Story #2342

Updated by Tom Clegg almost 6 years ago

This can cover an entire class of analysis tools / utilities with a single crunch script; pipeline/user will specify things like
* Source/binary distribution to download from Keep
* Command line arguments
* How to store/collate output

This should wrap some utility classes for translating @script_parameters@ to command line arguments, along these lines:

* https://github.com/biopython/biopython/blob/master/Bio/Application/__init__.py

These classes should be documented so they can help DRY up other bundled, custom, and third-party crunch scripts.

"mr-file-filter" from warehouse-apps did a simple version of this along these lines:
* provide shell command as a script_parameter
* flag to concatenate all outputs into one file, vs. 1:1 with input

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