I tried to add test-data folder to my repository in toolshed, but there aren't any option to add folder.
https://wiki.galaxyproject.org/CreateAndPopulateARepository
I found only the way to upload file.
AFAIK: It's a mercurial repository so directories in an uploaded archive will add directories to the updated repository.
Make a gzipped tarball of your repository containing all of the contents - eg if ./foo is the top level directory containing the tool xml and that test-data subdirectory (./foo/test-data) then something like:
tar -cz ./foo/* > myrepo.tar.gz
Upload myrepo.tar.gz using the upload option in your tool shed repository view.
The subdirectories and other contents should appear in the updated tool repository.
Suggestion: spin up a local tool shed and experiment there BEFORE you upload to any public toolshed. Recent laptops and desktops are likely to run both servers well enough for development.
sh run_tool_shed.sh --daemon
should just about do it - then localhost:9009 becomes your test playground - access to the logs will help a lot.
Thank you very much for the answer. The situation is a bit more complicated than that.
First, most of these tools have been tested. They are valid. I can install it back to my local galaxy after I deposit them on public toolshed. I did that with 9 of them.
Second, when I use sh run_tool_shed.sh --daemon, I can't create repository to put my tools there. There is no admin panel for me. I only have admin panel in local8080.
Third, in main toolshed, when I click "Repositories I own" and click at my repository, I cannot see the valid tools. However, if I change revision to other version and change back, then I see four of them. Thus, I think there is something wrong with the update of the tool on toolshed.
Second, when I use sh run_tool_shed.sh --daemon, I can't create repository to put my tools there. There is no admin panel for me. I only have admin panel in local8080.
To make a local administrator is the same for the toolshed as for Galaxy - add your account user email to the list of toolshed administrators in tool_shed_wsgi.ini and restart the toolshed - eg:
# this should be a comma-separated list of valid Galaxy users
admin_users = ross.lazarus@gmail.com,foo@bar.com
This http://gregvonkuster.org/galaxy-tool-shed-framework-building-galaxy-tools/ may also be useful.
Although I still can't create repository in local toolshed, but I found out the problem of my tools. It's some prohibit in comment that I just add. The "test-data" directory works as well. Thank you so much.
If Ross's answer helped to solve some of your other issues, "Accepting" the answer will help others to know it was a solution. Thanks! Jen
