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> wrote:
> On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning
> <bjoern.gruen...@pharmazie.uni-freiburg.de> 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
> And the Test Tool Shed repository has been updated:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/8f9023b30384
> 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:


The functional tests are passing on the Test Tool Shed,
so before I push this to the main Tool Shed, any other

> 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:

See this branch updating and extending that work:

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:

Inline image 1

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)?


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.


James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
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