# Galaxy workflow test file for galaxy-workflow.gxwf.yml (phix174_sra_landscape_spikein_sieve # / Workflow A). Assembled by implement-galaxy-workflow-test (phase 9) from galaxy-test-plan.yml, # galaxy-workflow.gxwf.yml, and test-data-refs.json. All job-input and output labels below are the # literal input/output ids from galaxy-workflow.gxwf.yml's inputs:/outputs: blocks. # # Two test cases, matching galaxy-test-plan.yml exactly: # 1. kmindex_wiring_smoke_generic_fixtures -- wiring/structural smoke test using each pinned # Tool Shed wrapper's own real upstream functional-test fixtures (generic, non-phiX174). # Existence-only assertions throughout; does not audit the am3 diagnostic. # 2. gene_e_j_am3_diagnostic_synthetic_lexicmap_index -- the flagship am3 content test, built # around a hand-constructed synthetic 3-decoy LexicMap hits fixture (see # test-data/synthetic_am3/). All output assertions in this case were verified by directly # executing the real vendored lexicmap_streamer.py (galaxy-user-tool.yml, LexicMapStreamer, # commit a51eb58d) against that fixture -- the reported values below are actual observed # script output, not guessed. # # KNOWN BLOCKING GAP (test case 2, carried from galaxy-test-plan.yml unresolved[0]/[1], both # blocking): `lexicmap_index_selection` in test case 2 is a PLACEHOLDER value # ("PhiX174E_J_Am3ToyIndex"). No real small kmindex/LexicMap index exists anywhere at test scale # (109 Logan kmindex shards and up to 25 LexicMap domain indices are multi-terabyte, # usegalaxy.org-hosted production data only), and no `lexicmap` or `kmindex` CLI was available in # this authoring environment to build and register one. Consequently: # - lexicmap_search (the real Tool Shed tool immediately upstream of lexicmap_streamer_tiling_qc # in the concrete workflow) cannot itself be made to emit the synthetic hits table below when # `planemo test` actually invokes this workflow end-to-end -- the tests-format `job:` block can # only bind values to top-level workflow input labels (confirmed against # references/schemas/tests-format.schema.json's `Job`/`TestJob` defs), and # `lexicmap_streamer_tiling_qc`'s `lexicmap_results` port is wired to an internal step output # (`lexicmap_search/out_file`), not a workflow input -- there is no schema-supported way to # inject a pre-built hits table directly onto that port from this file. # - The synthetic fixture (test-data/synthetic_am3/{E,J}.synthetic_lexicmap_hits.tsv plus the 3 # decoy reference FASTAs) is therefore staged as the validated ground truth this test case's # assertions were derived from, and as the input a future real-index-build pass (or a direct # component/tool-level test of lexicmap_streamer_tiling_qc alone) should reproduce against. # - See foundry-feedback.ledger.yml entry # `implement-galaxy-workflow-test-no-tests-format-path-to-intermediate-step-input` for the # schema-capability gap this exposed, and the plan's own unresolved[0]/[1] for the upstream # index-construction gap. # - A full `planemo test` run of this test case is therefore expected to fail or hang at # `lexicmap_search` today; this is a deliberate, already-documented deferral to phase 11 # (run-workflow-test), not an authoring omission. - doc: >- kmindex_wiring_smoke_generic_fixtures: structural/wiring smoke test for the kmindex containment-screen chain and lexicmap_search's multi-index-selection binding, using each pinned Tool Shed wrapper's own real upstream functional-test fixtures (generic, non-phiX174 sequences and indices). Proves the workflow's collection map-over, multi-select DB/index binding, and per-gene sensitivity-override wiring execute without error. Does NOT audit any biological content, including the Gene E am3 diagnostic (see the other test case for that). job: gene_query_panel: class: Collection collection_type: sample_sheet elements: - class: File identifier: E location: "https://raw.githubusercontent.com/galaxyproject/tools-iuc/main/tools/kmindex/test-data/query1.fasta" filetype: fasta - class: File identifier: J location: "https://raw.githubusercontent.com/galaxyproject/tools-iuc/main/tools/lexicmap/test-data/lexicmap_query3.fasta" filetype: fasta # Per-gene LexicMap sensitivity-override columns (align_min_match_pident, etc.) intentionally # left unset (no `rows:` block) -- not meaningful for generic non-phiX174 fixture content, # per galaxy-test-plan.yml test_cases[0].job_inputs[0]. # kmindex_db_selection / lexicmap_index_selection removed 2026-09-18: both ports are # `multiple: true` selects that reject a delimited string and require an array, which a # gxformat2 `text` input cannot carry. The index lists are now literals in the workflow's # kmindex_containment_screen / lexicmap_search step state, so they are no longer job inputs. kmindex_zvalue: 6 kmindex_threshold: 0.3 kmindex_output_format: "json" kmindex_fast: false lexicmap_top_n_genomes: 0 lexicmap_advanced_all: true tiling_qc_min_coverage: 0.8 tiling_qc_min_coverage_partial: 0.5 tiling_qc_min_pident: 60.0 tiling_qc_max_internal_stops: 0 tiling_qc_sample_cap: 10 tiling_qc_allow_frameshifts: false outputs: kmindex_accession_union: # Existence-only: the underlying index has no phiX174 biological relationship, so only # "the chain ran and produced non-empty output" is assertable. asserts: - has_size: { min: 1 } clean_full_length_cds_haplotypes: class: Collection element_tests: E: asserts: - has_size: { min: 1 } J: asserts: - has_size: { min: 1 } clean_haplotype_counts: class: Collection element_tests: E: asserts: - has_n_columns: { min: 2 } J: asserts: - has_n_columns: { min: 2 } flagged_audit_reasons: class: Collection element_tests: E: # "At least a header line is present." asserts: - has_n_lines: { min: 1 } per_gene_ingestion_summary: class: Collection element_tests: E: asserts: - has_text: { text: "{" } J: asserts: - has_text: { text: "{" } ingestion_manifest_all_genes: asserts: - has_n_lines: { n: 3, delta: 1 } gene_e_am3_quarantine_audit: # Existence-only: this case's "E" element is generic fixture sequence, not real phiX174 # gene E, so no am3 diagnostic content is expected here. asserts: - has_size: { min: 1 } - doc: >- gene_e_j_am3_diagnostic_synthetic_lexicmap_index: primary functional test for the paper's Sanger am3 spike-in diagnostic (freeform-summary.md Stage D2: genome position nt587 G->A causes a premature TGG->TAG stop at Gene E codon 7, gpE_W7*). Exercises lexicmap_streamer_tiling_qc -> {flatten_gene_summary_json_to_row -> join_gene_summary_rows_into_manifest} and -> extract_gene_e_am3_audit against a hand-built synthetic 3-decoy LexicMap hits fixture (test-data/synthetic_am3/) seeded with real cds/E.fasta and cds/J.fasta content: (1) a Gene-E wildtype-clean decoy (E_wildtype_ctrl, sseq == real E.fasta verbatim), (2) a Gene-E am3-positive decoy (E_am3_ctrl, sseq carries the exact nt587 G->A / codon-7 TGG->TAG substitution), (3) a Gene-J clean decoy (J_clean_ctrl, sseq == real J.fasta verbatim). All assertion values below were confirmed by directly executing the real vendored lexicmap_streamer.py against this fixture with the workflow's default tiling_qc_* parameters (see test-data/synthetic_am3/*.tsv header comments for full provenance). The kmindex chain shares the same job but is not this case's focus and is left unasserted (kmindex_accession_union), matching galaxy-test-plan.yml omissions[1]. KNOWN BLOCKING GAP: `lexicmap_index_selection` here is a placeholder ("PhiX174E_J_Am3ToyIndex") -- no real small LexicMap index backs it, and the tests-format `job:` block cannot bind the synthetic hits fixture directly onto lexicmap_streamer_tiling_qc's internal `lexicmap_results` port (see the file header comment above and galaxy-test-plan.yml unresolved[0]/[1]). A full `planemo test` run of this case is expected to fail/stall at lexicmap_search until a real toy index is constructed and registered; that construction is deferred to a later phase. job: gene_query_panel: class: Collection collection_type: sample_sheet elements: - class: File identifier: E path: test-data/E.fasta filetype: fasta - class: File identifier: J path: test-data/J.fasta filetype: fasta # Per-gene LexicMap sensitivity-override columns, in column_definitions order # (align_min_match_pident, align_min_match_len, seed_min_prefix, min_qcov_per_genome). # Populated for E (real per-gene values from logan_remaining_runs.json, per # test-data-refs.json); left null for J (falls back to wrapper defaults 70/50/17/unset). # NOTE: this skill bundle's packaged references do not document a worked `sample_sheet` / # `column_definitions` -> tests-format shape; this `rows:` block is a reasoned best-effort # construction against the tests-format.schema.json `Collection.rows` field (a dict of # column name -> per-row-aligned array) -- see the feedback ledger entry # `tests-format-schema-silent-on-sample-sheet-column-definitions-shape`. rows: align_min_match_pident: [60.0, null] align_min_match_len: [35, null] seed_min_prefix: [15, null] min_qcov_per_genome: [30.0, null] # kmindex_db_selection / lexicmap_index_selection removed 2026-09-18: both ports are # `multiple: true` selects that reject a delimited string and require an array, which a # gxformat2 `text` input cannot carry. The index lists are now literals in the workflow's # kmindex_containment_screen / lexicmap_search step state, so they are no longer job inputs. kmindex_zvalue: 6 kmindex_threshold: 0.3 kmindex_output_format: "json" kmindex_fast: false lexicmap_top_n_genomes: 0 lexicmap_advanced_all: true tiling_qc_min_coverage: 0.8 tiling_qc_min_coverage_partial: 0.5 tiling_qc_min_pident: 60.0 tiling_qc_max_internal_stops: 0 tiling_qc_sample_cap: 10 tiling_qc_allow_frameshifts: false outputs: clean_full_length_cds_haplotypes: # Gene E's clean cohort should contain exactly the wildtype-clean decoy (the am3-positive # decoy is routed to FLAGGED, not here). Gene J's clean cohort should contain its one clean # decoy. Confirmed via direct script execution: result_E.clean.accessions.fasta contains # only E_wildtype_ctrl; result_J.clean.accessions.fasta contains only J_clean_ctrl. class: Collection element_tests: E: asserts: - has_text: { text: "E_wildtype_ctrl" } J: asserts: - has_text: { text: "J_clean_ctrl" } clean_haplotype_counts: # Confirmed: header + exactly 1 clean-haplotype row for both E and J. class: Collection element_tests: E: asserts: - has_n_lines: { n: 2, delta: 1 } J: asserts: - has_n_lines: { n: 2, delta: 1 } flagged_accessions: # Confirmed: Gene E's flagged FASTA contains exactly the am3-positive decoy. class: Collection element_tests: E: asserts: - has_text: { text: "E_am3_ctrl" } flagged_audit_reasons: # Confirmed via direct script execution (result_E.flagged.tsv): # accession coverage mean_pident flag n_stops stop_codons hsps_merged # E_am3_ctrl 1.0000 99.63 PREMATURE_STOPS 1 7 1 # header + exactly 1 flagged row for E (stop_codons="7", matching the paper's gpE_W7* # codon-7 diagnostic). Gene J's flagged.tsv is header-only (0 flagged rows; clean decoy # only) -- confirmed exact 1-line file. class: Collection element_tests: E: asserts: - has_n_lines: { n: 2, delta: 1 } - has_text: { text: "7" } J: asserts: - has_n_lines: { n: 1, delta: 0 } per_gene_ingestion_summary: # Confirmed via direct script execution (result_E.summary.json / result_J.summary.json): # gene E total_accessions_evaluated=2, cohort_breakdown.flagged_premature_stops=1; # gene J total_accessions_evaluated=1. class: Collection element_tests: E: asserts: - has_json_property_with_value: { property: "total_accessions_evaluated", value: "2" } - has_json_property_with_value: { property: "flagged_premature_stops", value: "1" } J: asserts: - has_json_property_with_value: { property: "total_accessions_evaluated", value: "1" } ingestion_manifest_all_genes: asserts: - has_n_lines: { n: 3, delta: 1 } - has_text: { text: "gene" } gene_e_am3_quarantine_audit: # FLAGSHIP ASSERTION. Gene E element of flagged_tsv (extract_gene_e_am3_audit, # by_identifier "E"). Confirmed identical to result_E.flagged.tsv above: exactly 1 flagged # row (header + the single am3-positive decoy), identifying E_am3_ctrl with stop_codons="7" # -- the workflow-level, assertable analog of the paper's real finding that # 2,215,172/2,392,457 (92.59%) of evaluated Gene E accessions carry the nt587 G->A / # gpE_W7* substitution (real full-scale numbers recorded only as directional context in # test-data-refs.json, not asserted here). asserts: - has_n_lines: { n: 2, delta: 0 } - has_text: { text: "E_am3_ctrl" } - has_text: { text: "7" }