Plan: Fix `dotproduct` + `valueFrom` Scatter

Summary

Multi-parameter dotproduct scatter combined with valueFrom fails because the CWL parser assigns scatter_type to ALL step inputs when scatterMethod is present, not just the inputs actually listed in scatter.

Root Cause

File: lib/galaxy/tool_util/cwl/parser.py, lines 1205-1208

In InputProxy.to_dict():

if "scatterMethod" in self.step_proxy._step.tool:
    as_dict["scatter_type"] = self.step_proxy._step.tool.get("scatterMethod", "dotproduct")
else:
    as_dict["scatter_type"] = "dotproduct" if self.scatter else "disabled"

The self.scatter boolean correctly identifies whether this input is in the scatter list, but it’s only consulted in the else branch — when scatterMethod is absent. Multi-parameter scatter always specifies scatterMethod, so non-scattered inputs incorrectly get scatter_type = "dotproduct".

Downstream effect: In find_cwl_scatter_collections(), the non-scattered input (e.g., first which receives the full array for $(self[0].instr)) gets added to collections_to_match and scattered per-element. The valueFrom expression then receives a single record instead of the full array.

Single-parameter scatter never specifies scatterMethod, so those tests pass.

Code Changes

1. Fix the parser

File: lib/galaxy/tool_util/cwl/parser.py, lines 1205-1208

Replace:

if "scatterMethod" in self.step_proxy._step.tool:
    as_dict["scatter_type"] = self.step_proxy._step.tool.get("scatterMethod", "dotproduct")
else:
    as_dict["scatter_type"] = "dotproduct" if self.scatter else "disabled"

With:

if self.scatter:
    if "scatterMethod" in self.step_proxy._step.tool:
        as_dict["scatter_type"] = self.step_proxy._step.tool.get("scatterMethod", "dotproduct")
    else:
        as_dict["scatter_type"] = "dotproduct"
else:
    as_dict["scatter_type"] = "disabled"

Non-scattered inputs always get "disabled" regardless of scatterMethod presence.

2. Add unit test

File: test/unit/tool_util/test_cwl.py

Add test parsing scatter-valuefrom-wf4.cwl (the dotproduct + valueFrom workflow):

Assert echo_in1 has scatter_type = "dotproduct" and value_from set
Assert echo_in2 has scatter_type = "dotproduct" and no value_from
Assert first has scatter_type = "disabled" and value_from set

Follow pattern of existing test_workflow_scatter() at line 240.

3. Remove from RED_TESTS

File: scripts/cwl_conformance_to_test_cases.py

Remove wf_scatter_twoparam_dotproduct_valuefrom from RED_TESTS for v1.0, v1.1, v1.2.

Do NOT remove crossproduct+valueFrom variants — crossproduct itself isn’t implemented.

Testing Strategy

Write unit test asserting first gets scatter_type = "disabled" — RED
Apply parser fix — unit test GREEN
Run existing test_workflow_scatter — verify no regression
Run conformance test wf_scatter_twoparam_dotproduct_valuefrom (v1.2) — verify GREEN

Risk Assessment

The fix is narrow and correct: non-scattered inputs should never have a scatter type other than "disabled". Only inputs NOT in the scatter list on steps with scatterMethod are affected. No passing test relies on the incorrect behavior.

Critical Files

File	Change
`lib/galaxy/tool_util/cwl/parser.py`	Fix scatter_type assignment (lines 1205-1208)
`test/unit/tool_util/test_cwl.py`	Add unit test
`scripts/cwl_conformance_to_test_cases.py`	Remove 1 test from RED_TESTS (all 3 versions)

Unresolved Questions

The crossproduct+valuefrom tests also have this bug, but fixing it alone won’t make them pass (crossproduct isn’t implemented). Should we verify they fail with a different/better error after this fix?
Need to regenerate CWL conformance test cases after modifying RED_TESTS? (make generate-cwl-conformance-tests)
Is there a CI target that runs the CWL conformance suite, or only local run_tests.sh? (Answer: .github/workflows/cwl_conformance.yaml)

PLAN_GAP3_DOTPRODUCT_VALUEFROM

Plan: Fix dotproduct + valueFrom Scatter