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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 citation linters.

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

class galaxy.tool_util.linters.citations.CitationsMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.citations.CitationsNoText[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.citations.CitationsFound[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.citations.CitationsNoValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

galaxy.tool_util.linters.command module

This module contains linters for a tool’s command description.

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

class galaxy.tool_util.linters.command.CommandMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.command.CommandEmpty[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.command.CommandTODO[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.command.CommandInterpreterDeprecated[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.command.CommandInfo[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

galaxy.tool_util.linters.cwl module

Linter for CWL tools.

class galaxy.tool_util.linters.cwl.CWLValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.cwl.CWLInValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.cwl.CWLVersionMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.cwl.CWLVersionUnknown[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.cwl.CWLVersionGood[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.cwl.CWLDockerMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.cwl.CWLDockerGood[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.cwl.CWLDescriptionMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.cwl.CWLHelpTODO[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

galaxy.tool_util.linters.general module

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

class galaxy.tool_util.linters.general.ToolVersionMissing[source]

Bases: Linter

Tools must have a version

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolVersionPEP404[source]

Bases: Linter

Tools should have a PEP404 compliant version.

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolVersionWhitespace[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolVersionValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolNameMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolNameWhitespace[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolNameValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolIDMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolIDWhitespace[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolIDValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolProfileInvalid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolProfileLegacy[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ToolProfileValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.RequirementNameMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.RequirementVersionMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.RequirementVersionWhitespace[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.ResourceRequirementExpression[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.BioToolsValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.general.EDAMTermsValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

galaxy.tool_util.linters.help module

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

class galaxy.tool_util.linters.help.HelpMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.help.HelpEmpty[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.help.HelpPresent[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.help.HelpTODO[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.help.HelpInvalidRST[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.help.HelpValidRST[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

galaxy.tool_util.linters.help.rst_invalid(text: str) → 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.

class galaxy.tool_util.linters.inputs.InputsNum[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsMissingDataSource[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsDatasourceTags[source]

Bases: Linter

Lint that datasource tools have display and uihints tags

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsName[source]

Bases: Linter

Lint params define a name

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsNameRedundantArgument[source]

Bases: Linter

Lint params define a name

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsNameEmpty[source]

Bases: Linter

Lint params define a non-empty name

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsNameValid[source]

Bases: Linter

Lint params define valid cheetah placeholder

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsNameDuplicate[source]

Bases: Linter

Lint params with duplicate names

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsNameDuplicateOutput[source]

Bases: Linter

Lint params names that are also used in outputs

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsTypeChildCombination[source]

Bases: Linter

Lint for invalid parameter type child combinations

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsDataFormat[source]

Bases: Linter

Lint for data params wo format

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsDataOptionsMultiple[source]

Bases: Linter

Lint for data params with multiple options tags

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsDataOptionsAttrib[source]

Bases: Linter

Lint for data params with options that have invalid attributes

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsDataOptionsFilterAttribFiltersType[source]

Bases: Linter

Lint for valid filter types for data parameters if options set options_filter_attribute

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsDataOptionsFiltersType[source]

Bases: Linter

Lint for valid filter types for data parameters if options do not set options_filter_attribute

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsOptionsFiltersRequiredAttributes[source]

Bases: Linter

check required attributes of filters

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsOptionsRemoveValueFilterRequiredAttributes[source]

Bases: Linter

check required attributes of remove_value filter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsOptionsFiltersAllowedAttributes[source]

Bases: Linter

check allowed attributes of filters

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsOptionsRegexFilterExpression[source]

Bases: Linter

Check the regular expression of regexp filters

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsOptionsFiltersCheckReferences[source]

Bases: Linter

Check the references used in filters

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsDataOptionsFiltersRef[source]

Bases: Linter

Lint for set ref for filters of data parameters

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectDynamicOptions[source]

Bases: Linter

Lint for select with deprecated dynamic_options attribute

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionsDef[source]

Bases: Linter

Lint for valid ways to define select options

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionsDefConditional[source]

Bases: Linter

Lint for valid ways to define select options (for a select in a conditional)

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionValueMissing[source]

Bases: Linter

Lint for select option tags without value

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionDuplicateValue[source]

Bases: Linter

Lint for select option with same value

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionDuplicateText[source]

Bases: Linter

Lint for select option with same text

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionsMultiple[source]

Bases: Linter

Lint dynamic options select for multiple options tags

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionsDefinesOptions[source]

Bases: Linter

Lint dynamic options select for the potential to define options

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionsDeprecatedAttr[source]

