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: 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.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
ncbi_blastn_wrapper.xml
Description: ncbi_blastn_wrapper.xml
taxid_name.loc
Description: taxid_name.loc
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