Hello Peter, I've created teh following Trello card for this: https://trello.com/c/Vg12cS7o/1174-toolshed-frames-issue-with-readme-file-li... Thanks, Greg Von Kuster On Oct 8, 2013, at 10:44 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

Consider the following sequence:

1. Goto http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan

2. The README file explains this is for InterProScan 4, and has a link to http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5 for Bjoern's InterProScan 45 wrapper.

3. Click the link for InterProScan 5.

4. Notice the link opened within the frame, and you now have a nested tool shed menu.

5. Click on the link to InterPro itself, http://www.ebi.ac.uk/interpro/interproscan.html

6. Notice the double nested frame remains, and now the InterPro page is squeezed into the bottom left.

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This isn't specific to these repositories, e.g.

1. Goto http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go

2. The README file introduction refers to the tool being available on the main tool shed,

"It is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go "

3. Click on that link

4. Observe a double nested tool shed interface, with the Test Tool Shed at the top, and the Main Tool Shed nested within.

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Suggested fix: All links within Tool Shed README files should be modified to open full frame by adding target="_top" to them.

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