Hi all,

Some of my medium/long term plans for Galaxy involve running one tool which
then generates input parameters (and perhaps input files) for another tool.
This would be particularly powerful in combination with workflows.

One example is phylogenetics where you might have a model selection tool
which selects assorted parameters for tree building (e.g. Gamma on or off).

General model selection for classifiers might also benefit from such a flow
- e.g. Model selection on a subset of the data assessed on a test data set,
then running the best model on the full dataset.

I can see how I might solve this on a case by case basis, where for each
tool which I want to be able to call with a parameter file a wrapper script
would be needed, plus the tool would have a top level parameter selection
between values from a file, or values entered by the user in the normal way.
At least in some niche fields such parameter files already exist - for
example the Nexus file format (although many tools which support this as an
input format do so in a simplistic way and only look at the alignment or
trees, not the commands/settings).

However, I'm envisioning a general mechanism for providing (some or all of)
the inputs to a Galaxy tool via a file, which for extensibility and
consistency with the rest of Galaxy would be in XML. Galaxy would need a
nice viewer for this new datatype, which could appear in the history as just
another dataset. However, the key new functionality would be on any tool
dialogue (if a suitable tool parameter XML file was in the history) would be
a new option/button to apply settings from this file to the current form.
I'm imagining the new XML would include a list of tool IDs for which it can
be used on (e.g. Maximum likelihood model selection might produce settings
for both PhyML and RAxML, but these tools might have differently named
parameters in their Galaxy tool XML files).

Have the Galaxy team been thinking of anything like this already?


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