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galaxy.tools.parser package¶
Package responsible for parsing tools from files/abstract tool sources.
-
galaxy.tools.parser.
get_input_source
(content)[source]¶ Wrap an XML element in a XmlInputSource if needed.
If the supplied content is already an InputSource object, it is simply returned. This allow Galaxy to uniformly consume using the tool input source interface.
-
galaxy.tools.parser.
get_tool_source
(config_file=None, xml_tree=None, enable_beta_formats=True, tool_location_fetcher=None)[source]¶ Return a ToolSource object corresponding to supplied source.
The supplied source may be specified as a file path (using the config_file parameter) or as an XML object loaded with load_tool_with_refereces.
-
class
galaxy.tools.parser.
ToolOutputCollectionPart
(output_collection_def, element_identifier, output_def, parent_ids=[])[source]¶ Bases:
object
-
effective_output_name
¶
-
-
class
galaxy.tools.parser.
ToolSource
[source]¶ Bases:
object
This interface represents an abstract source to parse tool information from.
-
default_is_multi_byte
= False¶
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parse_id
()[source]¶ Parse an ID describing the abstract tool. This is not the GUID tracked by the tool shed but the simple id (there may be multiple tools loaded in Galaxy with this same simple id).
-
parse_tool_module
()[source]¶ Load Tool class from a custom module. (Optional).
If not None, return pair containing module and class (as strings).
-
parse_action_module
()[source]¶ Load Tool class from a custom module. (Optional).
If not None, return pair containing module and class (as strings).
-
parse_is_multi_byte
()[source]¶ Parse is_multi_byte from tool - TODO: figure out what this is and document.
-
parse_display_interface
(default)[source]¶ Parse display_interface - fallback to default for the tool type (supplied as default parameter) if not specified.
-
parse_request_param_translation_elem
()[source]¶ Return an XML element describing require parameter translation.
If we wish to support this feature for non-XML based tools this should be converted to return some sort of object interface instead of a RAW XML element.
-
parse_tmp_target
()[source]¶ Should be “pwd”, “shared_home”, “job_tmp”, “job_tmp_if_explicit”, or None.
-
parse_interpreter
()[source]¶ Return string containing the interpreter to prepend to the command (for instance this might be ‘python’ to run a Python wrapper located adjacent to the tool).
-
parse_redirect_url_params_elem
()[source]¶ Return an XML element describing redirect_url_params.
If we wish to support this feature for non-XML based tools this should be converted to return some sort of object interface instead of a RAW XML element.
-
parse_version_command
()[source]¶ Parse command used to determine version of primary application driving the tool. Return None to not generate or record such a command.
-
parse_version_command_interpreter
()[source]¶ Parse command used to determine version of primary application driving the tool. Return None to not generate or record such a command.
-
parse_parallelism
()[source]¶ Return a galaxy.jobs.ParallismInfo object describing task splitting or None.
Return boolean indicating whether tool should be hidden in the tool menu.
-
parse_requirements_and_containers
()[source]¶ Return pair of ToolRequirement and ContainerDescription lists.
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parse_provided_metadata_style
()[source]¶ Return style of tool provided metadata file (e.g. galaxy.json).
A value of of “default” indicates the newer galaxy.json style (the default for XML-based tools with profile >= 17.09) and a value of “legacy” indicates the older galaxy.json style.
A short description of these two styles can be found at https://github.com/galaxyproject/galaxy/pull/4437.
-
parse_provided_metadata_file
()[source]¶ Return location of provided metadata file (e.g. galaxy.json).
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parse_outputs
(tool)[source]¶ Return a pair of output and output collections ordered dictionaries for use by Tool.
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parse_stdio
()[source]¶ Builds lists of ToolStdioExitCode and ToolStdioRegex objects to describe tool execution error conditions.
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Submodules¶
galaxy.tools.parser.cwl module¶
-
class
galaxy.tools.parser.cwl.
CwlToolSource
(tool_file, strict_cwl_validation=True)[source]¶ Bases:
galaxy.tools.parser.interface.ToolSource
-
tool_proxy
¶
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galaxy.tools.parser.factory module¶
Constructors for concrete tool and input source objects.
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galaxy.tools.parser.factory.
get_tool_source
(config_file=None, xml_tree=None, enable_beta_formats=True, tool_location_fetcher=None)[source]¶ Return a ToolSource object corresponding to supplied source.
