Index

_

__init__() (galaxy.authnz.IdentityProvider method) (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.datatypes.dataproviders.base.FilteredDataProvider method) (galaxy.datatypes.dataproviders.base.LimitedOffsetDataProvider method) (galaxy.datatypes.dataproviders.base.MultiSourceDataProvider method) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider method) (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) (galaxy.datatypes.dataproviders.column.DictDataProvider method) (galaxy.datatypes.dataproviders.exceptions.InvalidDataProviderSource method) (galaxy.datatypes.dataproviders.exceptions.NoProviderAvailable method) (galaxy.datatypes.dataproviders.line.BlockDataProvider method) (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider method) (galaxy.datatypes.dataproviders.line.RegexLineDataProvider method) (galaxy.job_execution.datasets.DatasetPath method) (galaxy.job_execution.datasets.OutputsToWorkingDirectoryPathRewriter method) (galaxy.job_execution.datasets.TaskPathRewriter method) (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) (tool_shed.repository_types.metadata.Metadata method) (tool_shed.repository_types.metadata.TipOnly method)

A

ActiveWorkflowSchedulingPlugin (class in galaxy.workflow.schedulers) add_line_to_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) AlwaysReject (class in galaxy.auth.providers.alwaysreject) assemble_current_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) authenticate() (galaxy.auth.providers.alwaysreject.AlwaysReject method) (galaxy.auth.providers.AuthProvider method) (galaxy.auth.providers.localdb.LocalDB method) (galaxy.authnz.IdentityProvider method)

authenticate_user() (galaxy.auth.providers.alwaysreject.AlwaysReject method) (galaxy.auth.providers.AuthProvider method) (galaxy.auth.providers.localdb.LocalDB method) AuthProvider (class in galaxy.auth.providers)

B

Base64ChunkDataProvider (class in galaxy.datatypes.dataproviders.chunk) baseauth_headers() (in module galaxy_test.base.api_util) BiotoolsEntry (class in galaxy.tool_util.biotools.interface)

biotoolsID (galaxy.tool_util.biotools.interface.BiotoolsEntry attribute) (galaxy.tool_util.biotools.interface.ParsedBiotoolsEntry attribute) BlockDataProvider (class in galaxy.datatypes.dataproviders.line)

C

callback() (galaxy.authnz.IdentityProvider method) check_example_1() (in module galaxy_test.base.rules_test_data) check_example_2() (in module galaxy_test.base.rules_test_data) check_example_3() (in module galaxy_test.base.rules_test_data) check_example_4() (in module galaxy_test.base.rules_test_data) check_example_5() (in module galaxy_test.base.rules_test_data) check_example_6() (in module galaxy_test.base.rules_test_data)

ChunkDataProvider (class in galaxy.datatypes.dataproviders.chunk) ColumnarDataProvider (class in galaxy.datatypes.dataproviders.column) compute_fasta_length() (in module galaxy.datatypes.converters.fasta_to_len) convert_to_csv() (in module galaxy.datatypes.converters.tabular_csv) convert_to_tsv() (in module galaxy.datatypes.converters.tabular_csv) create_list_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) create_numeric_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) create_string_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method)

D

DataProvider (class in galaxy.datatypes.dataproviders.base) dataset_path_rewrites() (in module galaxy.job_execution.datasets) DatasetPath (class in galaxy.job_execution.datasets) DatasetPathRewriter (class in galaxy.job_execution.datasets)

DEFAULT_CHUNK_SIZE (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider attribute) DEFAULT_COMMENT_CHAR (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider attribute) DictDataProvider (class in galaxy.datatypes.dataproviders.column) disconnect() (galaxy.authnz.IdentityProvider method)

E

edam_info (galaxy.tool_util.biotools.interface.BiotoolsEntry property) edam_operations (galaxy.tool_util.biotools.interface.ParsedBiotoolsEntry attribute) edam_topics (galaxy.tool_util.biotools.interface.ParsedBiotoolsEntry attribute)

encode() (galaxy.datatypes.dataproviders.chunk.Base64ChunkDataProvider method) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider method) ensure_cwltool_available() (in module galaxy.tool_util.cwl.cwltool_deps) escape() (in module tool_shed.util.web_util)

