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Interestingly, planemo doesn't complain when e.g. doing shed_diffs:
Diffing repository ncbi_eutils_ecitmatch
wget -q --recursive -O- 'https://testtoolshed.g2.bx.psu.edu/repository/download?repository_id=b905112aa2141a77&changeset_revision=default&file_type=gz' | tar -xzf - -C /var/folders/4k/j29691bj6758ygzqjgpg8g6w0000gn/T/tool_shed_diff_9BsmES/_test-iuc_ --strip-components 1
-k or -r can be used together with -O only if outputting to a regular file.
mkdir "/var/folders/4k/j29691bj6758ygzqjgpg8g6w0000gn/T/tool_shed_diff_9BsmES/_workingdir_"; tar -xzf "/var/folders/4k/j29691bj6758ygzqjgpg8g6w0000gn/T/tmpAz5Pdq" -C "/var/folders/4k/j29691bj6758ygzqjgpg8g6w0000gn/T/tool_shed_diff_9BsmES/_workingdir_"; rm -rf /var/folders/4k/j29691bj6758ygzqjgpg8g6w0000gn/T/tmpAz5Pdq
cd "/var/folders/4k/j29691bj6758ygzqjgpg8g6w0000gn/T/tool_shed_diff_9BsmES"; diff -r _workingdir_ _test-iuc_
Should be fixed by incorporating galaxyproject/galaxy-lib#5
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