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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