The supplied source may be specified as a file path (using the config_file parameter) or as an XML object loaded with load_tool_with_refereces.
galaxy.tools.parser.interface module¶
-
class
galaxy.tools.parser.interface.
ToolSource
[source]¶ Bases:
object
This interface represents an abstract source to parse tool information from.
-
default_is_multi_byte
= False¶
-
parse_id
()[source]¶ Parse an ID describing the abstract tool. This is not the GUID tracked by the tool shed but the simple id (there may be multiple tools loaded in Galaxy with this same simple id).
-
parse_tool_module
()[source]¶ Load Tool class from a custom module. (Optional).
If not None, return pair containing module and class (as strings).
-
parse_action_module
()[source]¶ Load Tool class from a custom module. (Optional).
If not None, return pair containing module and class (as strings).
-
parse_is_multi_byte
()[source]¶ Parse is_multi_byte from tool - TODO: figure out what this is and document.
-
parse_display_interface
(default)[source]¶ Parse display_interface - fallback to default for the tool type (supplied as default parameter) if not specified.
-
parse_request_param_translation_elem
()[source]¶ Return an XML element describing require parameter translation.
If we wish to support this feature for non-XML based tools this should be converted to return some sort of object interface instead of a RAW XML element.
-
parse_tmp_target
()[source]¶ Should be “pwd”, “shared_home”, “job_tmp”, “job_tmp_if_explicit”, or None.
-
parse_interpreter
()[source]¶ Return string containing the interpreter to prepend to the command (for instance this might be ‘python’ to run a Python wrapper located adjacent to the tool).
-
parse_redirect_url_params_elem
()[source]¶ Return an XML element describing redirect_url_params.
If we wish to support this feature for non-XML based tools this should be converted to return some sort of object interface instead of a RAW XML element.
-
parse_version_command
()[source]¶ Parse command used to determine version of primary application driving the tool. Return None to not generate or record such a command.
-
parse_version_command_interpreter
()[source]¶ Parse command used to determine version of primary application driving the tool. Return None to not generate or record such a command.
-
parse_parallelism
()[source]¶ Return a galaxy.jobs.ParallismInfo object describing task splitting or None.
Return boolean indicating whether tool should be hidden in the tool menu.
-
parse_requirements_and_containers
()[source]¶ Return pair of ToolRequirement and ContainerDescription lists.
-
parse_provided_metadata_style
()[source]¶ Return style of tool provided metadata file (e.g. galaxy.json).
A value of of “default” indicates the newer galaxy.json style (the default for XML-based tools with profile >= 17.09) and a value of “legacy” indicates the older galaxy.json style.
A short description of these two styles can be found at https://github.com/galaxyproject/galaxy/pull/4437.
-
parse_provided_metadata_file
()[source]¶ Return location of provided metadata file (e.g. galaxy.json).
-
parse_outputs
(tool)[source]¶ Return a pair of output and output collections ordered dictionaries for use by Tool.
-
parse_stdio
()[source]¶ Builds lists of ToolStdioExitCode and ToolStdioRegex objects to describe tool execution error conditions.
-
-
class
galaxy.tools.parser.interface.
PagesSource
(page_sources)[source]¶ Bases:
object
Contains a list of Pages - each a list of InputSources - each item in the outer list representing a page of inputs. Pages are deprecated so ideally this outer list will always be exactly a singleton.
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inputs_defined
¶
-
-
class
galaxy.tools.parser.interface.
InputSource
[source]¶ Bases:
object
-
default_optional
= False¶
-
get
(key, value=None)[source]¶ Return simple named properties as string for this input source. keys to be supported depend on the parameter type.
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get_bool
(key, default)[source]¶ Return simple named properties as boolean for this input source. keys to be supported depend on the parameter type.
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parse_sanitizer_elem
()[source]¶ Return an XML description of sanitizers. This is a stop gap until we can rework galaxy.tools.parameters.sanitize to not explicitly depend on XML.
-
parse_validator_elems
()[source]¶ Return an XML description of sanitizers. This is a stop gap until we can rework galaxy.tools.parameters.validation to not explicitly depend on XML.
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parse_static_options
()[source]¶ Return list of static options if this is a select type without defining a dynamic options.
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class
galaxy.tools.parser.interface.
