Python Module Index

g | t
 
g
galaxy
    galaxy.actions
    galaxy.actions.library
    galaxy.app
    galaxy.app_unittest_utils
    galaxy.app_unittest_utils.galaxy_mock
    galaxy.app_unittest_utils.tools_support
    galaxy.auth
    galaxy.auth.providers
    galaxy.auth.providers.alwaysreject
    galaxy.auth.providers.ldap_ad
    galaxy.auth.providers.localdb
    galaxy.auth.providers.pam_auth
    galaxy.auth.util
    galaxy.authnz
    galaxy.authnz.custos_authnz
    galaxy.authnz.managers
    galaxy.authnz.psa_authnz
    galaxy.celery
    galaxy.celery.tasks
    galaxy.config
    galaxy.config.config_manage
    galaxy.config.schema
    galaxy.config.script
    galaxy.config_watchers
    galaxy.datatypes
    galaxy.datatypes.annotation
    galaxy.datatypes.anvio
    galaxy.datatypes.assembly
    galaxy.datatypes.binary
    galaxy.datatypes.blast
    galaxy.datatypes.checkers
    galaxy.datatypes.chrominfo
    galaxy.datatypes.constructive_solid_geometry
    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.fastq_to_fqtoc
    galaxy.datatypes.converters.fastqsolexa_to_fasta_converter
    galaxy.datatypes.converters.fastqsolexa_to_qual_converter
    galaxy.datatypes.converters.gff_to_bed_converter
    galaxy.datatypes.converters.gff_to_interval_index_converter
    galaxy.datatypes.converters.interval_to_bed_converter
    galaxy.datatypes.converters.interval_to_bedstrict_converter
    galaxy.datatypes.converters.interval_to_fli
    galaxy.datatypes.converters.interval_to_interval_index_converter
    galaxy.datatypes.converters.lped_to_fped_converter
    galaxy.datatypes.converters.lped_to_pbed_converter
    galaxy.datatypes.converters.maf_to_fasta_converter
    galaxy.datatypes.converters.maf_to_interval_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.pileup_to_interval_index_converter
    galaxy.datatypes.converters.ref_to_seq_taxonomy_converter
    galaxy.datatypes.converters.tabular_csv
    galaxy.datatypes.converters.vcf_to_interval_index_converter
    galaxy.datatypes.converters.wiggle_to_simple_converter
    galaxy.datatypes.coverage
    galaxy.datatypes.data
    galaxy.datatypes.dataproviders
    galaxy.datatypes.dataproviders.base
    galaxy.datatypes.dataproviders.chunk
    galaxy.datatypes.dataproviders.column
    galaxy.datatypes.dataproviders.dataset
    galaxy.datatypes.dataproviders.decorators
    galaxy.datatypes.dataproviders.exceptions
    galaxy.datatypes.dataproviders.external
    galaxy.datatypes.dataproviders.hierarchy
    galaxy.datatypes.dataproviders.line
    galaxy.datatypes.display_applications
    galaxy.datatypes.display_applications.application
    galaxy.datatypes.display_applications.parameters
    galaxy.datatypes.display_applications.util
    galaxy.datatypes.flow
    galaxy.datatypes.genetics
    galaxy.datatypes.gis
    galaxy.datatypes.goldenpath
    galaxy.datatypes.graph
    galaxy.datatypes.hdf5
    galaxy.datatypes.images
    galaxy.datatypes.interval
    galaxy.datatypes.isa
    galaxy.datatypes.media
    galaxy.datatypes.metacyto
    galaxy.datatypes.metadata
    galaxy.datatypes.microarrays
    galaxy.datatypes.molecules
    galaxy.datatypes.mothur
    galaxy.datatypes.msa
    galaxy.datatypes.neo4j
    galaxy.datatypes.ngsindex
    galaxy.datatypes.phylip
    galaxy.datatypes.plant_tribes
    galaxy.datatypes.proteomics
    galaxy.datatypes.qiime2
    galaxy.datatypes.qualityscore
