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galaxy.tool_util.linters package

This package contains linting functions for Galaxy tools.

Submodules

galaxy.tool_util.linters.citations module

This module contains a citation lint function.

Citations describe references that should be used when consumers of the tool publish results.

galaxy.tool_util.linters.citations.lint_citations(tool_xml, lint_ctx)[source]

Ensure tool contains at least one valid citation.

galaxy.tool_util.linters.command module

This module contains a linting function for a tool’s command description.

A command description describes how to build the command-line to execute from supplied inputs.

galaxy.tool_util.linters.command.lint_command(tool_xml, lint_ctx)[source]

Ensure tool contains exactly one command and check attributes.

galaxy.tool_util.linters.command.get_command(tool_xml)[source]

Get command XML element from supplied XML root.

galaxy.tool_util.linters.cwl module

Linter for CWL tools.

galaxy.tool_util.linters.cwl.lint_cwl_validation(tool_source, lint_ctx)[source]

Determine in CWL tool validates against spec.

galaxy.tool_util.linters.cwl.lint_new_draft(tool_source, lint_ctx)[source]

Determine in CWL tool is valid, modern draft.

galaxy.tool_util.linters.cwl.lint_docker_image(tool_source, lint_ctx)[source]
galaxy.tool_util.linters.cwl.lint_description(tool_source, lint_ctx)[source]

galaxy.tool_util.linters.general module

This module contains linting functions for general aspects of the tool.

galaxy.tool_util.linters.general.lint_general(tool_source, lint_ctx)[source]

Check tool version, name, and id.

galaxy.tool_util.linters.help module

This module contains a linting function for a tool’s help.

galaxy.tool_util.linters.help.lint_help(tool_xml, lint_ctx)[source]

Ensure tool contains exactly one valid RST help block.

galaxy.tool_util.linters.help.rst_invalid(text: str) → Union[bool, str][source]

Predicate to determine if text is invalid reStructuredText. Return False if the supplied text is valid reStructuredText or a string indicating the problem.

galaxy.tool_util.linters.inputs module

This module contains a linting functions for tool inputs.

galaxy.tool_util.linters.inputs.lint_inputs(tool_source: ToolSource, lint_ctx: LintContext)[source]

Lint parameters in a tool’s inputs block.

galaxy.tool_util.linters.inputs.lint_repeats(tool_source: ToolSource, lint_ctx)[source]

Lint repeat blocks in tool inputs.

galaxy.tool_util.linters.outputs module

This module contains a linting functions for tool outputs.

galaxy.tool_util.linters.outputs.lint_output(tool_source: ToolSource, lint_ctx: LintContext)[source]

Check output elements, ensure there is at least one and check attributes.

galaxy.tool_util.linters.stdio module

This module contains a linting functions for tool error detection.

galaxy.tool_util.linters.stdio.lint_stdio(tool_source, lint_ctx)[source]

galaxy.tool_util.linters.tests module

This module contains a linting functions for tool tests.

galaxy.tool_util.linters.tests.check_compare_attribs(element, lint_ctx, test_idx)[source]
galaxy.tool_util.linters.tests.lint_tests(tool_xml, lint_ctx)[source]

galaxy.tool_util.linters.xml_order module

This module contains a linting functions for tool XML block order.

For more information on the IUC standard for XML block order see - https://github.com/galaxy-iuc/standards.

galaxy.tool_util.linters.xml_order.lint_xml_order(tool_xml, lint_ctx)[source]