ToolStdioRegex
[source]¶ Bases:
object
This is a container for the <stdio> element’s regex subelement. The regex subelement has a “match” attribute, a “sources” attribute that contains “output” and/or “error”, and a “level” attribute that contains “warning” or “fatal”.
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class
galaxy.tools.parser.interface.
ToolStdioExitCode
[source]¶ Bases:
object
This is a container for the <stdio> element’s <exit_code> subelement. The exit_code element has a range of exit codes and the error level.
galaxy.tools.parser.output_actions module¶
Support for dynamically modifying output attributes.
-
class
galaxy.tools.parser.output_actions.
ToolOutputActionGroup
(parent, config_elem)[source]¶ Bases:
object
Manages a set of tool output dataset actions directives
-
tag
= 'group'¶
-
tool
¶
-
-
class
galaxy.tools.parser.output_actions.
ToolOutputActionConditionalWhen
(parent, config_elem, value)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionGroup
-
tag
= 'when'¶
-
-
class
galaxy.tools.parser.output_actions.
ValueToolOutputActionConditionalWhen
(parent, config_elem, value)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen
-
tag
= 'when value'¶
-
-
class
galaxy.tools.parser.output_actions.
DatatypeIsInstanceToolOutputActionConditionalWhen
(parent, config_elem, value)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionConditionalWhen
-
tag
= 'when datatype_isinstance'¶
-
-
class
galaxy.tools.parser.output_actions.
ToolOutputActionConditional
(parent, config_elem)[source]¶ Bases:
object
-
tag
= 'conditional'¶
-
tool
¶
-
-
class
galaxy.tools.parser.output_actions.
ToolOutputAction
(parent, elem)[source]¶ Bases:
object
-
tag
= 'action'¶
-
tool
¶
-
-
class
galaxy.tools.parser.output_actions.
ToolOutputActionOption
(parent, elem)[source]¶ Bases:
object
-
tag
= 'object'¶
-
tool
¶
-
-
class
galaxy.tools.parser.output_actions.
NullToolOutputActionOption
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOption
-
tag
= 'null_option'¶
-
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class
galaxy.tools.parser.output_actions.
FromFileToolOutputActionOption
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOption
-
tag
= 'from_file'¶
-
-
class
galaxy.tools.parser.output_actions.
FromParamToolOutputActionOption
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOption
-
tag
= 'from_param'¶
-
-
class
galaxy.tools.parser.output_actions.
FromDataTableOutputActionOption
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOption
-
tag
= 'from_data_table'¶
-
-
class
galaxy.tools.parser.output_actions.
MetadataToolOutputAction
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputAction
-
tag
= 'metadata'¶
-
-
class
galaxy.tools.parser.output_actions.
FormatToolOutputAction
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputAction
-
tag
= 'format'¶
-
-
class
galaxy.tools.parser.output_actions.
ToolOutputActionOptionFilter
(parent, elem)[source]¶ Bases:
object
-
tag
= 'filter'¶
-
tool
¶
-
-
class
galaxy.tools.parser.output_actions.
ParamValueToolOutputActionOptionFilter
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter
-
tag
= 'param_value'¶
-
-
class
galaxy.tools.parser.output_actions.
InsertColumnToolOutputActionOptionFilter
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter
-
tag
= 'insert_column'¶
-
-
class
galaxy.tools.parser.output_actions.
MultipleSplitterFilter
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter
-
tag
= 'multiple_splitter'¶
-
-
class
galaxy.tools.parser.output_actions.
ColumnStripFilter
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter
-
tag
= 'column_strip'¶
-
-
class
galaxy.tools.parser.output_actions.
ColumnReplaceFilter
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter
-
tag
= 'column_replace'¶
-
-
class
galaxy.tools.parser.output_actions.
MetadataValueFilter
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter
-
tag
= 'metadata_value'¶
-
-
class
galaxy.tools.parser.output_actions.
BooleanFilter
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter
-
tag
= 'boolean'¶
-
-
galaxy.tools.parser.output_actions.
action_type
¶ alias of
galaxy.tools.parser.output_actions.FormatToolOutputAction
-
galaxy.tools.parser.output_actions.
filter_type
¶ alias of
galaxy.tools.parser.output_actions.ColumnReplaceFilter
-
galaxy.tools.parser.output_actions.
option_type
¶ alias of
galaxy.tools.parser.output_actions.FromDataTableOutputActionOption
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class
galaxy.tools.parser.output_actions.
