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Switches hardcoded credentials to secure Galaxy-provided secrets, enhancing authentication safety and flexibility for users. Updates descriptions and help text for better clarity about functionality, input formats, and credential requirements.
And fixes environment variables access in command line.
Expands the tool's scope from imaging data to arbitrary data files by updating descriptions, input parameter types, and help text. Improves usability for broader biological study submissions.
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This pull request adds a new Galaxy tool
biostudies_upload, which enables users to upload data to the BioStudies database at EMBL-EBI using Aspera high-speed transfer.The tool uses the new
credentialsrequirement available in Galaxy since version 25.1 to handle secrets in a user-friendly way.Tests are expected to fail since there is no current way of providing credentials in the testing environment for now.