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/0b161baa7f87d514c94fd1b3976af20bdc00c4c9
https://github.com/peterjc/galaxy_blast/commit/5234e32a277595044ec6d2a7002d93f9fb3011c7
http://blastedbio.blogspot.co.uk/2012/05/blast-tabular-missing-descriptions.html

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-re...@montana.galaxyproject.org> wrote:
>
> Sharable link:         
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> Repository name:       blast_reporting
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