I digged some more and I guess I could use the rename dataset option in a workflow, but I can't find how I can rename a dataset using the original input name.
I tried to use the same notation as those used in the tools (such as ${input.name}) but that just treats the input.name as a user provided parameter, which is NOT my intention.

Is there any way I can rename a dataset using information from the orginal input dataset name? It seems a trivially obvious thing to be able to do, but I can't figure it out...Hopefully this is just an oversight on my part!

Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru

On Dec 31, 2011, at 2:26 PM, Thon deBoer wrote:

Hi,

I am trying to pass some key-value pairs to the result of a tool (such as the original sample name) but I cannot find a way to do this in the galaxy XML tool definitions.

I am simply trying to retain in all the data files I produce, the name of the original sample which the results are related to.
Now I have to follow the history of a result just to see which original data file sample my results came from (and when using hidden files, this is almost impossible, since all results refer to some arbitrary number my data set had ("Tophat on data 30" is not going to help me, if I have 140 samples with all the same name)...

Is there some way to pass some key-value pairs to a tools output? Can tags be assigned in the Tool definition? Can I set metadata tags programmatically?

Any help would be appreciated...

Regards,

Thon de Boer, Ph.D.
Bioinformatics Guru

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