comparison Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-2.ga @ 2:48b020a0d2f7 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
author drosofff
date Fri, 13 May 2016 05:46:40 -0400
parents 3d8eb2c065c7
children ba15c770fd40
comparison
equal deleted inserted replaced
1:3d8eb2c065c7 2:48b020a0d2f7
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