Hi all,

I'm trying to update one of my saved workflows which was created
using an old version of the filter tool BEFORE this tool had the
option "Number of header lines to skip". In order to get rid of the
nag message on using the tool, I want to re-save the workflow
using the default 0 for this.

This missing parameter was also causing problems trying to
import the *.ga file for this old workflow,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016223.html

The (now out of date) copy of the Workflow is on the Tool Shed,
but to update it I am working on the same Galaxy instance used
to create it (where TMHMM and SignalP were manually installed
and have been updated since):
http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow

1. Log into Galaxy
2. Click on workflows (top menu)
3. Find my workflow, select "Edit" from the dropdown menu
4. Observe warning:

Workflow loaded with changes
Problems were encountered loading this workflow (possibly a result of
tool upgrades). Please review the following parameters and then save.

    Step 3: Filter
        No value found for 'Number of header lines to skip', used default
    Step 6: Filter
        No value found for 'Number of header lines to skip', used default

5. Click on these workflow steps, verify this new parameter is
set to zero.
6. Save the workflow, observe blue progress bar pops up.
7. Close the workflow
9. Save the workflow to disk as a *.ga file
8. Open the workflow again for editing

Expected result: New parameter recorded, and
tool versions updated.

Actual result: No change, same warning appears.
No sign of the new setting in the freshly save *.ga file.
Tool versions not changed.

Workaround: Change the default values to one ("1"),
save, close, reopen, no warning, change values back
to zero ("0"), save, close, reopen, Happy.

Is this simply a bug where the workflow editor wrongly
assumes no changes have been made (despite there
being two major types of change - the new header_lines
parameter, and the versions of the tools)?

Peter
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