galaxy/doc/schema_template.md

Galaxy Tool XML File

The XML File for a Galaxy tool, generally referred to as the "tool config file" or "wrapper", serves a number of purposes. First, it lays out the user interface for the tool (e.g. form fields, text, help, etc.). Second, it provides the glue that links your tool to Galaxy by telling Galaxy how to invoke it, what options to pass, and what files it will produce as output.

If you find a bug please report it here.

This document serves as reference documentation. If you would like to learn how to build tools for Galaxy, Planemo features a number of tutorials on building Galaxy tools that would better serve that purpose.

$tag:tool://element[@name='tool'] $tag:tool|description://element[@name='tool']//element[@name='description'] $tag:tool|macros://complexType[@name='Macros'] $tag:tool|edam_topics://complexType[@name='EdamTopics'] $tag:tool|edam_operations://complexType[@name='EdamOperations'] $tag:tool|requirements://complexType[@name='Requirements'] $tag:tool|requirements|requirement://complexType[@name='Requirement'] $tag:tool|requirements|container://complexType[@name='Container'] $tag:tool|code://complexType[@name='Code'] $tag:tool|stdio://complexType[@name='Stdio'] $tag:tool|stdio|exit_code://complexType[@name='ExitCode'] hide_attributes $tag:tool|stdio|regex://complexType[@name='Regex'] hide_attributes $tag:tool|version_command://complexType[@name='VersionCommand'] $tag:tool|command://element[@name='tool']//element[@name='command'] hide_attributes $tag:tool|environment_variables://complexType[@name='EnvironmentVariables'] $tag:tool|environment_variables|environment_variable://complexType[@name='EnvironmentVariable'] $tag:tool|configfiles://complexType[@name='ConfigFiles'] $tag:tool|configfiles|configfile://complexType[@name='ConfigFile'] $tag:tool|configfiles|inputs://complexType[@name='ConfigInputs'] $tag:tool|inputs://complexType[@name='Inputs'] $tag:tool|inputs|section://complexType[@name='Section'] $tag:tool|inputs|repeat://complexType[@name='Repeat'] $tag:tool|inputs|conditional://complexType[@name='Conditional'] $tag:tool|inputs|conditional|when://complexType[@name='ConditionalWhen'] $tag:tool|inputs|param://complexType[@name='Param'] $tag:tool|inputs|param|validator://complexType[@name='Validator'] $tag:tool|inputs|param|option://complexType[@name='ParamOption'] $tag:tool|inputs|param|conversion://complexType[@name='ParamConversion'] $tag:tool|inputs|param|options://complexType[@name='ParamOptions'] $tag:tool|inputs|param|options|column://complexType[@name='Column'] $tag:tool|inputs|param|options|filter://complexType[@name='Filter'] $tag:tool|inputs|param|sanitizer://complexType[@name='Sanitizer'] $tag:tool|inputs|param|sanitizer|valid://complexType[@name='SanitizerValid'] $tag:tool|inputs|param|sanitizer|valid|add://complexType[@name='SanitizerValidAdd'] $tag:tool|inputs|param|sanitizer|valid|remove://complexType[@name='SanitizerValidRemove'] $tag:tool|inputs|param|sanitizer|mapping://complexType[@name='SanitizerMapping'] $tag:tool|inputs|param|sanitizer|mapping|add://complexType[@name='SanitizerMappingAdd'] $tag:tool|inputs|param|sanitizer|mapping|remove://complexType[@name='SanitizerMappingRemove'] $tag:tool|request_param_translation://complexType[@name='RequestParameterTranslation'] $tag:tool|request_param_translation|request_param://complexType[@name='RequestParameter'] $tag:tool|request_param_translation|request_param|append_param://complexType[@name='RequestParameterAppend'] $tag:tool|request_param_translation|request_param|append_param|value://complexType[@name='RequestParameterAppendValue'] $tag:tool|request_param_translation|request_param|value_translation://complexType[@name='RequestParameterValueTranslation'] $tag:tool|request_param_translation|request_param|value_translation|value://complexType[@name='RequestParameterValueTranslationValue'] $tag:tool|outputs://complexType[@name='Outputs'] $tag:tool|outputs|data://complexType[@name='Data'] $tag:tool|outputs|data|filter://complexType[@name='OutputFilter'] $tag:tool|outputs|data|change_format://complexType[@name='ChangeFormat'] $tag:tool|outputs|data|change_format|when://complexType[@name='ChangeFormatWhen'] $tag:tool|outputs|data|actions://complexType[@name='Actions'] $tag:tool|outputs|data|actions|conditional://complexType[@name='ActionsConditional'] $tag:tool|outputs|data|actions|conditional|when://complexType[@name='ActionsConditionalWhen'] $tag:tool|outputs|data|actions|action://complexType[@name='Action'] $tag:tool|outputs|data|discover_datasets://complexType[@name='OutputDiscoverDatasets'] $tag:tool|outputs|collection://complexType[@name='Collection'] $tag:tool|outputs|collection|filter://complexType[@name='OutputFilter'] $tag:tool|outputs|collection|discover_datasets://complexType[@name='OutputCollectionDiscoverDatasets'] $tag:tool|tests://complexType[@name='Tests'] $tag:tool|tests|test://complexType[@name='Test'] $tag:tool|tests|test|param://complexType[@name='TestParam'] $tag:tool|tests|test|repeat://complexType[@name='TestRepeat'] $tag:tool|tests|test|section://complexType[@name='TestSection'] $tag:tool|tests|test|conditional://complexType[@name='TestConditional'] $tag:tool|tests|test|output://complexType[@name='TestOutput'] $tag:tool|tests|test|output|discover_dataset://complexType[@name='TestDiscoveredDataset'] $tag:tool|tests|test|output|metadata://complexType[@name='TestOutputMetadata'] $tag:tool|tests|test|output|assert_contents://group[@name='TestOutputElement']//element[@name='assert_contents'] $tag:tool|tests|test|output_collection://complexType[@name='TestOutputCollection'] $tag:tool|tests|test|assert_command://group[@name='TestParamElement']//element[@name='assert_command'] $tag:tool|tests|test|assert_stdout://group[@name='TestParamElement']//element[@name='assert_stdout'] $tag:tool|tests|test|assert_stderr://group[@name='TestParamElement']//element[@name='assert_stderr'] $tag:tool|help://element[@name='tool']//element[@name='help'] $tag:tool|citations://complexType[@name='Citations'] $tag:tool|citations|citation://complexType[@name='Citation']