Hi Joachim, Thanks for the info! but I could not register on your instance...and thus could not check your wrapper. :-( Please help! Thanks, Rui On Wed, Sep 11, 2013 at 12:59 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<http://toolshed.bits.vib.be/view/joachim/deseq2>
Cheers, Joachim
Joachim Jacob Contact details: http://www.bits.vib.be/index.**php/about/80-team<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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