This is probably something only the Galaxy devs can answer, but I thought I'd 
give it a shot in the wider community. Some of you are doing some very 
complicated stuff.

If you have a workflow with several input blocks, you might have multiple fastq 
files you need to provide. A good example of this is paired-end analysis - it 
doesn't really matter in which order you provide the fastq files for R1 and R2, 
but providing just one or the other twice requires user intervention.

It would be really nice if Galaxy assigned a unique value from the history to 
runtime parameters (tool params and input modules) before reusing datasets. I'm 
trying to get the initial form for running a workflow as close as possible to 
"right" to reduce the number of steps a user has to go through. So, in this 
example, R1 would be assigned to one input and R2 to another (or the reverse), 
as the initial defaults.

Is that what the "context" parameter of ToolParameter.get_initial_value() is 
for? I see that is used for repeat-group and conditionals, but it's used to 
store all the eligible values, not just the ones chosen from the history so 
far. For other tools, it accumulates the input values chosen for the tool.

Would it be consistent with the design to modify templates/workflow/run.mako to 
accumulate a dictionary of datasets used, instead of clearing it for each 
module? Since InputDataModule uses DataToolParameter, I think I can make the 
change in DataToolParameter and get input blocks and tools in one fell swoop, 
and history items would not be reused across the entire workflow, providing the 
number of runtime parameters did not exceed the number of compatible history 

John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584

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