxy-dev] Blast+: new feature filter/mask... by taxid before job in one
On Wed, Jun 12, 2013 at 11:45 AM, Berner, Thomas <thomas.berner(a)jki.bund.de> wrote:
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.
) 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
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
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?