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.c...@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_xml.html#data-managers > > Peter C. > > On Mon, Sep 17, 2018 at 10:56 PM Peter van Heusden <p...@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/__init__.py#L120 >> >> from: >> >> >> https://github.com/galaxyproject/galaxy/blob/dev/lib/tool_shed/tools/data_table_manager.py#L88 >> >> 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 >> >> >>
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