StringFunctionFilter
(parent, elem)[source]¶ Bases:
galaxy.tools.parser.output_actions.ToolOutputActionOptionFilter
-
tag
= 'string_function'¶
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galaxy.tools.parser.output_collection_def module¶
This module define an abstract class for reasoning about Galaxy’s dataset collection after jobs are finished.
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galaxy.tools.parser.output_collection_def.
dataset_collector_descriptions_from_elem
(elem, legacy=True)[source]¶
-
galaxy.tools.parser.output_collection_def.
dataset_collector_descriptions_from_list
(discover_datasets_dicts)[source]¶
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class
galaxy.tools.parser.output_collection_def.
DatasetCollectionDescription
(**kwargs)[source]¶ Bases:
object
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class
galaxy.tools.parser.output_collection_def.
ToolProvidedMetadataDatasetCollection
(**kwargs)[source]¶ Bases:
galaxy.tools.parser.output_collection_def.DatasetCollectionDescription
-
discover_via
= 'tool_provided_metadata'¶
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galaxy.tools.parser.output_objects module¶
-
class
galaxy.tools.parser.output_objects.
ToolOutputBase
(name, label=None, filters=None, hidden=False)[source]¶
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class
galaxy.tools.parser.output_objects.
ToolOutput
(name, format=None, format_source=None, metadata_source=None, parent=None, label=None, filters=None, actions=None, hidden=False, implicit=False)[source]¶ Bases:
galaxy.tools.parser.output_objects.ToolOutputBase
Represents an output datasets produced by a tool. For backward compatibility this behaves as if it were the tuple:
(format, metadata_source, parent)
-
dict_collection_visible_keys
= ['name', 'format', 'label', 'hidden']¶
-
-
class
galaxy.tools.parser.output_objects.
ToolOutputCollection
(name, structure, label=None, filters=None, hidden=False, default_format='data', default_format_source=None, default_metadata_source=None, inherit_format=False, inherit_metadata=False)[source]¶ Bases:
galaxy.tools.parser.output_objects.ToolOutputBase
Represents a HistoryDatasetCollectionAssociation of output datasets produced by a tool.
- <outputs>
- <collection type=”list” label=”${tool.name} on ${on_string} fasta”>
- <discover_datasets pattern=”__name__” ext=”fasta” visible=”True” directory=”outputFiles” />
</collection> <collection type=”paired” label=”${tool.name} on ${on_string} paired reads”>
<data name=”forward” format=”fastqsanger” /> <data name=”reverse” format=”fastqsanger”/></collection>
<outputs>
-
dict_collection_visible_keys
= ['name', 'default_format', 'label', 'hidden', 'inherit_format', 'inherit_metadata']¶
-
__init__
(name, structure, label=None, filters=None, hidden=False, default_format='data', default_format_source=None, default_metadata_source=None, inherit_format=False, inherit_metadata=False)[source]¶
-
dynamic_structure
¶
-
dataset_collector_descriptions
¶
-
class
galaxy.tools.parser.output_objects.
ToolOutputCollectionStructure
(collection_type, collection_type_source=None, collection_type_from_rules=None, structured_like=None, dataset_collector_descriptions=None)[source]¶ Bases:
object
galaxy.tools.parser.util module¶
galaxy.tools.parser.xml module¶
-
class
galaxy.tools.parser.xml.
XmlToolSource
(xml_tree, source_path=None, macro_paths=None)[source]¶ Bases:
galaxy.tools.parser.interface.ToolSource
Responsible for parsing a tool from classic Galaxy representation.
-
class
galaxy.tools.parser.xml.
StdioParser
(root)[source]¶ Bases:
object
-
parse_stdio_exit_codes
(stdio_elem)[source]¶ Parse the tool’s <stdio> element’s <exit_code> subelements. This will add all of those elements, if any, to self.stdio_exit_codes.
-
-
class
galaxy.tools.parser.xml.
XmlPagesSource
(root)[source]¶ Bases:
galaxy.tools.parser.interface.PagesSource
-
inputs_defined
¶
-
-
class
galaxy.tools.parser.xml.
XmlInputSource
(input_elem)[source]¶