view test-data/params.json @ 22:d033ffc1c161 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d44a94772c58903157edfc12c2a67819cfe252a9"
author iuc
date Wed, 24 Feb 2021 18:58:38 +0000
parents 419cd817299c
children
line wrap: on
line source

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