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Add more docs on existing dynamic tool output features. #526

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merged 2 commits into from Aug 5, 2016

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jmchilton commented Aug 1, 2016

Document the mysterious galaxy.json.

xref galaxyproject/galaxy#2697


This stub of a section provides some initial documentation on tool provided
metadata. Galaxy allows any of datasets to be discovered after a tool has been
executed and allows tool's to specify metadata for these datasets. Whenever

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@nsoranzo

nsoranzo Aug 4, 2016

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s/tool's/tools/

==============================

This stub of a section provides some initial documentation on tool provided
metadata. Galaxy allows any of datasets to be discovered after a tool has been

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@nsoranzo

nsoranzo Aug 4, 2016

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s/any of datasets/any dataset/

sounds better to my non--native speaker ear.

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@peterjc

peterjc Aug 4, 2016

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I agree

possible, Galaxy's datatypes and more structured outputs should
be used to collect metadata.

If arbitrary an number of outputs is needed but no special metadata must be set,

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@nsoranzo

nsoranzo Aug 4, 2016

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s/arbitrary an/an arbitrary/

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

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@nsoranzo

nsoranzo Aug 4, 2016

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s/populated/populated,/

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
the dictionary (in lieu of ``filename`` above) and should be the databaes id of the

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@nsoranzo

nsoranzo Aug 4, 2016

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s/databaes/database/

\.\.\. handle arbitrary output data formats?
-------------------------------------------------

If the output format of a tool's output cannot isn't known ahead of time,

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@nsoranzo

nsoranzo Aug 4, 2016

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s/cannot isn't known/is not known/


If the output format of a tool's output cannot isn't known ahead of time,
Galaxy can be instructed to "sniff" the output and determine the data type
using the same method used for uploads. Adding the ``auto_format="true"`

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@nsoranzo

nsoranzo Aug 4, 2016

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Missing "`" at the end of this line.

@jmchilton jmchilton merged commit 940523f into galaxyproject:master Aug 5, 2016

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jmchilton commented Aug 5, 2016

Thanks for the detailed review @nsoranzo - I fixed up things with 983d4aa I believe.

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