Incoming References (63)

• advance-galaxy-draft-steprelated mold— Advance the gxformat2 draft by one step: pick the next drafty step, resolve a wrapper, implement the step, and validate.
• Cleanup, sync, and publish non-empty resultsrelated mold— Clean sparse mapped outputs, keep sibling collections aligned, then gate report publishing on non-empty results.
• Collection: build list paired with Apply Rulesrelated mold— Use Apply Rules to promote identifier columns into a list:paired collection, with optional cleanup first.
• Collection: build named bundlerelated mold— Use BUILD_LIST to assemble named outputs into a collection bundle for publishing or downstream fan-in.
• Collection: cleanup after map-over failurerelated mold— Use FILTER_EMPTY or FILTER_FAILED after map-over when bad elements would break downstream collection steps.
• Collection: flatten after fan-outrelated mold— Use FLATTEN to collapse nested collection outputs to a flat list once the outer axis no longer matters.
• Collection: split identifier via rulesrelated mold— Use Apply Rules regex columns to split one collection identifier into nested list identifiers.
• Collection: swap nesting with Apply Rulesrelated mold— Use Apply Rules to regroup a list:list collection by swapping outer and inner identifier columns.
• Collection: unbox singletonrelated mold— Use __EXTRACT_DATASET__ with which: first when a one-element collection must become a dataset.
• Parameter: compose runtime text parameterrelated mold— Use compose_text_param to build connected text expressions from constants plus runtime scalar values.
• Conditional: gate on non-empty resultrelated mold— Derive a boolean from empty or non-empty data, then use when to skip reporting or export steps.
• Conditional: route between alternative outputsrelated mold— Use when-gated alternatives plus pick_value to merge binary or one-of-N routes into one downstream value.
• Conditional: run optional steprelated mold— Use a workflow boolean connected as inputs.when to skip an optional Galaxy step or branch.
• Conditional: transform or pass throughrelated mold— Gate an optional transform, then use pick_value to pass transformed data when present or original data otherwise.
• Parameter: derive from filerelated mold— Read a one-value dataset with param_value_from_file, including count recipes that feed typed parameters.
• Fan-in bundle, consume, and flattenrelated mold— Bundle parallel outputs into a collection consumer, then flatten nested results for pooled downstream processing.
• Galaxy: collection patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy collection transformation patterns.
• Galaxy: conditionals patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy when and pick_value conditional patterns.
• Galaxy: genomic interval patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy genomic interval operations and recipes on coordinate features.
• Galaxy: sequence patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy operations on sequence records (FASTA) — interconvert, reformat, merge, length, extract/mask by region.
• Galaxy: tabular patternsrelated mold— Use this MOC to choose corpus-grounded Galaxy tabular transformation patterns.
• Collection: harmonize by sortlist from identifiersrelated mold— Use SORTLIST with sort_type:file to reorder one collection by another collection's identifiers.
• Interval: consensus regions by multi-intersectrelated mold— Find features reproducible across replicates: multi-intersect per-replicate sets, threshold by replicate count, then intersect back against the merged call.
• Interval: compute coveragerelated mold— Two coverage modes: genome-wide depth as a bedgraph (genomecoveragebed) and reads counted in given regions (coveragebed). Same family, different question.
• Interval: build a mask by set algebrarelated mold— Compute regions from regions: concatenate candidate intervals, merge into non-overlapping spans, then subtract the set to keep. The gops_* set-algebra recipe.
• Interval: merge overlapping featuresrelated mold— Collapse overlapping or book-ended intervals within one set into single spans; bedtools mergebed or the gops_merge Operate-on-Genomic-Intervals tool.
• Interval: filter or annotate by overlaprelated mold— Keep, drop, or annotate coordinate features by overlap with a second feature set; bedtools intersect (BED) or vcfvcfintersect (VCF), mapped over a collection.
• Interval: window or flank featuresrelated mold— Extend features by a fixed or fractional amount to build neighborhood windows, clamped to chromosome ends; bedtools slopbed with a genome file.
• Interval: windowed coverage around featuresrelated mold— Quantify signal in fixed neighborhoods around point features: window the features (slop), collapse overlaps (merge), then count reads in each window (coverage).
• Manifest to mapped collection lifecyclerelated mold— Use a manifest or table to build a collection, map a tool per row, then relabel or reshape outputs.
• Parameter: map workflow enum to tool parameterrelated mold— Use map_param_value to translate workflow enum values into downstream tool codes, flags, or snippets.
• Collection: regex relabel via tabularrelated mold— Derive collection element identifiers in a tabular mapping, then apply them with RELABEL_FROM_FILE.
• Sequence: relabel FASTA headers via tabularrelated mold— Edit FASTA headers you cannot easily regex in place: fasta2tab, rewrite column 1 with find/replace, then tab2fasta back. The high-value sequence recipe.