F

filter() (galaxy.datatypes.dataproviders.base.FilteredDataProvider method) (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) (galaxy.datatypes.dataproviders.line.BlockDataProvider method) (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider method) (galaxy.datatypes.dataproviders.line.RegexLineDataProvider method) filter_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method)

filter_by_columns() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) filter_by_regex() (galaxy.datatypes.dataproviders.line.RegexLineDataProvider method) FilteredDataProvider (class in galaxy.datatypes.dataproviders.base) FilteredLineDataProvider (class in galaxy.datatypes.dataproviders.line) from_json() (galaxy.tool_util.biotools.interface.BiotoolsEntry static method) function (galaxy.tool_util.biotools.interface.BiotoolsEntry attribute)

G

galaxy module galaxy.actions module galaxy.app_unittest_utils module galaxy.auth.providers module galaxy.auth.providers.alwaysreject module galaxy.auth.providers.localdb module galaxy.authnz module galaxy.datatypes module galaxy.datatypes.converters module galaxy.datatypes.converters.bed_to_gff_converter module galaxy.datatypes.converters.fasta_to_len module galaxy.datatypes.converters.fasta_to_tabular_converter module galaxy.datatypes.converters.fastqsolexa_to_fasta_converter module galaxy.datatypes.converters.fastqsolexa_to_qual_converter module galaxy.datatypes.converters.gff_to_bed_converter module galaxy.datatypes.converters.lped_to_fped_converter module galaxy.datatypes.converters.lped_to_pbed_converter module galaxy.datatypes.converters.parquet_to_csv_converter module galaxy.datatypes.converters.pbed_ldreduced_converter module galaxy.datatypes.converters.pbed_to_lped_converter module galaxy.datatypes.converters.picard_interval_list_to_bed6_converter module galaxy.datatypes.converters.ref_to_seq_taxonomy_converter module galaxy.datatypes.converters.tabular_csv module galaxy.datatypes.dataproviders.base module galaxy.datatypes.dataproviders.chunk module galaxy.datatypes.dataproviders.column module galaxy.datatypes.dataproviders.exceptions module galaxy.datatypes.dataproviders.line module galaxy.datatypes.display_applications module galaxy.datatypes.util module galaxy.forms module galaxy.job_execution module galaxy.job_execution.actions module galaxy.job_execution.datasets module galaxy.managers module galaxy.managers.markdown_parse module galaxy.selenium module galaxy.selenium.scripts module galaxy.selenium.toolbox module galaxy.selenium.toolbox.filters module galaxy.tool_shed module galaxy.tool_shed.galaxy_install module galaxy.tool_shed.galaxy_install.metadata module galaxy.tool_shed.galaxy_install.repository_dependencies module galaxy.tool_shed.galaxy_install.tools module galaxy.tool_shed.metadata module galaxy.tool_shed.repository_type module galaxy.tool_shed.tools module galaxy.tool_shed.util module galaxy.tool_util module galaxy.tool_util.biotools.interface module galaxy.tool_util.client module galaxy.tool_util.cwl.cwltool_deps module

