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.c...@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 <d...@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. > > -------------------------------------------------------------------------- > > > 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. > > -------------------------------------------------------------------------- > > 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" > } > }, > > -------------------------------------------------------------------------- > > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
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