    galaxy.datatypes.registry
    galaxy.datatypes.sequence
    galaxy.datatypes.sniff
    galaxy.datatypes.spaln
    galaxy.datatypes.speech
    galaxy.datatypes.tabular
    galaxy.datatypes.text
    galaxy.datatypes.tracks
    galaxy.datatypes.triples
    galaxy.datatypes.upload_util
    galaxy.datatypes.util
    galaxy.datatypes.util.generic_util
    galaxy.datatypes.util.gff_util
    galaxy.datatypes.util.maf_utilities
    galaxy.datatypes.xml
    galaxy.dependencies
    galaxy.di
    galaxy.exceptions
    galaxy.exceptions.error_codes
    galaxy.files
    galaxy.files.sources
    galaxy.files.sources.anvil
    galaxy.files.sources.basespace
    galaxy.files.sources.dropbox
    galaxy.files.sources.ftp
    galaxy.files.sources.galaxy
    galaxy.files.sources.googlecloudstorage
    galaxy.files.sources.googledrive
    galaxy.files.sources.onedata
    galaxy.files.sources.posix
    galaxy.files.sources.s3
    galaxy.files.sources.s3fs
    galaxy.files.sources.ssh
    galaxy.files.sources.webdav
    galaxy.files.unittest_utils
    galaxy.files.uris
    galaxy.forms
    galaxy.forms.forms
    galaxy.job_execution
    galaxy.job_execution.actions
    galaxy.job_execution.actions.post
    galaxy.job_execution.compute_environment
    galaxy.job_execution.datasets
    galaxy.job_execution.output_collect
    galaxy.job_execution.ports
    galaxy.job_execution.ports.view
    galaxy.job_execution.setup
    galaxy.job_metrics
    galaxy.job_metrics.formatting
    galaxy.job_metrics.instrumenters
    galaxy.job_metrics.instrumenters.cgroup
    galaxy.job_metrics.instrumenters.core
    galaxy.job_metrics.instrumenters.cpuinfo
    galaxy.job_metrics.instrumenters.env
    galaxy.job_metrics.instrumenters.hostname
    galaxy.job_metrics.instrumenters.meminfo
    galaxy.job_metrics.instrumenters.uname
    galaxy.job_metrics.safety
    galaxy.jobs
    galaxy.jobs.command_factory
    galaxy.jobs.dynamic_tool_destination
    galaxy.jobs.handler
    galaxy.jobs.manager
    galaxy.jobs.mapper
    galaxy.jobs.rule_helper
    galaxy.jobs.rules
    galaxy.jobs.runners
    galaxy.jobs.runners.chronos
    galaxy.jobs.runners.cli
    galaxy.jobs.runners.condor
    galaxy.jobs.runners.drmaa
    galaxy.jobs.runners.godocker
    galaxy.jobs.runners.kubernetes
    galaxy.jobs.runners.local
    galaxy.jobs.runners.pbs
    galaxy.jobs.runners.pulsar
    galaxy.jobs.runners.slurm
    galaxy.jobs.runners.state_handler_factory
    galaxy.jobs.runners.state_handlers
    galaxy.jobs.runners.state_handlers.resubmit
    galaxy.jobs.runners.tasks
    galaxy.jobs.runners.univa
    galaxy.jobs.runners.util
    galaxy.jobs.runners.util.cli
    galaxy.jobs.runners.util.cli.factory
    galaxy.jobs.runners.util.cli.job
    galaxy.jobs.runners.util.cli.job.lsf
    galaxy.jobs.runners.util.cli.job.pbs
    galaxy.jobs.runners.util.cli.job.slurm
    galaxy.jobs.runners.util.cli.job.slurm_torque
    galaxy.jobs.runners.util.cli.job.torque
    galaxy.jobs.runners.util.cli.shell
    galaxy.jobs.runners.util.cli.shell.local
    galaxy.jobs.runners.util.cli.shell.rsh
    galaxy.jobs.runners.util.condor
    galaxy.jobs.runners.util.env
    galaxy.jobs.runners.util.external
    galaxy.jobs.runners.util.job_script
    galaxy.jobs.runners.util.kill
    galaxy.jobs.runners.util.process_groups
    galaxy.jobs.runners.util.pykube_util
    galaxy.jobs.runners.util.sudo
    galaxy.jobs.splitters
