version: "1.0.1"

Galaxy Ground-Truth Expansion (Manual, per item)

Purpose: expand each benchmark item’s acceptable ground-truth tools (multiple correct answers) by manually reviewing the query and the underlying tutorial context. This skill exists because automated, “template-like” expansions can easily introduce incorrect alternatives.

This skill is for maintaining data/benchmark/v1_items.jsonl and keeping data/benchmark/v1_items_readable.md in sync.

Non-negotiable rules

• Expansion is manual: review one query + one tool at a time.
• Do not use “pattern rules”, “keyword triggers”, or “template expansions” to add tools in bulk.
• Only add an alternative tool if it is clearly acceptable for the same user intent in Galaxy.
• Only add tool IDs that exist on the target server (usegalaxy.org) tool universe.
• Prefer a small, high-precision set of alternatives over a large noisy set.

What “acceptable alternative” means

An alternative tool is acceptable if, given the query as written:

• A typical Galaxy user could reasonably choose either tool to accomplish the task, and
• The tool is not a different analysis step (e.g., a preprocessing step vs a downstream step), and
• The tool is not an unrelated visualization/reporting helper, and
• The alternative does not change the task semantics (e.g., long-read vs short-read aligner).

Inputs / outputs

• Input benchmark: data/benchmark/v1_items.jsonl
• Output benchmark (in-place updates): data/benchmark/v1_items.jsonl
• Readable export: data/benchmark/v1_items_readable.md
• Tool catalogs (usegalaxy.org): data/tool_catalog/

Why IO details + help text matter (discovery + validation)

io_details (IO fields in the catalog) are useful for two reasons:

1. Discovery (finding plausible alternatives): tools that can plausibly substitute each other often share

IO structure (e.g., both take tabular data + require a data_column target, both output a trained model, etc.).

1. Validation (preventing false positives): even if names/help text look similar, IO mismatch usually means

the tools are not interchangeable for the same step.

tool_help_text adds the missing semantic layer: it can confirm whether a tool genuinely supports the specific algorithm/operation implied by the query (e.g., “SVM”, “one-hot encoding”, “hyperparameter search”), and whether that support can be constrained to match the intent (e.g., “SVM-only”).

Step 0 — Make sure you have the tool universe

Build or refresh the catalog from usegalaxy.org (recommended: panel tools):

python3 -m scripts.catalog.build_usegalaxy_tool_catalog --server https://usegalaxy.org --in-panel --include-io-details

If you need the full installed universe:

python3 -m scripts.catalog.build_usegalaxy_tool_catalog --server https://usegalaxy.org --no-in-panel --include-io-details

Non-negotiable for expansion: the tool catalog must include input/output details.

• This skill assumes each tool entry in the catalog JSONL includes IO-related fields such as:
• input_params_flat (preferred summary)
• inputs_raw / outputs_raw (raw Galaxy tool parameter schema)
• If your catalog JSONL does not contain IO fields, rebuild it with --include-io-details before expanding ground truth.

Use these as references:

• data/tool_catalog/usegalaxy_org_tools.jsonl / data/tool_catalog/usegalaxy_org_index.json
• data/tool_catalog/usegalaxy_org_all_tools.jsonl / data/tool_catalog/usegalaxy_org_all_index.json

Notes on the tool catalog builder:

• The catalog is built by python3 -m scripts.catalog.build_usegalaxy_tool_catalog.
• --include-io-details enriches each JSONL entry with IO-related fields used by this expansion workflow.

Step 1 — Pick an item to expand

Work item-by-item. For a given id in data/benchmark/v1_items.jsonl:

1. Read the query (and ensure it does not mention datasets or the tool name).
2. Note the current single ground-truth tool in tools[0] and metadata.tool_focus.
3. Identify the tutorial (tutorial_id) and, if needed, open the tutorial markdown in training-material/.

Step 2 — Propose alternatives (manual)

For each proposed alternative tool:

1. Confirm it exists on usegalaxy.org (tool ID must be present in the catalog index).
2. Confirm it matches the query intent (not just “related”).
3. Prefer tools that appear in the same tutorial for the same step (strong evidence).
4. If the alternative is not in the tutorial, require stronger justification (e.g., a well-known equivalent Galaxy tool).
5. IO compatibility check (required):

• Compare the candidate tool’s expected inputs and outputs against the original tool using the catalog IO fields.
• Only add an alternative if a typical user could swap it in without changing the overall step semantics.
• If IO details are missing/unclear for either tool, do not expand for that item yet (rebuild the catalog with IO details).

1. Help text check (recommended):

• Use tool_help_text (if available) to confirm task semantics and important constraints.
• If tool_help_text is missing for a critical decision, consider regenerating the helptext-enriched catalog first.

