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.
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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