    galaxy.jobs.splitters.basic
    galaxy.jobs.splitters.multi
    galaxy.jobs.stock_rules
    galaxy.main
    galaxy.main_config
    galaxy.managers
    galaxy.managers.annotatable
    galaxy.managers.api_keys
    galaxy.managers.base
    galaxy.managers.citations
    galaxy.managers.cloud
    galaxy.managers.cloudauthzs
    galaxy.managers.collections
    galaxy.managers.collections_util
    galaxy.managers.configuration
    galaxy.managers.context
    galaxy.managers.datasets
    galaxy.managers.datatypes
    galaxy.managers.deletable
    galaxy.managers.display_applications
    galaxy.managers.executables
    galaxy.managers.folders
    galaxy.managers.genomes
    galaxy.managers.group_roles
    galaxy.managers.group_users
    galaxy.managers.groups
    galaxy.managers.hdas
    galaxy.managers.hdcas
    galaxy.managers.histories
    galaxy.managers.history_contents
    galaxy.managers.interactivetool
    galaxy.managers.jobs
    galaxy.managers.lddas
    galaxy.managers.libraries
    galaxy.managers.library_datasets
    galaxy.managers.licenses
    galaxy.managers.markdown_parse
    galaxy.managers.markdown_util
    galaxy.managers.metrics
    galaxy.managers.model_stores
    galaxy.managers.pages
    galaxy.managers.quotas
    galaxy.managers.ratable
    galaxy.managers.rbac_secured
    galaxy.managers.remote_files
    galaxy.managers.roles
    galaxy.managers.secured
    galaxy.managers.session
    galaxy.managers.sharable
    galaxy.managers.taggable
    galaxy.managers.tags
    galaxy.managers.tool_data
    galaxy.managers.tools
    galaxy.managers.users
    galaxy.managers.visualizations
    galaxy.managers.workflows
    galaxy.metadata
    galaxy.metadata.set_metadata
    galaxy.model
    galaxy.model.base
    galaxy.model.custom_types
    galaxy.model.database_heartbeat
    galaxy.model.database_utils
    galaxy.model.dataset_collections
    galaxy.model.dataset_collections.builder
    galaxy.model.dataset_collections.matching
    galaxy.model.dataset_collections.registry
    galaxy.model.dataset_collections.structure
    galaxy.model.dataset_collections.subcollections
    galaxy.model.dataset_collections.type_description
    galaxy.model.dataset_collections.types
    galaxy.model.dataset_collections.types.list
    galaxy.model.dataset_collections.types.paired
    galaxy.model.deferred
    galaxy.model.index_filter_util
    galaxy.model.item_attrs
    galaxy.model.mapping
    galaxy.model.metadata
    galaxy.model.migrations
    galaxy.model.migrations.scripts
    galaxy.model.migrations.util
    galaxy.model.none_like
    galaxy.model.orm
    galaxy.model.orm.engine_factory
    galaxy.model.orm.now
    galaxy.model.orm.scripts
    galaxy.model.orm.util
    galaxy.model.scoped_session
    galaxy.model.search
    galaxy.model.security
    galaxy.model.store
    galaxy.model.store.build_objects
    galaxy.model.store.discover
    galaxy.model.store.load_objects
    galaxy.model.tags
    galaxy.model.tool_shed_install
    galaxy.model.tool_shed_install.mapping
    galaxy.model.triggers
    galaxy.model.triggers.history_update_time_field
    galaxy.model.triggers.update_audit_table
    galaxy.model.triggers.utils
    galaxy.model.unittest_utils
    galaxy.model.unittest_utils.data_app
    galaxy.model.unittest_utils.store_fixtures
    galaxy.model.view
    galaxy.model.view.utils
    galaxy.objectstore
    galaxy.objectstore.azure_blob
