It is not necessarily bad. If we all test each others tools (dependencies, interface, output,...) we might get to the best of all worlds :-) (I have planned to test Björns wrapper)

One of the points of differentiation is also how 'integrated' a tool needs to be: e.g. Ross' tool for diff expression (combining a complete pipelin), and my tool just on DE with DESeq2. I like to keep things granular on the level of the tools.


Cheers,
Joachim

Joachim Jacob.
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 09/11/2013 10:56 AM, Peter Cock wrote:
Wow - that makes at least five Deseq2 wrappers for Galaxy
available or in progress :(

Bjoern's wrapper on the (test) tool shed,
http://testtoolshed.g2.bx.psu.edu/view/bgruening/deseq2

Ross' combined wrapper for edgeR, DESeq2 and voom in one tool:
http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models

Joachim's wrapper on the Tool Shed
http://toolshed.bits.vib.be/view/joachim/deseq2

Vipin's which is soon to be released to the (Test?) Tool Shed,
https://github.com/ratschlab/oqtans_tools/tree/master/DESeq2

And Rui's is working on one too.

This does seem like duplicated effort & a source of confusion
for end users and Galaxy administrators (a problem not unique
to deseq2, but affecting many Galaxy wrappers).

I appreciate there will be different needs, and one wrapper
may not suit all, but I would prefer if the default behaviour
for Galaxy tool wrapper authors was to collaborate on one
good wrapper rather than writing competing ones.

When I started work on a new wrapper I tried to announce
this on the mailing list to find out if anyone else was already
tackling the same tool - and that seemed to work quite well.
Of course, the volume of emails on galaxy-dev has grown
quite a lot over the last few years so that may not be as
effective, but the archives should be searchable.

Perhaps we need to improve communication in some way?
One option would be to encourage greater use of the Test
Tool Shed for works in progress to give them visibility?
You could even have the Tool Shed itself require a search
step before creating a new repository to avoid accidental
duplication of effort? Or maybe a wiki page of wrappers
in progress?

(And maybe we should split this into a new thread)

Regards,

Peter


On Wed, Sep 11, 2013 at 8:59 AM, Joachim Jacob | VIB |
<joachim.ja...@vib.be> wrote:
Hi Rui,

I should provide a 'sample metadata table', a tabular file with one column
the names of your samples, the other column the associated metadata (e.g.
type).

This is how I've done it in my DESeq2 wrapper. :-) Feel free to check the
interface at http://toolshed.bits.vib.be/view/joachim/deseq2


Cheers,
Joachim

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team



On 09/11/2013 01:15 AM, ruiwang.sz wrote:
Hi All,

we are making a wrapper for deseq2, and there is a step where
control/experimental conditions
need to be determined. For example, it would be a column like the
following in the input file

Type
CTC
CTC
LM
LM
PT
PT

and we want the select list to contain

CTC
LM
PT

In other words, we want to filter out the 'Type' and have only distinct
ones in the select list. We could
make it in two steps, generate a intermediate file for this but it would
be nice that we could directly
retrieve the distinct types to make the list. I took a look at the tool
config wiki, but didn't see anything
(maybe because it was a quick scan). Does anyone have any tip on this?
we'll really appreciate.

Thanks,
Rui


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