Bases: Linter

Lint dynamic options select deprecated attributes

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionsFromDatasetAndDatatable[source]

Bases: Linter

Lint dynamic options select for from_dataset and from_data_table

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionsMetaFileKey[source]

Bases: Linter

Lint dynamic options select: meta_file_key attribute can only be used with from_dataset

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsBoolDistinctValues[source]

Bases: Linter

Lint booleans for distinct true/false value

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsBoolProblematic[source]

Bases: Linter

Lint booleans for problematic values, i.e. truevalue being false and vice versa

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectSingleCheckboxes[source]

Bases: Linter

Lint selects that allow only a single selection but display as checkboxes

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectMandatoryCheckboxes[source]

Bases: Linter

Lint selects that are mandatory but display as checkboxes

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectMultipleRadio[source]

Bases: Linter

Lint selects that allow only multiple selections but display as radio

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.InputsSelectOptionalRadio[source]

Bases: Linter

Lint selects that are optional but display as radio

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorParamIncompatible[source]

Bases: Linter

Lint for validator type - parameter type incompatibilities

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorAttribIncompatible[source]

Bases: Linter

Lint for incompatibilities between validator type and given attributes

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorHasText[source]

Bases: Linter

Lint that parameters that need text have text

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorHasNoText[source]

Bases: Linter

Lint that parameters that need no text have no text

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorExpression[source]

Bases: Linter

Lint that checks expressions / regexp (ignoring FutureWarning)

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorExpressionFuture[source]

Bases: Linter

Lint that checks expressions / regexp FutureWarnings

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorMinMax[source]

Bases: Linter

Lint for min/max for validator that need it

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorDatasetMetadataEqualValue[source]

Bases: Linter

Lint dataset_metadata_equal needs value or value_json

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorDatasetMetadataEqualValueOrJson[source]

Bases: Linter

Lint dataset_metadata_equal needs either value or value_json

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorMetadataCheckSkip[source]

Bases: Linter

Lint metadata needs check or skip

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorTableName[source]

Bases: Linter

Lint table_name is present if needed

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ValidatorMetadataName[source]

Bases: Linter

Lint metadata_name is present if needed

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ConditionalParamTypeBool[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ConditionalParamType[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ConditionalParamIncompatibleAttributes[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ConditionalWhenMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ConditionalOptionMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.inputs.ConditionalOptionMissingBoolean[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

galaxy.tool_util.linters.outputs module

galaxy.tool_util.linters.stdio module

This module contains a linting functions for tool error detection.

class galaxy.tool_util.linters.stdio.StdIOAbsenceLegacy[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.stdio.StdIOAbsence[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.stdio.StdIORegex[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

galaxy.tool_util.linters.tests module

This module contains a linting functions for tool tests.

class galaxy.tool_util.linters.tests.TestsMissing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsMissingDatasource[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsAssertsMultiple[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsAssertsHasNQuant[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsAssertsHasSizeQuant[source]

Bases: Linter

has_size needs at least one of size (or value), min, max

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsAssertsHasSizeOrValueQuant[source]

Bases: Linter

has_size should not have size and value

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsAssertionValidation[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsCaseValidation[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsExpectNumOutputs[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsParamInInputs[source]

Bases: Linter

really simple linter that test parameters are also present in the inputs

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsOutputName[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsOutputDefined[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsOutputCorresponding[source]

Bases: Linter

Linter checking if test/output corresponds to outputs/data

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsOutputCollectionCorresponding[source]

Bases: Linter

Linter checking if test/collection corresponds to outputs/output_collection

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsOutputCompareAttrib[source]

Bases: Linter

Linter checking compatibility of output attributes with the value of the compare attribute

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsOutputCheckDiscovered[source]

Bases: Linter

Linter checking that discovered elements of outputs are tested with a count attribute or listing some discovered_dataset

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsOutputCollectionCheckDiscovered[source]

Bases: Linter

Linter checking that discovered elements of output collections are tested with a count attribute or listing some elements

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsOutputCollectionCheckDiscoveredNested[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsOutputFailing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsExpectNumOutputsFailing[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsHasExpectations[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsNoValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

class galaxy.tool_util.linters.tests.TestsValid[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context

galaxy.tool_util.linters.xml_order module

This module contains a linter for tool XML block order.

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

class galaxy.tool_util.linters.xml_order.XMLOrder[source]

Bases: Linter

classmethod lint(tool_source: ToolSource, lint_ctx: LintContext)[source]: should add at most one message to the lint context