    galaxy.objectstore.cloud
    galaxy.objectstore.irods
    galaxy.objectstore.pithos
    galaxy.objectstore.pulsar
    galaxy.objectstore.s3
    galaxy.objectstore.s3_multipart_upload
    galaxy.objectstore.unittest_utils
    galaxy.queue_worker
    galaxy.queues
    galaxy.quota
    galaxy.schema
    galaxy.schema.fetch_data
    galaxy.schema.fields
    galaxy.schema.remote_files
    galaxy.schema.schema
    galaxy.schema.tasks
    galaxy.schema.types
    galaxy.security
    galaxy.security.idencoding
    galaxy.security.object_wrapper
    galaxy.security.passwords
    galaxy.security.ssh_util
    galaxy.security.validate_user_input
    galaxy.security.vault
    galaxy.selenium
    galaxy.selenium.cli
    galaxy.selenium.context
    galaxy.selenium.driver_factory
    galaxy.selenium.has_driver
    galaxy.selenium.jupyter_context
    galaxy.selenium.navigates_galaxy
    galaxy.selenium.scripts
    galaxy.selenium.scripts.dump_tour
    galaxy.selenium.sizzle
    galaxy.selenium.smart_components
    galaxy.selenium.toolbox
    galaxy.selenium.toolbox.filters
    galaxy.structured_app
    galaxy.tool_shed
    galaxy.tool_shed.galaxy_install
    galaxy.tool_shed.galaxy_install.install_manager
    galaxy.tool_shed.galaxy_install.installed_repository_manager
    galaxy.tool_shed.galaxy_install.metadata
    galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager
    galaxy.tool_shed.galaxy_install.repository_dependencies
    galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
    galaxy.tool_shed.galaxy_install.tools
    galaxy.tool_shed.galaxy_install.tools.data_manager
    galaxy.tool_shed.galaxy_install.tools.tool_panel_manager
    galaxy.tool_shed.galaxy_install.update_repository_manager
    galaxy.tool_shed.metadata
    galaxy.tool_shed.metadata.metadata_generator
    galaxy.tool_shed.repository_type
    galaxy.tool_shed.tools
    galaxy.tool_shed.tools.data_table_manager
    galaxy.tool_shed.tools.tool_validator
    galaxy.tool_shed.util
    galaxy.tool_shed.util.basic_util
    galaxy.tool_shed.util.container_util
    galaxy.tool_shed.util.hg_util
    galaxy.tool_shed.util.metadata_util
    galaxy.tool_shed.util.repository_util
    galaxy.tool_shed.util.shed_util_common
    galaxy.tool_shed.util.tool_dependency_util
    galaxy.tool_shed.util.tool_util
    galaxy.tool_util
    galaxy.tool_util.biotools
    galaxy.tool_util.biotools.interface
    galaxy.tool_util.biotools.source
    galaxy.tool_util.client
    galaxy.tool_util.client.staging
    galaxy.tool_util.cwl
    galaxy.tool_util.cwl.cwltool_deps
    galaxy.tool_util.cwl.parser
    galaxy.tool_util.cwl.representation
    galaxy.tool_util.cwl.runnable
    galaxy.tool_util.cwl.runtime_actions
    galaxy.tool_util.cwl.schema
    galaxy.tool_util.cwl.util
    galaxy.tool_util.deps
    galaxy.tool_util.deps.brew_exts
    galaxy.tool_util.deps.brew_util
    galaxy.tool_util.deps.commands
    galaxy.tool_util.deps.conda_compat
    galaxy.tool_util.deps.conda_util
    galaxy.tool_util.deps.container_classes
    galaxy.tool_util.deps.container_resolvers
    galaxy.tool_util.deps.container_resolvers.explicit
    galaxy.tool_util.deps.container_resolvers.mulled
    galaxy.tool_util.deps.container_volumes
    galaxy.tool_util.deps.containers
    galaxy.tool_util.deps.dependencies
    galaxy.tool_util.deps.docker_util
    galaxy.tool_util.deps.dockerfiles
    galaxy.tool_util.deps.installable
