Adding galaxy-dev list in CC as suggested by Peter.

Il giorno mer, 06/02/2013 alle 16.57 +0000, Peter Cock ha scritto: 
> On Tue, Feb 5, 2013 at 11:45 AM, Nicola Soranzo <sora...@crs4.it> wrote:
> > Dear Peter,
> > I have created a simple Galaxy tool for DustMasker of the NCBI BLAST+
> > suite, which I think would be a useful addition to the ncbi_blast_plus
> > repository you're maintaining in the Galaxy Tool Shed.
> >
> > You can find it and hopefully pull it from:
> >
> > https://bitbucket.org/nsoranzo/ncbi_blast_plus
> >
> > Kind regards,
> > Nicola
> 
> Hi Nicola,
> 
> Thanks for getting involved - we can discuss this on the galaxy-dev
> mailing list if you prefer? For now I have CC'd Edward Kirton as he
> is/was working on masking in BLAST databases for Galaxy.
> 
> I can see the new file
> tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml however it refers to
> multiple new file formats - where are they defined?
> 
> * acclist
> * maskinfo_asn1_bin
> * maskinfo_asn1_text
> * seqloc_asn1_bin
> * seqloc_asn1_text

Hi Peter,
I added these file formats mostly as placeholders for a future
implementation. Now I have changed a bit the tool by removing acclist
and seqloc_xml formats since they are not recognized by the last
versions of dustmasker (I also sent an email to
blast-h...@ncbi.nlm.nih.gov to inform them of this bug).
As before, you can find the new version at:

https://bitbucket.org/nsoranzo/ncbi_blast_plus

I stripped the old commit and did a new one, not a very good practice,
sorry about that.

> Have you looked at the (commented out) bits in the makeblastdb wrapper
> which would perhaps be relevant? This is something Edward Kirton wrote
> which I haven't integrated yet:
> 
>     <!-- SEQUENCE MASKING OPTIONS -->
>     <!-- TODO
>     <repeat name="mask_data" title="Provide one or more files
> containing masking data">
>         <param name="file" type="data" format="asnb" label="File
> containing masking data" help="As produced by NCBI masking
> applications (e.g. dustmasker, segmasker, windowmasker)" />
>     </repeat>
>     <repeat name="gi_mask" title="Create GI indexed masking data">
>         <param name="file" type="data" format="asnb" label="Masking
> data output file" />
>     </repeat>
>     -->
> 
> Perhaps all you need to offer in ncbi_dustmasker_wrapper.xml is
> 'fasta' and 'asnb' (binary ASN) formats? Edward - did you have an
> 'asnb' definition?

'fasta' and 'interval' are the ones I'm interested for my use case.

'maskinfo_asn1_bin' is probably the one referenced as 'asnb' in the
cited code (ASN1 is a general data serialization format like XML). A
file in this format can be given as input to "makeblastdb -mask_data".

Nicola
-- 
Nicola Soranzo, Ph.D.
CRS4
Bioinformatics Program
Loc. Piscina Manna
09010 Pula (CA), Italy
http://www.bioinformatica.crs4.it/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to