Clap: Consider supporting the CWL standard CommandLineTool for YAML specification of a CLI interface

[mr-c]

Bug or Feature Request Summary

Specification: https://www.commonwl.org/v1.0/CommandLineTool.html
User guide: https://www.commonwl.org/user_guide/

CWL project homepage: https://www.commonwl.org/

If some properties that you have aren't yet in CWL you can add them as "vendor extensions" and retain compatibility. We'd want to study your extensions for possible future inclusion.

[CreepySkeleton]

I haven't read the spec completely but looks pretty interesting. cc @clap-rs/admins What do you think?

[pksunkara]

So, I looked over the spec and I am really hesitant to support it. It will have too much noise compared to clap's yaml which will make it harder for users to use.

[mr-c]

@pksunkara What do you think about CWL export from clap-using apps?

[pksunkara]

I don't mind that, but it will have to go clap_generate crate and even then, I am not sure this is not niche.

[CreepySkeleton]

@mr-c The main goal of clap is to provide a flexible an feature-full parser for command line arguments, but the full scope of CWL is way beyond this goal. I don't think we'll ever consider supporting all of it.

About CLI part only - well, if it's all about building clap::App from corresponding cwl.yaml file it can be seen as "yet another format akin to YAML and TOML". We are considering to make use of serde (#1630). If/when we manage to implement it, you will be free to make your own implementation of it , like serde_json or serde_yaml.

Even if we decide not to support it, you are still free to make your own "converter" crate that reads cwl.yaml and builds the corresponding clap::App.

I'm closing this because I'm almost sure we don't want to maintain such an implementation in this repo.

[Dylan-DPC]

I'd like to consider this in the future. Let's keep it open.

[mr-c]

@Dylan-DPC @CreepySkeleton I am happy to write a Google Summer of Code proposal and co-mentor alongside a rust person to work on CWL export from clap applications.

[luizirber]

This is pretty much exactly why I used the YAML feature to write my CLI. I had previously handwritten the equivalent command (compute) in CWL, and I think it would be extremely useful to have both more Rust CLIs in bioinformatics and larger adoption of CWL tool descriptions.

[pksunkara]

@codesections Could this come under documentation crate? Can one of the generators be CWL?

[medcelerate]

I would absolutely love this feature set, would make our biofx tools more powerful and easier to add to workflows.

[Dylan-DPC]

Let's discuss this once we are done with the 3.0.0 release