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Implement profile="XX.XX" on tools, better defaults for newer tools.
- set -e in tool command scripts. - Disable implicit extra file collection. All dynamic extra file collection requires a <discover_datasets tag. - Disable format="input" - require explicit metadata targets (metadata_source, format_source). - Disable interpreter= - hacky and doesn't work as expected in too many circumstances. Use $__tool_directory__. - Disable $param_file - grepping the command for the string is impercise. If useful we can add flag to match the flag used to produce inputs as a JSON file. - Disable default version of 1.0.0, the IUC has made it clear they prefer all tools have an explicit version. Fixes #1609.
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