Add ENA Webin cli as a Galaxy tool

[bedroesb]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

This work is done in collaboration with ENA to make bring submission/validation functionalities of ENA to Galaxy. This tool will live next to the ena_upload Galaxy tool which is focused on RAW read submissions. This tool will be focused on Assemblies and other types of analysis submissions. The goal is to make it work well in combination with the ena_upload Galaxy tool.

To Do's

• Fetch credentials from User settings
• Interactive way of filling in metadata for submission
• Have main cli on BioConda
• Test with latest version Webin CLI
• Agree on a tool name
• Update README
• Write more tests
• Align this work with the ena_upload Galaxy tool
  • Initial POC with receipt coming from ena_upload
• Check if current form is still compliant valid for assembly submissions
• Add the option to submit metadata through uploading a manifest file

[bedroesb]

@bgruening Is it normal that I get an error like this "No repository named ena_webin_cli found with owner iuc" "remote_repository_url" https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli does not yet exist off course but don't know if that is the problem.

[bgruening]

No this is not normal, can you add a citation and then we see this is just a wired mix up.

[bedroesb]

@bgruening I think this is ready for review!

[bgruening]

I know its a larger rearchitecture, but do you think its feasilbly that we hide the web-cli tool in a pythons script and read the credetials straight from the YML file in python?

That way we do not expose any credentials as ENV var. We read the password from the yaml and pass them with subprocess to the cli-command.

[bgruening]

Suggested change

	<description>Submission of consensus sequences to the European Nucleotide Archive (ENA)</description>
	<description>Submission of consensus sequences to the ENA</description>

[bedroesb]

I personally like the more verbose description 🤔

[bedroesb]

Thanks for the review! I will get back to it soon!

[bedroesb]

@bgruening Thanks a lot for merging. I did start with a more secure wrapping, and I plan to make a PR for it. I was wondering if the tool could be installed also on usegalaxy.eu?

[bgruening]

If you need it feel free to add it to https://github.com/usegalaxy-eu/usegalaxy-eu-tools