On Thu, Feb 21, 2013 at 6:12 PM, Carlos Borroto
<carlos.borr...@gmail.com> wrote:
> On Wed, Feb 20, 2013 at 9:57 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> [*] This is one reason why I've just switched the default BLAST+
>> output from the standard 12 column output to the extended 24
>> column output in v0.0.17 of the wrappers:
>> http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
>
> Hi Peter,
>
> Would you consider adding the option to set a custom tabular output? I
> would like to be able to select exactly which fields to include. For
> example the alignment data I rarely need it and if I choose 24 column
> output I'll be wasting a lot of space by including it.
>
> I'll be happy to provide patch.
>
> And yes, I'll be very happy to be able to set custom column names in
> the workflow for tabular outputs.
>
> Regards,
> Carlos

Hi Carlos,

I had deliberately avoid letting users pick the columns - it is
doable, but has two major downsides. First a more complex
GUI (if we don't allow the order to change then it is still ~24
options), and then the worse problem of it being hard to know
what the output columns are in later work. If the columns are
consistent, it is much easier to write general instructions (e.g.
for filtering on percentage identity). If Galaxy let us label the
columns on the current 'tabular' format, then I'd be more
positive about this, but until that happens I would prefer not
to offer arbitrary columns in the BLAST tabular output.

In the mean time, would you prefer I revert the default to 12
column tabular output? Just how big are your BLAST files if
the extra disk space is a serious concern (compared to raw
sequencing data)?

(Separately I was asking about how to offer automatic datatype
conversion - that would allow easy conversion of BLAST XML
or even BLAST archive ASN.1 format into tabular on demand,
making them viable default output formats from a usability point
of view - but both of those are larger than the default 12 column
or even 24 column tabular formats.)

Regards,

Peter
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