Hello again Thomas,

Unfortunately I forgot about your email from last summer - which
was shortly before the GCC2013 conference where we had some
productive discussions about the BLAST+ wrappers, e.g.
http://wiki.galaxyproject.org/Events/GCC2013/BoF

Further replies in-line below...

Peter wrote:
> 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.

That's done now, and will be in the forthcoming v0.1.0 release of the
Galaxy BLAST wrappers - available for early testing here:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus

>> 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

The BLAST+ wrappers have turned into a team effort, managed from
this GitHub repository: https://github.com/peterjc/galaxy_blast/

On Fri, Jun 14, 2013 at 1:59 PM, Berner, Thomas
<thomas.ber...@jki.bund.de> wrote:
> 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

Now we have an issue tracker for the BLAST+ wrappers, I've filed an
enhancement issue on this with notes from your email - I don't think
the negative filtering by taxid would work though:

https://github.com/peterjc/galaxy_blast/issues/36

If you have a GitHub account you are welcome to subscribe to the
issue and comment there - or reply by email.

Regards,

Peter
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