Hi James,

I realize I didn't do a good job explaining, but your suggestion
sounds promising. How can I make something into a dataset?

Here's what I'm hoping to achieve:
User runs Tool1, uploading a text file and specifying some parameters.
Tool1 uses this to write out a serialized R object. Somehow this
object is persisted in Galaxy (made into a dataset).
Now the user can run Tool2 or Tool3, which each take the dataset
created in the previous step, plus some parameters of their own.

So I guess the only part I am missing is how to turn the output of
Tool1 into a dataset. Is there a way to do this other than downloading
it to my local computer and then uploading it to Galaxy? That seems


On Tue, Sep 18, 2012 at 3:41 PM, James Taylor <ja...@jamestaylor.org> wrote:
> Dan, I may not be following, but why not make the serialized R object
> a dataset (of its own datatype). Then the user can just pass it to the
> downstream tools just by specifying one parameter.
> -- jt
> On Tue, Sep 18, 2012 at 3:00 PM, Dan Tenenbaum <dtene...@fhcrc.org> wrote:
>> I want the user to upload a text file, then pass that text file, along
>> with several parameters, (in something we'll call Tool1) which I use
>> to create a serialized R object. That object is then used in several
>> other tools. I don't want the user to have to download and then
>> re-upload the serialized object. I want it to just be available after
>> the user runs Tool1.
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