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fix and complete metadata setting docs #1167

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fix and complete metadata setting docs #1167

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839a639
fix and complete metadata setting docs
bernt-matthias May 4, 2021
69fb863
start to describe new metadata format
bernt-matthias May 6, 2021
a38ef63
added some links
bernt-matthias Aug 5, 2021
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33 changes: 30 additions & 3 deletions docs/_writing_tool_metadata.rst
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Expand Up @@ -19,7 +19,33 @@ to build a manifest file.

A tool may also produce a file called ``galaxy.json`` during execution. If
upon a job's completion this file is populated, Galaxy will expect to find metadata
about outputs in it.
about outputs in it.

The current format of the metadata file -- which has been introduced in release 17.09 --
is described in the following. The legacy format is described at the end of this section.

----------------------------------------------------------------
Metadata format
----------------------------------------------------------------

Original PR https://github.com/galaxyproject/galaxy/pull/4437

Simple data sets:

TODO

Discovered data sets:

TODO

Collections:

https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_dynamic_nested_from_json_elements.xml
https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_dynamic_nested_from_json.xml

----------------------------------------------------------------
Legacy metadata format
----------------------------------------------------------------

The format of this file is a bit quirky - each line of this file should be a JSON
dictionary. Each such dictionary should contain a ``type`` attribute - this type
Expand All @@ -42,10 +68,11 @@ Examples of tools using ``new_primary_dataset`` entries:

The ``type`` of an entry may also be ``dataset``. In this case the metadata
descriptions describe an explicit output (one with its own corresponding ``output``
element definition). In this case, an entry called ``dataset`` should appear in
element definition). In this case, an entry called ``dataset_id`` should appear in
the dictionary (in lieu of ``filename`` above) and should be the database id of the
output dataset. Such entries may contain all of the other fields described above except
``metadata``.
``metadata``. Note that the output needs to set ``format="auto"`` in order to set the
format.

Example tool using a ``dataset`` entry:

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