Hi Damion,
I see your blast_reporting tool is now on the Main Tool Shed. https://toolshed.g2.bx.psu.edu/view/damion/blast_reporting
I am a little confused about your tabular output options:
<option value="std" selected="True">Standard 12 columns</option> <option value="std+seqs">Standard 12 columns + sequences</option> <option value="ext">Extended 24 columns</option> <option value="ext+">Extended 26 columns</option> <option value="custom">Only field selections below</option>
In comparison my blastxml_to_tabular currently offers:
<option value="std" selected="True">Tabular (standard 12 columns)</option> <option value="ext">Tabular (extended 25 columns)</option> <option value="cols">Tabular (select columns to output)</option>
For the moment my pick-you-own columns choices are limited here to the 25 columns (unlike the BLAST+ wrappers which offers more). See: https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus
In ncbi_blast_plus the extended output used to be 24 columns, my 25th column is the description (BLAST+ field salltitles, added in BLAST+ 2.2.28).
https://github.com/peterjc/galaxy_blast/commit/0b161baa7f87d514c94fd1b3976af... https://github.com/peterjc/galaxy_blast/commit/5234e32a277595044ec6d2a7002d9... http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions....
Your in-tool help and the blast_reporting.py comments show you've picked different extra columns:
Column 25 pcov Percentage coverage Column 26 sallseqdescr All subject Seq-descr(s), separated by a ','
I'm guessing these names map to NCBI BLAST+ fields qcovs or qcovhsp, and salltitles? Could you check and adopt the NCBI names?
It is unfortunately the choice of fields has diverged.
Could you switch your columns 25 and 26 round in your "ext+" output so that we agree on the first 25 columns? And expand your "ext" output to add the descriptions and so match the 25 column extended output in ncbi_blast_plus too?
Thanks,
Peter
P.S. There is a problem in your markdown for the README.md file, shown as a "Unexpected indentation." error when viewed on the Tool Shed. https://toolshed.g2.bx.psu.edu/view/damion/blast_reporting
On Tue, Mar 3, 2015 at 1:46 AM, galaxy-no-reply@montana.galaxyproject.org wrote:
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