Nicola Soranzo
3180b63166
Generate intermediate rst file instead of html Move generation to doc/Makefile Use pandoc to generate table of contents and fragment ids. Remove nested inline markup (not supported by reStructuredText) Fix https and other links.
5.2 KiB
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|version_command://complexType[@name='VersionCommand'] $tag:tool|command://element[@name='tool']//element[@name='command'] hide_attributes $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|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|configfiles://complexType[@name='ConfigFiles'] $tag:tool|configfiles|configfile://complexType[@name='ConfigFile'] $tag:tool|configfiles|inputs://complexType[@name='ConfigInputs'] $tag:tool|environment_variables://complexType[@name='EnvironmentVariables'] $tag:tool|environment_variables|environment_variable://complexType[@name='EnvironmentVariable'] $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|code://complexType[@name='Code'] $tag:tool|requirements://complexType[@name='Requirements'] $tag:tool|requirements|requirement://complexType[@name='Requirement'] $tag:tool|requirements|container://complexType[@name='Container'] $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|help://element[@name='tool']//element[@name='help'] $tag:tool|citations://complexType[@name='Citations'] $tag:tool|citations|citation://complexType[@name='Citation']