galaxy.tool_util.edam_util module galaxy.tool_util.linters module galaxy.tool_util.linters.citations module galaxy.tool_util.linters.command module galaxy.tool_util.linters.general module galaxy.tool_util.linters.xml_order module galaxy.tool_util.locations module galaxy.tool_util.locations.file module galaxy.tool_util.ontologies module galaxy.tool_util.unittest_utils module galaxy.tool_util.unittest_utils.sample_data module galaxy.version module galaxy.visualization module galaxy.visualization.data_providers module galaxy.visualization.data_providers.cigar module galaxy.visualization.genome module galaxy.visualization.plugins module galaxy.visualization.plugins.utils module galaxy.visualization.tracks module galaxy.webapps module galaxy.webapps.base module galaxy.webapps.galaxy module galaxy.webapps.galaxy.controllers module galaxy.webapps.galaxy.services module galaxy.webapps.openapi module galaxy.work module galaxy.workflow module galaxy.workflow.refactor module galaxy.workflow.schedulers module galaxy_ext module galaxy_ext.container_monitor module galaxy_ext.expressions module galaxy_ext.metadata module galaxy_test module galaxy_test.api module galaxy_test.api.cwl module galaxy_test.base module galaxy_test.base.api_util module galaxy_test.base.constants module galaxy_test.base.env module galaxy_test.base.rules_test_data module galaxy_test.base.workflow_fixtures module galaxy_test.driver module galaxy_test.driver.test_logging module galaxy_test.performance module galaxy_test.selenium module galaxy_test.selenium.jupyter module get_admin_api_key() (in module galaxy_test.base.api_util) get_changesets_for_setting_metadata() (tool_shed.repository_types.metadata.Metadata method) (tool_shed.repository_types.metadata.TipOnly method) get_column_type() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) get_command() (in module galaxy.tool_util.linters.command) get_default_parsers() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) get_ip_address() (in module galaxy_test.base.env) get_path_rewriter() (in module galaxy.job_execution.datasets) get_ref_based_read_seq_and_cigar() (in module galaxy.visualization.data_providers.cigar) get_tool_source_path() (galaxy.tool_util.locations.file.HttpToolResolver method) (galaxy.tool_util.locations.ToolLocationResolver method) get_user_api_key() (in module galaxy_test.base.api_util) getMissval() (in module galaxy.datatypes.converters.lped_to_pbed_converter)

H

handle_last_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method)

HasSettings (class in galaxy.datatypes.dataproviders.base) HttpToolResolver (class in galaxy.tool_util.locations.file)

I

IdentityProvider (class in galaxy.authnz) init_new_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method)

InvalidDataProviderSource is_new_block() (galaxy.datatypes.dataproviders.line.BlockDataProvider method) is_valid_for_type() (tool_shed.repository_types.metadata.Metadata method)

L

LimitedOffsetDataProvider (class in galaxy.datatypes.dataproviders.base) lint_citations() (in module galaxy.tool_util.linters.citations) lint_command() (in module galaxy.tool_util.linters.command) lint_general() (in module galaxy.tool_util.linters.general)

lint_xml_order() (in module galaxy.tool_util.linters.xml_order) load_edam_tree() (in module galaxy.tool_util.edam_util) LocalDB (class in galaxy.auth.providers.localdb) logout() (galaxy.authnz.IdentityProvider method)

