Hi there,

we would like to use planemo autoupdate to upgrade our workflows, as they contain lots of subworkflows and planemo already offers recursive update functionality.

Unfortunately, the actual update is only performed if a tool from the main public toolshed is out of date in the workflow. If only tools from private tool sheds are out-of-date the update is skipped.

If such a tool is present, however, the update is performed correctly for ALL tools in the workflow.

@mvdbeek pointed out in galaxyproject/bioblend#475 that this may well be due to hard-coding of the main public tool shed in planemo. I was able to confirm that tools from our private TS are correctly considered when we change the line below to reference our private tool shed.

As @mvdbeek points out it would probably be a good solution to infer the correct tool shed address from the tool ID.