On Mon, Dec 2, 2013 at 3:37 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning <bjoern.gruening@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/eb1e522a864e5274a2d274a49fcb1...
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: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/72170c3f515a 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/d79afc03522768323494818a40a... See this branch updating and extending that work: https://github.com/peterjc/galaxy_blast/tree/blastxml_jj 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: [image: 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)? Peter