• Collection: relabel via rules and find/replacerelated mold— Use Apply Rules, identifier extraction, find/replace, and relabeling for structural fan-out cleanup.
• Reshape, relabel, and remap by collection axisrelated mold— Use Apply Rules and deterministic relabeling when domain fan-out creates the wrong map-over axis.
• Sequence: compute record lengthsrelated mold— Emit a (id, length) table from a FASTA so downstream tabular steps can filter, sort, or threshold records by length; fasta_compute_length.
• Sequence: extract or mask by regionrelated mold— Turn coordinates into sequence: extract FASTA at BED intervals (getfasta), mask regions by BED (maskfasta), or extract transcripts from a GFF (gffread).
• Sequence: interconvert FASTA and tabularrelated mold— Move sequence records between FASTA and a (header, sequence) table so tabular tools can edit them; fasta2tab one way, tab2fasta back.
• Sequence: merge FASTA and filter uniquerelated mold— Concatenate several FASTA files into one and drop duplicate records by sequence identity in a single step; fasta_merge_files_and_filter_unique_sequences.
• Sequence: reformat FASTA line widthrelated mold— Rewrap FASTA records to a fixed sequence-line width so downstream tools and viewers get canonical 60/70/80-column output; cshl_fasta_formatter.
• Collection: sync collections by identifierrelated mold— Use collection_element_identifiers with FILTER_FROM_FILE or RELABEL_FROM_FILE to align sibling collections.
• Tabular: compute a new columnrelated mold— Use column_maker (Add_a_column1) with strict error_handling to insert/replace a computed column. Per-expression-kind auto_col_types rule.
• Tabular: concatenate collection to tablerelated mold— Use collapse_dataset to row-bind a collection of tabulars into one table, with optional element IDs and header dedupe.
• Tabular: cut and reorder columnsrelated mold— Use Cut1 with a comma-separated cN list to project — and reorder — columns. Listing out of order is the canonical reorder idiom.
• Tabular: filter rows by column valuerelated mold— Use Filter1 with a Python expression over cN columns to drop rows. Highest-frequency tabular row filter in IWC.
• Tabular: filter rows by regexrelated mold— Use tp_grep_tool for whole-line regex row filters on tabular input. Grep1 is the legacy alternative.
• Tabular: group and aggregaterelated mold— Use datamash_ops for grouped tabular aggregation: multi-column grouping, collapse, countunique, min/max, and reductions.
• Tabular: join on keyrelated mold— Use tp_easyjoin_tool for two-tabular key joins; use tp_multijoin_tool for many files and query_tabular for SQL joins.
• Tabular: pivot collection to widerelated mold— Use collection_column_join to outer-join a collection of 2-column id/value tables into one wide table.
• Tabular: prepend headerrelated mold— Use tp_awk_tool to prepend a constant header line, optionally skipping or reformatting an existing first row.
• Tabular: relabel by row counterrelated mold— Use tp_awk_tool to replace each row or label with deterministic sample_N values from awk NR.
• Tabular: split taxonomy stringrelated mold— Use tp_awk_tool to split semicolon-delimited taxonomy strings into explicit rank columns with missing-rank handling.
• Tabular: SQL queryrelated mold— Use query_tabular when SQL semantics justify it: windows, joins, anti-joins, or fused project+compute over tabulars.
• Tabular: synthesize BED from 3-column inputrelated mold— Use tp_awk_tool to convert chrom/start/end rows into 6-column BED, subtracting 1 from start and setting constants.
• Tabular: to collection by rowrelated mold— Use split_file_to_collection split_by:col to fan a tabular into collection elements by row/key.
• Galaxy tool and job failure referencerelated mold— Reference for Galaxy tool stdio rules, job failure detection, job states, and job API failure surfaces.
• Galaxy workflow draft formatrelated mold— gxformat2 draft superset: wrapper-tier TODOs (tool_id, tool_state, port names) plus _plan_state / _plan_context / _plan_in / _plan_out per tool step.
• Nextflow operators to Galaxy collection recipesrelated mold— Classifies common Nextflow operators as Galaxy wiring, collection semantics, explicit steps, or review triggers.
• Nextflow-to-Galaxy channel shape mappingrelated mold— Maps common Nextflow channel, tuple, and path shapes to Galaxy dataset and collection shapes.
• Galaxy tool discovery recommendationrelated mold— JSON Schema for Tool Shed discovery hit, weak, and miss recommendations.
• Galaxy tool summary manifestrelated mold— JSON Schema for the deterministic per-tool manifest emitted by `galaxy-tool-cache summarize`.
• Galaxy workflow draft (gxformat2 superset)related mold— JSON Schema for `class: GalaxyWorkflowDraft` — gxformat2 with `TODO_*` sentinels and `_plan_*` planning fields per draft step.
• Galaxy ParsedToolrelated mold— JSON Schema for the upstream Galaxy `ParsedTool` model, vendored from `@galaxy-tool-util/schema`.