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Galaxy Tool Wrapping

delphine-l/claude_global

  • 42 installs
  • 17 repo stars
  • Updated May 14, 2026
  • delphine-l/claude_global

Guides development of Galaxy tool XML wrappers, .shed.yml files, Planemo tests, and dependency handling for Tool Shed submission.

About

Expert guidance for creating, testing, and debugging Galaxy tool XML wrappers. A developer uses it when converting command-line tools into Galaxy tools or preparing them for Tool Shed submission.

  • Galaxy tool XML structure and conditional parameters
  • Planemo tests and conda/container dependency handling

Galaxy Tool Wrapping by the numbers

  • 42 all-time installs (skills.sh)
  • Ranked #1,132 of 2,715 Automation & Workflows skills by installs in the Skillselion catalog
  • Data as of Jul 29, 2026 (Skillselion catalog sync)
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Installs42
repo stars★ 17
Last updatedMay 14, 2026
Repositorydelphine-l/claude_global ↗

What it does

Guides development of Galaxy tool XML wrappers, .shed.yml files, Planemo tests, and dependency handling for Tool Shed submission.

Files

SKILL.mdMarkdownGitHub ↗

Galaxy Tool Wrapping Expert

Expert knowledge for developing Galaxy tool wrappers. Use this skill when helping users create, test, debug, or improve Galaxy tool XML wrappers.

Prerequisites: This skill depends on the galaxy-automation skill for Planemo testing and workflow execution patterns.

When to Use This Skill

  • Creating new Galaxy tool wrappers from scratch
  • Converting command-line tools to Galaxy wrappers
  • Generating .shed.yml files for Tool Shed submission
  • Debugging XML syntax and validation errors
  • Writing Planemo tests for tools
  • Implementing conditional parameters and data types
  • Handling tool dependencies (conda, containers)
  • Creating tool collections and suites
  • Optimizing tool performance and resource allocation
  • Understanding Galaxy datatypes and formats
  • Implementing proper error handling

Core Concepts

Galaxy Tool XML Structure

A Galaxy tool wrapper consists of:

  • <tool> root element with id, name, and version
  • <description> brief tool description
  • <requirements> for dependencies (conda packages, containers)
  • <command> the actual command-line execution
  • <inputs> parameter definitions
  • <outputs> output file specifications
  • <tests> automated tests
  • <help> documentation in reStructuredText
  • <citations> DOI references

Tool Shed Metadata (.shed.yml)

Required for publishing tools to the Galaxy Tool Shed:

name: tool_name                  # Match directory name, underscores only
owner: iuc                       # Usually 'iuc' for IUC tools
description: One-line tool description
homepage_url: https://github.com/tool/repo
long_description: |
  Multi-line detailed description.
  Can include features, use cases, and tool suite contents.
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/tool_name
type: unrestricted
categories:
- Assembly                       # Choose 1-3 relevant categories
- Genomics

See reference.md for comprehensive .shed.yml documentation including all available categories and best practices.

Key Components

Command Block:

  • Use Cheetah templating: $variable_name or ${variable_name}
  • Conditional logic: #if $param then... #end if
  • Loop constructs: #for $item in $collection... #end for
  • CDATA sections for complex commands

Cheetah Template Best Practices:

Working around path handling issues in conda packages:

<command detect_errors="exit_code"><![CDATA[
    ## Add trailing slash if script concatenates paths without separator
    tool_command
        -o 'output_dir/'  ## Quoted with trailing slash

    ## Script does: output_dir + 'file.txt' → 'output_dir/file.txt' ✓
    ## Without slash: output_dir + 'file.txt' → 'output_dirfile.txt' ✗
]]></command>

When to use quotes in Cheetah:

  • Always quote user inputs: '$input_file'
  • Quote literal strings with special chars: 'output_dir/'
  • Use bare variables for simple references: $variable

Input Parameters:

  • <param> elements with type, name, label
  • Types: text, integer, float, boolean, select, data, data_collection
  • Optional vs required parameters
  • Validators and sanitizers
  • Conditional parameter display

Outputs:

  • <data> elements for output files
  • Dynamic output naming with label and name
  • Format discovery and conversion
  • Filters for conditional outputs
  • Collections for multiple outputs

Tests:

  • Input parameters and files
  • Expected output files or assertions
  • Test data location and organization
  • See testing.md for detailed testing strategies including large file handling