M

main() (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_ldreduced_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) (in module galaxy.datatypes.converters.tabular_csv) makeLDreduced() (in module galaxy.datatypes.converters.pbed_ldreduced_converter) MAX_CHUNK_SIZE (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider attribute) Metadata (class in tool_shed.repository_types.metadata) mock_trans() (in module galaxy.tool_util.unittest_utils) module galaxy galaxy.actions galaxy.app_unittest_utils galaxy.auth.providers galaxy.auth.providers.alwaysreject galaxy.auth.providers.localdb galaxy.authnz galaxy.datatypes galaxy.datatypes.converters galaxy.datatypes.converters.bed_to_gff_converter galaxy.datatypes.converters.fasta_to_len galaxy.datatypes.converters.fasta_to_tabular_converter galaxy.datatypes.converters.fastqsolexa_to_fasta_converter galaxy.datatypes.converters.fastqsolexa_to_qual_converter galaxy.datatypes.converters.gff_to_bed_converter galaxy.datatypes.converters.lped_to_fped_converter galaxy.datatypes.converters.lped_to_pbed_converter galaxy.datatypes.converters.parquet_to_csv_converter galaxy.datatypes.converters.pbed_ldreduced_converter galaxy.datatypes.converters.pbed_to_lped_converter galaxy.datatypes.converters.picard_interval_list_to_bed6_converter galaxy.datatypes.converters.ref_to_seq_taxonomy_converter galaxy.datatypes.converters.tabular_csv galaxy.datatypes.dataproviders.base galaxy.datatypes.dataproviders.chunk galaxy.datatypes.dataproviders.column galaxy.datatypes.dataproviders.exceptions galaxy.datatypes.dataproviders.line galaxy.datatypes.display_applications galaxy.datatypes.util galaxy.forms galaxy.job_execution galaxy.job_execution.actions galaxy.job_execution.datasets galaxy.managers galaxy.managers.markdown_parse galaxy.selenium galaxy.selenium.scripts galaxy.selenium.toolbox galaxy.selenium.toolbox.filters galaxy.tool_shed galaxy.tool_shed.galaxy_install galaxy.tool_shed.galaxy_install.metadata galaxy.tool_shed.galaxy_install.repository_dependencies galaxy.tool_shed.galaxy_install.tools galaxy.tool_shed.metadata galaxy.tool_shed.repository_type galaxy.tool_shed.tools galaxy.tool_shed.util galaxy.tool_util galaxy.tool_util.biotools.interface galaxy.tool_util.client galaxy.tool_util.cwl.cwltool_deps galaxy.tool_util.edam_util galaxy.tool_util.linters galaxy.tool_util.linters.citations galaxy.tool_util.linters.command galaxy.tool_util.linters.general galaxy.tool_util.linters.xml_order galaxy.tool_util.locations galaxy.tool_util.locations.file galaxy.tool_util.ontologies galaxy.tool_util.unittest_utils galaxy.tool_util.unittest_utils.sample_data galaxy.version galaxy.visualization galaxy.visualization.data_providers galaxy.visualization.data_providers.cigar galaxy.visualization.genome galaxy.visualization.plugins galaxy.visualization.plugins.utils galaxy.visualization.tracks galaxy.webapps galaxy.webapps.base galaxy.webapps.galaxy galaxy.webapps.galaxy.controllers galaxy.webapps.galaxy.services galaxy.webapps.openapi galaxy.work galaxy.workflow galaxy.workflow.refactor galaxy.workflow.schedulers galaxy_ext galaxy_ext.container_monitor galaxy_ext.expressions galaxy_ext.metadata galaxy_test galaxy_test.api galaxy_test.api.cwl galaxy_test.base galaxy_test.base.api_util galaxy_test.base.constants galaxy_test.base.env galaxy_test.base.rules_test_data galaxy_test.base.workflow_fixtures galaxy_test.driver galaxy_test.driver.test_logging galaxy_test.performance galaxy_test.selenium galaxy_test.selenium.jupyter tool_shed tool_shed.dependencies tool_shed.dependencies.repository tool_shed.dependencies.tool tool_shed.dependencies.tool.tag_attribute_handler tool_shed.galaxy_install tool_shed.grids tool_shed.managers tool_shed.metadata tool_shed.repository_types tool_shed.repository_types.metadata tool_shed.test tool_shed.test.base tool_shed.test.base.common tool_shed.test.functional tool_shed.tools tool_shed.util tool_shed.util.web_util

MultiSourceDataProvider (class in galaxy.datatypes.dataproviders.base)

N

needs_shell_quoting() (in module galaxy.tool_util.cwl.cwltool_deps)

NoProviderAvailable NullDatasetPathRewriter (class in galaxy.job_execution.datasets)

O

OpenObject (class in galaxy.visualization.plugins.utils)

OutputsToWorkingDirectoryPathRewriter (class in galaxy.job_execution.datasets)

P

parse_column_at_index() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_columns_from_line() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_filter() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) parse_value() (galaxy.datatypes.dataproviders.column.ColumnarDataProvider method) ParsedBiotoolsEntry (class in galaxy.tool_util.biotools.interface) plugin_type (galaxy.auth.providers.alwaysreject.AlwaysReject attribute) (galaxy.auth.providers.AuthProvider property) (galaxy.auth.providers.localdb.LocalDB attribute) (galaxy.workflow.schedulers.WorkflowSchedulingPlugin property)

process_action_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_actions_group_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_actions_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_config() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_install_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_package_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) process_repository_tag_set() (tool_shed.dependencies.tool.tag_attribute_handler.TagAttributeHandler method) pruneLD() (in module galaxy.datatypes.converters.pbed_ldreduced_converter)

