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...



-----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> 
> 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 



Attachment: ncbi_blastn_wrapper.xml
Description: ncbi_blastn_wrapper.xml

Attachment: taxid_name.loc
Description: taxid_name.loc

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