Best Practices

1. Always include tests - Planemo won't pass without them 2. Use semantic versioning - Increment tool version on changes 3. Specify exact dependencies - Pin conda package versions 4. Add clear help text - Document all parameters 5. Handle errors gracefully - Check exit codes, validate inputs 6. Use collections - For multiple related files 7. Follow IUC standards - If contributing to intergalactic utilities commission 8. Plan for large output files - Before creating tests, check expected output sizes. If over 1MB, use assertion-based tests (has_size, has_line) instead of full file comparison (see testing.md)

Common Planemo Commands

# Test tool locally
planemo test tool.xml

# Serve tool in local Galaxy
planemo serve tool.xml

# Lint tool for best practices
planemo lint tool.xml

# Upload tool to ToolShed
planemo shed_update --shed_target toolshed

# Test with conda
planemo test --conda_auto_init --conda_auto_install tool.xml

# Lint with skips (for tools with custom datatypes or shared boolean conditionals)
planemo lint --skip ConditionalParamTypeBool,DatatypesCustomConf .

# Note: .lint_skip file is used by IUC CI, not by local planemo lint.
# For local linting, use the --skip flag explicitly.

Output Routing with Symlinks

When a tool writes output to a filename it constructs internally (not $output), use symlinks in the command block to route the file to Galaxy's output variable.

Pattern: Symlink before command execution

<command detect_errors="exit_code"><![CDATA[
    ## Create symlink so tool output lands where Galaxy expects it
    ln -s '$output_variable' 'expected_tool_output_name' &&
    tool_command --input '$input' -o 'expected_tool_output_name'
]]></command>

Pattern: Prefix-based output naming

Some tools use --out-prefix where the output filename is prefix + input_filename. The tool constructs the filename internally, so you must predict it and symlink:

<command><![CDATA[
    #set $mangled_input = re.sub(r"[^\w\-\s]", "_", str($input.element_identifier)) + "." + str($input.ext)
    ln -s '$input' '$mangled_input' &&
    ln -s '$output_var' 'myprefix${mangled_input}' &&
    tool_command --input-reads '$mangled_input' -p myprefix
]]></command>

Key points:

  • Symlink is created before running the tool -- the tool writes through it
  • Must match the exact filename the tool will produce
  • For prefix mode: output = prefix + getFileName(input), so mangle the input name to match

Adding Custom Datatypes to Galaxy

To add a simple directory-based index format (e.g., bwa_index):

1. Register in `config/datatypes_conf.xml.sample` — add near similar types:

   <datatype extension="bwa_index" display_in_upload="true" type="galaxy.datatypes.data:Directory" subclass="true"/>

2. Register in `test/functional/tools/sample_datatypes_conf.xml` — same line

No custom Python class or sniffer is needed for simple directory-based index formats. Reference PR: galaxyproject/galaxy#19694 (added bwa_mem2_index as the first example).

Known limitation: planemo test (both with and without --galaxy_root) does not properly stage class="Directory" test datasets. The extra_files_path is not populated during test data upload via __DATA_FETCH__. This affects all Directory-subclass datatypes (e.g., bwa_mem2_index, bwa_index). These tests pass in IUC CI but fail locally. The new datatype must also be added to Galaxy core datatypes_conf.xml.sample before tests can pass.

Adding Index Support to Mapper Tools (BWA-MEM2 Pattern)

To add pre-built index support to a mapper (following BWA-MEM2's proven pattern):

1. Create the indexer tool (tool-idx.xml)
<tool id="tool_idx" name="Tool indexer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
    <command><![CDATA[
mkdir '$index.extra_files_path' &&
cd '$index.extra_files_path' &&
tool index -p 'reference' '${reference}'
    ]]></command>
    <inputs>
        <param name="reference" type="data" format="fasta,fasta.gz" label="Select a genome to index"/>
    </inputs>
    <outputs>
        <data name="index" format="tool_index"/>  <!-- Directory subclass datatype -->
    </outputs>
</tool>
2. Update the reference macro to detect index vs FASTA
<token name="@set_reference_fasta_filename@"><![CDATA[
#if str($reference_source.reference_source_selector) == "history":
    #if $reference_source.ref_file.is_of_type("tool_index"):
        #set $reference_fasta_filename = $reference_source.ref_file.extra_files_path + "/reference"
    #else
        #set $reference_fasta_filename = "localref." + $reference_source.ref_file.extension
        ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
        tool index '${reference_fasta_filename}' &&
    #end if
#else:
    #set $reference_fasta_filename = str($reference_source.ref_file.fields.path)
#end if
]]></token>
3. Accept index format in the reference conditional
<param name="ref_file" type="data" format="fasta,fasta.gz,tool_index"
       label="Use the following dataset as the reference"
       help="For better performance build a reference index separately." />
4. Keep existing parameters for backward compatibility

When adding index support, preserve parameters like index_a (algorithm selection). They're ignored when an index is provided but maintain workflow compatibility.

