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
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