Peter, Thanks for noticing this -- the text in the UI should definitely reflect which output it's referring to. "Hide output_pos", etc. https://trello.com/c/KAtwLSiV/1069-workflow-actions-cosmetic-issues -Dannon On Wed, Aug 21, 2013 at 7:16 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:

Hi all,

I have found two potential bugs with how workflow actions are described to the user when running a workflow.

I am looking over the "run workflow" dialogue for this workflow, (I currently get a warning due to the filter tool having a new "Number of header lines to skip" option) http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow

I manually imported the *.ga file due to issues with the Tool Shed workflow import, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016209.html

I am running the latest galaxy-dist,

$ sudo -u galaxy hg head changeset: 10411:c42567f43aa7 tag: tip user: greg date: Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy.

changeset: 10408:6822f41bc9bb branch: stable parent: 10393:d05bf67aefa6 user: Dave Bouvier <dave@bx.psu.edu> date: Mon Aug 19 13:06:17 2013 -0400 summary: Fix for case where running functional tests might overwrite certain files in database/files.

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For step 2, the details view says:

Actions: Hide this dataset. Hide this dataset.

I find that confusing, and initially thought there might be a bug or duplicated action. Actually it is just a misleading summary as this tool can produce TWO outputs:

"post_job_actions": { "HideDatasetActionoutput_neg": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_neg" }, "HideDatasetActionoutput_pos": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_pos" } },

Perhaps the "Hide this dataset" message could be less ambiguous by using the output variable names (as in some of the other action descriptions)?

There are similar problems with the next steps too.

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Steps 6 and 7 are also odd. For step 6 the details view says:

Actions: Hide this dataset. Rename output 'out_file1' to 'Filtered SignalP results'. Hide this dataset. Rename output 'out_file1' to 'Filtered SignalP results'.

Likewise for step 7,

Actions: Hide this dataset. Rename output 'output_pos' to 'Secreted proteins'. Hide this dataset. Rename output 'output_pos' to 'Secreted proteins'.

Again, there seems to be a duplication of the messages. It should be hiding one output, and renaming the other, e.g.

"post_job_actions": { "HideDatasetActionoutput_neg": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_neg" }, "RenameDatasetActionoutput_pos": { "action_arguments": { "newname": "Secreted proteins" }, "action_type": "RenameDatasetAction", "output_name": "output_pos" } },

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In some ways this is just a harmless cosmetic issue, but it does seem confusing to me.

Thanks,

Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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