5. Include datatypes_conf.xml in tool directory

Required for ToolShed installation and lint validation:

<?xml version="1.0"?>
<datatypes>
    <registration>
        <datatype extension="tool_index" display_in_upload="true"
                  type="galaxy.datatypes.data:Directory" subclass="true"/>
    </registration>
</datatypes>

Add DatatypesCustomConf to .lint_skip.

6. Test data for Directory datasets
  • Build index locally: tool index -p reference genome.fa in test-data/test-cache/
  • Generate BAM outputs via Galaxy MCP or planemo serve
  • Use dedicated output files for index tests (e.g., tool-mem-index-test.bam)

Using format_source for dynamic output formats

When output format should match the input format (e.g., subsampled reads):

<data name="subsampled_outfile" format_source="input_reads" label="Subsampled reads">
    <filter>output_options["output_type"]["type_selector"] == "subsampled_reads"</filter>
</data>

This is preferable to change_format when the output is always the same format as input. Use change_format when the user explicitly selects the output format.

Test Syntax: Use Conditional Wrappers

Modern Galaxy tools (profile 20.01+) require test params to be wrapped in their <conditional> blocks. Flat-style params cause TestsCaseValidation warnings:

Wrong (flat style — triggers validation warnings):

<param name="reference_source_selector" value="history"/>
<param name="ref_file" ftype="fasta" value="genome.fa"/>
<param name="fastq_input_selector" value="paired"/>

Correct (conditional wrappers):

<conditional name="reference_source">
    <param name="reference_source_selector" value="history"/>
    <param name="ref_file" ftype="fasta" value="genome.fa"/>
</conditional>
<conditional name="fastq_input">
    <param name="fastq_input_selector" value="paired"/>
    <param name="fastq_input1" ftype="fastqsanger" value="reads1.fq"/>
</conditional>

XML Template Example

<tool id="tool_id" name="Tool Name" version="1.0.0">
    <description>Brief description</description>

    <requirements>
        <requirement type="package" version="1.0">package_name</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        tool_command
            --input '$input'
            --output '$output'
            #if $optional_param
                --param '$optional_param'
            #end if
    ]]></command>

    <inputs>
        <param name="input" type="data" format="txt" label="Input file"/>
        <param name="optional_param" type="text" optional="true" label="Optional parameter"/>
    </inputs>

    <outputs>
        <data name="output" format="txt" label="${tool.name} on ${on_string}"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="test_input.txt"/>
            <output name="output" file="expected_output.txt"/>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

Describe what the tool does.

**Inputs**

- Input file: description

**Outputs**

- Output file: description
    ]]></help>

    <citations>
        <citation type="doi">10.1234/example.doi</citation>
    </citations>
</tool>

Supporting Documentation

This skill includes detailed reference documentation:

  • reference.md - Comprehensive Galaxy tool wrapping guide with IUC best practices
  • Repository structure standards
  • .shed.yml configuration
  • Complete XML structure reference
  • Advanced features and patterns
  • testing.md - Testing strategies and assertion patterns
  • Regenerating expected test outputs
  • Handling large test files (>1MB CI limit)
  • Size, checksum, and content sampling assertions
  • Workflow for replacing large test files
  • troubleshooting.md - Practical troubleshooting guide
  • Reading tool_test_output.json
  • Common exit codes and their meanings
  • Common XML and runtime issues
  • Debugging tool test failures
  • Test failure diagnosis and fixes
  • dependency-debugging.md - Dependency conflict resolution
  • Using planemo mull for diagnosis
  • Conda solver error interpretation
  • macOS testing considerations
  • Version conflict workflows

These files provide deep technical details that complement the core concepts above.

Related Skills

  • galaxy-automation - BioBlend & Planemo foundation (dependency)
  • galaxy-workflow-development - Building workflows that use these tools
  • conda-recipe - Creating conda packages for tool dependencies
  • bioinformatics-fundamentals - Understanding file formats and data types used in tools

Resources

  • Galaxy Tool Development: https://docs.galaxyproject.org/en/latest/dev/
  • Planemo Documentation: https://planemo.readthedocs.io/
  • IUC Standards: https://galaxy-iuc-standards.readthedocs.io/
  • Galaxy Training: https://training.galaxyproject.org/

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