Step 3 — Apply the change (edit JSONL)

Update only the target item:

• Append additional tool IDs to the item’s tools list (keep the original tool first).
• Add metadata.ground_truth_alternatives = true
• Add metadata.ground_truth_alternatives_note with a short human note, e.g.:
• “Manual: Tabular Learner also fits this tabular ML training intent.”
• “Manual: HISAT2 and RNA STAR are both spliced aligners for RNA-seq mapping.”
• “Manual: SVM classifier can also be trained with Tabular Learner when configured to compare only SVM models.”

Do not add “bulk source” tags or apply the same change across many items without reviewing each one.

Step 4 — Re-export the readable view

python3 -m scripts.benchmark.export_readable --input data/benchmark/v1_items.jsonl --output data/benchmark/v1_items_readable.md

Step 5 — Spot-check

Open the relevant section in data/benchmark/v1_items_readable.md and verify:

• The query still makes sense and does not mention datasets/tools.
• The listed tools are plausible alternatives (no obvious false positives).

Notes

• Do not commit secrets (API keys). usegalaxy.org /api/tools does not require an API key.
• If you previously applied any automated expansions, remove them before proceeding with manual expansion.

Worked example — SVM classifier → Tabular Learner

Scenario: the gold tool is the dedicated SVM classifier tool:

• toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/<version>

Candidate alternative: the AutoML-style tool:

• toolshed.g2.bx.psu.edu/repos/goeckslab/tabular_learner/tabular_learner/<version>

Discovery process

1. Read `tool_help_text` for `tabular_learner`:

> "This tool uses PyCaret to train and evaluate machine learning models. It compares different models on a dataset and provides the best model based on the performance metrics."

PyCaret is an AutoML library that wraps multiple sklearn-style models. This suggests it might include SVM.

1. Read `inputs_raw` → `model_selection` conditional:

Found the classification_models select parameter with these options:

• Logistic Regression
• K Neighbors Classifier
• Naive Bayes
• Decision Tree Classifier
• SVM - Linear Kernel
• SVM - Radial Kernel
• MLP Classifier
• Ridge Classifier
• Random Forest Classifier
• Ada Boost Classifier
• Gradient Boosting Classifier
• ...

This confirms tabular_learner can be restricted to SVM-only by selecting only SVM - Linear Kernel and/or SVM - Radial Kernel.

1. IO compatibility check:

• Both tools accept tabular input (csv, tabular).
• Both require a target column (data_column type parameter).
• Both output a trained model.
• ✅ IO structure is compatible.

Decision

Accept as alternative — user can configure tabular_learner to compare only SVM models (Linear/Radial kernel), making it functionally equivalent to the dedicated SVM classifier for this step.

Example queries that justify this expansion

• "I want to train an SVM classifier and evaluate accuracy with a proper train/test split. Which tool in Galaxy can do this?"
• "I need a support vector machine classifier for my feature matrix. What Galaxy tool should I run?"

Metadata note to add

"ground_truth_alternatives_note": "Manual: Tabular Learner can train SVM classifiers when model selection is restricted to SVM-Linear/Radial."

Worked example — Keras model fit → Ludwig experiment

Scenario: the gold tool is Keras-based deep learning:

• toolshed.g2.bx.psu.edu/repos/bgruening/keras_model_builder/keras_model_builder/<version>
• toolshed.g2.bx.psu.edu/repos/bgruening/keras_train_and_eval/keras_train_and_eval/<version>

Candidate alternative: Ludwig declarative deep learning:

• toolshed.g2.bx.psu.edu/repos/goeckslab/ludwig_experiment/ludwig_experiment/<version>

Discovery process

1. Read `tool_help_text` for `ludwig_experiment`:

> "Generic Learner Experiment: train on one (portion of) dataset and evaluate the model performance on another (portion of) dataset."

This is a training + evaluation tool, which matches the Keras train_and_eval step.

1. Check Ludwig's capabilities (from tool description/docs):

Ludwig supports multiple model architectures including:

• Feedforward Neural Networks (FNN)
• Convolutional Neural Networks (CNN)
• Recurrent Neural Networks (RNN)
• Transformers

All of these are also achievable with Keras.

1. IO compatibility check:

• Both accept tabular/structured input data.
• Both output trained models and evaluation metrics.
• ✅ IO structure is compatible for the "train + evaluate" step.

Decision

Accept as alternative — Ludwig can build equivalent architectures (FNN, CNN, RNN) via its declarative config, performing the same analysis step: train → evaluate → output model + metrics.

Example queries that justify this expansion

• "I want to train a feedforward neural network on my tabular dataset and evaluate its performance. Which Galaxy tool should I use?"
• "I need to train a CNN for image classification and get performance metrics. What tool can do this?"

Metadata note to add

"ground_truth_alternatives_note": "Manual: Ludwig experiment can train equivalent neural network architectures (FNN/CNN/RNN) with train+eval workflow."