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.jacob@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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