Sending tool output to input parameters of downstream tool(s)

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Sending tool output to input parameters of downstream tool(s)

Peter Cock
Hi all,

I was recently wondering how it might be possible for
an output from tool A to be used as a parameter when
calling tool B (without modifying tool B to take a data
configuration file or anything like that).

To clarify, I'm thinking about simple parameters like
a single integer/float/string like "median insert size"
or "average coverage" which map to a single input
parameter in a downstream tool.

Workflow parameters basic $variable support is
similar to what I'm thinking about here, see:

Perhaps one day in addition to tool outputs being files,
they can include setting $variables (local to the history),
which could then be used within downstream tools?
I can see this has downsides with tracking the providence
of each variable though... thus:

Another idea would be extra filetypes for each parameter
type (Unix philosophy - make everything into a file), e.g.
integer_parameter, float_parameter, ... which "Tool A"
could define as an output, and write to. Galaxy would
then need to offer these history entries to the user when
a later tool (e.g. "Tool B") asked for a parameter of that
type (e.g. an integer, or a float).

(This idea could be extended further, with data files
using JSON or something to hold a structured set of
parameter values which Galaxy could then offer to
fill later tool's inputs.)

Crazy, or is there some mileage in this idea?

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