Idea #2342
Updated by Tom Clegg about 10 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