R

random_name() (in module galaxy_test.base.api_util) readlines() (galaxy.datatypes.dataproviders.base.DataProvider method) refresh() (galaxy.authnz.IdentityProvider method) RegexLineDataProvider (class in galaxy.datatypes.dataproviders.line) restrict_test() (in module galaxy.selenium.toolbox.filters) rewrite_dataset_path() (galaxy.job_execution.datasets.DatasetPathRewriter method) (galaxy.job_execution.datasets.NullDatasetPathRewriter method) (galaxy.job_execution.datasets.OutputsToWorkingDirectoryPathRewriter method) (galaxy.job_execution.datasets.TaskPathRewriter method)

rgConv() (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter)

S

schedule() (galaxy.workflow.schedulers.ActiveWorkflowSchedulingPlugin method) scheme (galaxy.tool_util.locations.file.HttpToolResolver attribute) (galaxy.tool_util.locations.ToolLocationResolver property) settings (galaxy.datatypes.dataproviders.base.DataProvider attribute) (galaxy.datatypes.dataproviders.base.FilteredDataProvider attribute) (galaxy.datatypes.dataproviders.base.LimitedOffsetDataProvider attribute) (galaxy.datatypes.dataproviders.base.MultiSourceDataProvider attribute) (galaxy.datatypes.dataproviders.chunk.Base64ChunkDataProvider attribute) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider attribute) (galaxy.datatypes.dataproviders.column.ColumnarDataProvider attribute) (galaxy.datatypes.dataproviders.column.DictDataProvider attribute) (galaxy.datatypes.dataproviders.line.BlockDataProvider attribute) (galaxy.datatypes.dataproviders.line.FilteredLineDataProvider attribute) (galaxy.datatypes.dataproviders.line.RegexLineDataProvider attribute)

setup_keep_outdir() (in module galaxy_test.base.env) shutdown() (galaxy.workflow.schedulers.WorkflowSchedulingPlugin method) simplify_edam_dict() (in module galaxy.tool_util.biotools.interface) simplify_edam_dicts() (in module galaxy.tool_util.biotools.interface) startup() (galaxy.workflow.schedulers.WorkflowSchedulingPlugin method) stop_err() (in module galaxy.datatypes.converters.fastqsolexa_to_fasta_converter) (in module galaxy.datatypes.converters.fastqsolexa_to_qual_converter)

T

t_data_downloader_for() (in module galaxy.tool_util.unittest_utils) TagAttributeHandler (class in tool_shed.dependencies.tool.tag_attribute_handler) target_url_parts() (in module galaxy_test.base.env) TaskPathRewriter (class in galaxy.job_execution.datasets) timenow() (in module galaxy.datatypes.converters.lped_to_fped_converter) (in module galaxy.datatypes.converters.lped_to_pbed_converter) (in module galaxy.datatypes.converters.pbed_ldreduced_converter) (in module galaxy.datatypes.converters.pbed_to_lped_converter) TipOnly (class in tool_shed.repository_types.metadata) tool_shed module tool_shed.dependencies module tool_shed.dependencies.repository module tool_shed.dependencies.tool module tool_shed.dependencies.tool.tag_attribute_handler module tool_shed.galaxy_install module tool_shed.grids module tool_shed.managers module

tool_shed.metadata module tool_shed.repository_types module tool_shed.repository_types.metadata module tool_shed.test module tool_shed.test.base module tool_shed.test.base.common module tool_shed.test.functional module tool_shed.tools module tool_shed.util module tool_shed.util.web_util module ToolLocationResolver (class in galaxy.tool_util.locations) topic (galaxy.tool_util.biotools.interface.BiotoolsEntry attribute) truncate() (galaxy.datatypes.dataproviders.base.DataProvider method)

V

validate_galaxy_markdown() (in module galaxy.managers.markdown_parse)

validate_source() (galaxy.datatypes.dataproviders.base.DataProvider method) (galaxy.datatypes.dataproviders.chunk.ChunkDataProvider method)

W

with_path_for_job() (galaxy.job_execution.datasets.DatasetPath method) WorkflowSchedulingPlugin (class in galaxy.workflow.schedulers)

write() (galaxy.datatypes.dataproviders.base.DataProvider method) writelines() (galaxy.datatypes.dataproviders.base.DataProvider method)