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.
Peter