Re: [galaxy-dev] creating a galaxy dataset within a galaxy tool

2012-09-18 Thread Dan Tenenbaum
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. Someh

Re: [galaxy-dev] creating a galaxy dataset within a galaxy tool

2012-09-18 Thread James Taylor
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 wrote: > I want the user to upload a text file, th

[galaxy-dev] creating a galaxy dataset within a galaxy tool

2012-09-18 Thread Dan Tenenbaum
I'd like to have a tool that does not actually return anything (is that possible?) but writes a file to the directory where Galaxy stores uploaded data files, and tells Galaxy about it (perhaps that involves writing to a database?). My tool is written in R. Here is my scenario: I want the user to