# author-galaxy-tool-wrapper scenarios

Concrete cases for `author-galaxy-tool-wrapper`, exercised against the abstract
properties in `eval.md`. Each case binds a fixture and states its expected
values; the `eval.md` oracle is applied to whatever the case produces.

## Case: conda-only Nextflow process

- fixture: Nextflow process summary with a bioconda-only environment directive,
  explicit command, declared inputs, declared outputs, and minimal test fixture
  evidence.
- expect: authors a Galaxy `GalaxyUserTool` YAML definition whose
  container/package evidence matches the conda spec, whose `shell_command`
  preserves the process command intent, and whose UDT passes structural
  validation plus mandatory critic review.

## Case: biocontainers Docker URI

- fixture: Nextflow process summary with a BioContainers Docker URI, command
  stanza, input/output declarations, and no acceptable Tool Shed discovery hit.
- expect: derives a plausible conda-equivalent requirement set, preserves
  command-stanza fidelity, and records uncertainty where container-to-conda
  mapping is not directly evidenced.

## Case: discovery fallthrough against IWC-wrapped tools

- fixture: process needs corresponding to IWC-wrapped tools such as fastp and
  samtools where wrapper discovery should normally succeed.
- expect: does not author a duplicate UDT unless discovery evidence is
  unacceptable; explains why the fallthrough was justified and compares the
  authored UDT shape against the existing IWC wrapper's behavior.