Hi,
There's a small bug with the "hide dataset" button in the workflow editor - once any dataset is marked as "output" (by clicking on the star icon), there's no way to show all the datasets, even if the user manually un-checked every star icon for every workflow step.
meaning: If I have a workflow that *used* to have one step marked as "output", unmarking it (so that no dataset is marked is "output", implying all datasets should be retained in the history) doesn't work - galaxy insists on hiding all the other datasets.
Steps to reproduce: 1. Import this workflow: http://main.g2.bx.psu.edu/u/foobar/w/hiddendatasetstest2
2. Edit this workflow. Notice that only the last two steps are marked as "output". don't change anything, close with (or without) saving.
3. Run this workflow. Notice that Steps 1,2,3,5,6 have "Action: Hide this dataset." - as expected. Only steps 4,7 are marked as "output". No need to actually execute the workflow.
4. Edit the workflow again. Remove the "output" mark from steps 4,7 ("Add Column" and "compute"). No dataset is marked as output - at least from the user POV, it's implied that all datasets should be kept in the history (just like when editing a new workflow). Save the workflow, close the workflow.
5. Run this workflow. Notice that steps 1,2,3,5,6 STILL have "Action: hide this dataset" - this is the bug.
So the only workaround is to run the workflow, then "extract workflow from history" to get a "clean" copy of the workflow without any datasets hidden.
Thanks to Marek Kudla for meticulously experimenting with this issue.
-gordon