Run galaxy with default tools included

[bernt-matthias]

I wanted to test some Galaxy tools and needed the collection operations. So I thought it might be a good idea to serve planemo with Galaxy's default tools installed:

Not sure what happens if some one calls planemo test/serve on one of the builtin tools....

Alternatively one could use --extra_tools but then the tools are just installed flat in the tool menu.

[mvdbeek]

Can you expose a --tool_conf argument instead (and check that --shed_tool_conf doesn't do the job already) ?

[bernt-matthias]

Can you expose a --tool_conf argument instead?

Could be done I guess. But it would be inconvenient for users who so not have a clone of Galaxy.

[mvdbeek]

Fine, but then at least make this optional ?

[jmchilton]

Could we have --extra_tools be able to take toolbox conf in addition to actual tools and directory. Also I guess we use the name stock tools in the workflow docs for planemo - so maybe add like a flag --include_stock_tools that is short-hand for enabling the behavior here (--extra_tools with a the tool conf sample as the target).

[bernt-matthias]

Can you expose a --tool_conf argument instead (and check that --shed_tool_conf doesn't do the job already) ?

Seems that --shed_tool_conf already does the trick (at least with --galaxy_root and using the sample tool conf from this directory).