Hi Thomas,

are you interested in implementing it on your own?

I'm not an blast expert, so sorry for the question, but is there an
public repository where all unit-counts can be download as
wmasker.obinary format, preferable in the correct folder structure as
described in http://www.ncbi.nlm.nih.gov/books/NBK1763/. Or do you need
to create such files on your own?

What we/you probably can do is to create a new windowmasker.loc file
pointing to each taxid and add a that new parameter to the wrapper.
 
Cheers,
Björn

> 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
> 
>  
> 
> 
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