Consider adding deprecated tag to all deprecated tools directly at http://usegalaxy.org

[jennaj]

Certain tools in the tool panel now have the new deprecated tag in the tool menu, other do not. Could we add for all tools under the "Deprecated" subsection at the bottom of the panel, per-tool?

Example: GATK tools, Cloudmap tools

Use case: User searches for a tool with tool panel search. Filtered tools are returned as the search result. The "Deprecate" tool section delimiter is not presented in this view.

The tool section header itself could have a deprecated tag (section headers are part of the search results) but since we are tagging other tools directly now (Tophat is one example), it would be consistent (and useful!) to also to tag each of these other deprecated tools individually.

@martenson I think you tagged Tophat or helped to organize that? Would you have time to review this idea and if you agree, decide the best way to inform users, through the UI, if a tool is deprecated? My ideas above are just some simple options. Tool forms could also have a deprecated tag or annotation in the full tool name/description, yet I have mixed feeling on that - seems a bit repetitive and would be much more work (?), although useful for some use cases (reruns, etc). Whatever is decided as the final method to expose "deprecated" metadata in all tool panel views is fine with me. Search filtered or not or other places (ex: a workflow editor tool itself and/or workflow "view" (structure) and/or at workflow execution time) are other places where "deprecated" tags could be exposed & associated with tools directly. The primary point is that users do not seem to be getting that info. And some are coming into the analysis from rerunning older workflows.

Other ideas welcome!