hifiasm: fix --primary output, --hg-size decimals, test typos, modern profile#7985
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alpapan wants to merge 3 commits into
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hifiasm: fix --primary output, --hg-size decimals, test typos, modern profile#7985alpapan wants to merge 3 commits into
alpapan wants to merge 3 commits into
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… profile * Fix duplicate output names causing primary_contig_graph to disappear when --primary is enabled. The output was declared multiple times under the same name, so Galaxy registered only the last (filter-disabled) one. The "Primary off mode" primary contig output is now named bp_primary_contig_graph; hap1/hap2 std labels are suffixed "(balanced haplotype)" to disambiguate from the trio outputs. * Wire the --primary toggle correctly: drop the unconditional --primary in the command line and fix the broken nested cheetah #if so the user-facing checkbox actually controls the flag. * --hg-size: accept decimal values (e.g. 1.3g). The sanitizer was stripping the dot, turning 1.3g into 13g silently. Added "." to the valid character set and tightened the validator regex. * Tests: wrap reads/mode_selector in <conditional name="mode"> so tests validate under modern Galaxy tool profiles; fix max_kooc -> max_kocc (Test 9) and hom-cov -> hom_cov (Test 11) typos; fix Test 5 trio param placement (reads at trio level, trio_input_selector inside trioinput). * Add profile="23.0" (was implicitly the legacy 16.01 profile) and bump VERSION_SUFFIX to 4.
bgruening
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May 13, 2026
RZ9082
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May 13, 2026
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Could you also please remove the .lint_skip file, and fix the linting errors if there are any?
* Use @Profile@ token (25.0) instead of hardcoded profile attr. * Replace `#if $assembly_options.primary: --primary #end if` with direct `$assembly_options.primary` substitution (canonical Galaxy idiom for booleans with truevalue/falsevalue). * Switch `name="primary"` to `argument="--primary"` so the param identifier auto-derives from the CLI flag; help text trimmed. * Fix test 17: `expect_num_outputs` 5 -> 6 (the noseq_files collection is counted), and switch the hap2 content assertion from `^S` regex to `has_size value="0"` since hifiasm emits an empty hap2 GFA for the tiny hifiasm-in1.fa.gz fixture. * Remove tools/hifiasm/.lint_skip; planemo lint is now clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
bgruening
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May 15, 2026
| </output> | ||
| <output name="hap2_contigs_std" ftype="gfa1"> | ||
| <assert_contents> | ||
| <has_size value="0"/> |
bgruening
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May 15, 2026
| </assert_command> | ||
| <output name="bp_primary_contig_graph" ftype="gfa1"> | ||
| <assert_contents> | ||
| <has_text_matching expression="^S"/> |
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is there just nothing included? Or why is this test so flax/loose?
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Summary
A handful of bug fixes and test/profile cleanup in
tools/hifiasm/hifiasm.xml.Bug fixes
primary_contig_graphdisappears when the--primarycheckbox is set. Three<data>elements share the nameprimary_contig_graph; Galaxy only registers the last, whose filter requires the opposite checkbox state. The Primary-off primary contig output is now namedbp_primary_contig_graph, and thehap1_contigs_std/hap2_contigs_stdlabels are suffixed with "(balanced haplotype)" to disambiguate from the trio outputs (resolves aOutputsLabelDuplicatedFilterwarning).--primarytoggle was a no-op. The command section had an unconditional--primaryand a broken nested#if(the'blank'branch was inside the'set'branch and could never fire). Reorganised so the user-facing checkbox actually controls the flag while preserving "primary on" as the default.--hg-sizesilently drops decimal points. Entering1.3gwas sanitised to13g. Added.to the sanitizer's valid set and tightened the validator regex to^[0-9]+(\.[0-9]+)?[kKmMGg]?$. Help text updated.Tests / lint
<param name="reads">+<param name="mode_selector">inside<conditional name="mode">for the standard / ONT tests, so they validate under modern Galaxy tool profile versions (resolves 15×TestsCaseValidation).readsmoved to trio level;trio_input_selectormoved insidetrioinputto match the actual input structure.max_kooc→max_kocc(resolvesTestsParamInInputsERROR).hom-cov→hom_cov(param name is derived fromargument="--hom-cov", hyphens become underscores).--primaryOFF path (balanced haplotype outputs).profile="23.0"(was implicitly legacy16.01) and bumpVERSION_SUFFIXto4.Test plan
planemo lint— clean (no warnings, no errors).planemo testagainst existing test data.--hg-sizeto1.3gand confirm the command line carries1.3g, not13g.