Il 2013-12-04 20:48 Jim Johnson ha scritto:
On 12/4/13, 10:21 AM, Peter Cock wrote:
On Mon, Dec 2, 2013 at 3:37 PM, Peter Cock
<p.j.a.c...@googlemail.com [1]> wrote:
> On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning
> <bjoern.gruen...@pharmazie.uni-freiburg.de [2]> wrote:
>>>
>>> Great. I'll probably merge the c25 branch and push that
>>> to the Test Tool Shed next week (adding the descriptions
>>> as a new 25th column to the default extended tabular
>>> output).
>>
>> +1
>
> Done, see this and the preceding commits:
>
https://github.com/peterjc/galaxy_blast/commit/eb1e522a864e5274a2d274a49fcb15c313e93d69
[3]
>
> And the Test Tool Shed repository has been updated:
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/8f9023b30384
[4]
>
> We'll also be running this update locally for a little more
> testing, but I'd appreciate some of you also testing this,
> e.g. via the Test Tool Shed on your own local (development)
> Galaxy instances.
>
> If there are no problems, that can probably go out to the
> main Tool Shed by the end of the week.
I pushed another update to the Test Tool Shed addressing
a slight change in the autogenerated IDs used in the BLAST
XML output, and an overlooked mention of 24 columns:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/72170c3f515a
[5]
The functional tests are passing on the Test Tool Shed,
so before I push this to the main Tool Shed, any other
comments?
> I'll look at the pick-your-own column output for the next
> revision of the NCBI BLAST+ wrappers.
I've been working on this using JJ's work on column picking
in the BLAST XML to tabular tool - viewable here:
https://github.com/jmchilton/galaxy_blast/commit/d79afc03522768323494818a40aac10513a6fa09
[6]
See this branch updating and extending that work:
https://github.com/peterjc/galaxy_blast/tree/blastxml_jj [7]
I'm considering splitting the column picker into three, the
standard 12 columns, the further 13 used in our extended
25 column output, and a third category for any other columns
offered by BLAST+ (like the taxonomy columns added in
BLAST+ 2.2.28).
Here's a screenshot showing the column picker offering
the 25 columns, split in two:
Note that (following JJ's earlier work) these all include the column
numbers as used in the standard 12 column BLAST tabular output,
or our extended 25 column output.
Note I would not intend to number the final set of "extra" columns.
Do people think this is helpful, or potentially confusing (since
the
column numbering will change in a custom selection)?
Peter
Splitting into 3 sections seems like a good idea.
That makes it easier to select groups of columns.
I also think labeling the column options with the column number in
the standard tabular outputs will be useful to users.
I also like the splitting into 3 sections, but I think that the column
numbering may be confusing and I would prefer it's not included.
Nicola
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
