Yes that was my conclusion, thanks Peter. As a result I switched to a new table named (shapeit2_ref) and a new tool name (data_manager_shapeit2_reference) and from planemo side upload seemed to succeed but the tool is in an error state. I resorted to manually editing the tool-data table. Data managers are a bit of an ugly duckling part of Galaxy - not receiving as much love as other kinds of tools. Peter On Tue, 18 Sep 2018 at 14:22 Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Peter vH,
I wonder if adding columns is not supported - because some tools would define the table without the extra column? You might have to define a new data table instead (with largely the same content). But to be clear, I am not an expert in this area of Galaxy.
However, it does seem the IUC could lay out some *.loc file best practises for tool authors. There is currently a TODO entry here:
https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xm...
Peter C.
On Mon, Sep 17, 2018 at 10:56 PM Peter van Heusden <pvh@sanbi.ac.za> wrote:
A bit more tracing leads me to suspect that what is happening is that a merge is being called here:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/data/__ini...
from:
https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/tools/data_ta...
i.e. the toolshed maintains an in-memory copy of tool-data tables and if the list of columns in an incoming tool-data table is not the same as the in-memory version the error I saw happens.
Which leaves me with the question: how is one meant to update the column list of a tool data table?
Peter