    galaxy.tool_util.deps.mulled
    galaxy.tool_util.deps.mulled.get_tests
    galaxy.tool_util.deps.mulled.mulled_build
    galaxy.tool_util.deps.mulled.mulled_build_channel
    galaxy.tool_util.deps.mulled.mulled_build_files
    galaxy.tool_util.deps.mulled.mulled_build_tool
    galaxy.tool_util.deps.mulled.mulled_hash
    galaxy.tool_util.deps.mulled.mulled_list
    galaxy.tool_util.deps.mulled.mulled_search
    galaxy.tool_util.deps.mulled.mulled_update_singularity_containers
    galaxy.tool_util.deps.mulled.util
    galaxy.tool_util.deps.requirements
    galaxy.tool_util.deps.resolvers
    galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages
    galaxy.tool_util.deps.resolvers.conda
    galaxy.tool_util.deps.resolvers.galaxy_packages
    galaxy.tool_util.deps.resolvers.homebrew
    galaxy.tool_util.deps.resolvers.lmod
    galaxy.tool_util.deps.resolvers.modules
    galaxy.tool_util.deps.resolvers.resolver_mixins
    galaxy.tool_util.deps.resolvers.tool_shed_packages
    galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages
    galaxy.tool_util.deps.singularity_util
    galaxy.tool_util.deps.views
    galaxy.tool_util.edam_util
    galaxy.tool_util.fetcher
    galaxy.tool_util.lint
    galaxy.tool_util.linters
    galaxy.tool_util.linters.citations
    galaxy.tool_util.linters.command
    galaxy.tool_util.linters.cwl
    galaxy.tool_util.linters.general
    galaxy.tool_util.linters.help
    galaxy.tool_util.linters.inputs
    galaxy.tool_util.linters.outputs
    galaxy.tool_util.linters.stdio
    galaxy.tool_util.linters.tests
    galaxy.tool_util.linters.xml_order
    galaxy.tool_util.loader
    galaxy.tool_util.loader_directory
    galaxy.tool_util.locations
    galaxy.tool_util.locations.dockstore
    galaxy.tool_util.locations.file
    galaxy.tool_util.locations.http
    galaxy.tool_util.ontologies
    galaxy.tool_util.ontologies.ontology_data
    galaxy.tool_util.output_checker
    galaxy.tool_util.parser
    galaxy.tool_util.parser.cwl
    galaxy.tool_util.parser.factory
    galaxy.tool_util.parser.interface
    galaxy.tool_util.parser.output_actions
    galaxy.tool_util.parser.output_collection_def
    galaxy.tool_util.parser.output_objects
    galaxy.tool_util.parser.stdio
    galaxy.tool_util.parser.util
    galaxy.tool_util.parser.xml
    galaxy.tool_util.parser.yaml
    galaxy.tool_util.provided_metadata
    galaxy.tool_util.toolbox
    galaxy.tool_util.toolbox.base
    galaxy.tool_util.toolbox.filters
    galaxy.tool_util.toolbox.integrated_panel
    galaxy.tool_util.toolbox.lineages
    galaxy.tool_util.toolbox.lineages.factory
    galaxy.tool_util.toolbox.lineages.interface
    galaxy.tool_util.toolbox.panel
    galaxy.tool_util.toolbox.parser
    galaxy.tool_util.toolbox.views
    galaxy.tool_util.toolbox.views.definitions
    galaxy.tool_util.toolbox.views.edam
    galaxy.tool_util.toolbox.views.interface
    galaxy.tool_util.toolbox.views.sources
    galaxy.tool_util.toolbox.views.static
    galaxy.tool_util.toolbox.watcher
    galaxy.tool_util.unittest_utils
    galaxy.tool_util.unittest_utils.sample_data
    galaxy.tool_util.verify
    galaxy.tool_util.verify.asserts
    galaxy.tool_util.verify.asserts.archive
    galaxy.tool_util.verify.asserts.hdf5
    galaxy.tool_util.verify.asserts.size
    galaxy.tool_util.verify.asserts.tabular
    galaxy.tool_util.verify.asserts.text
    galaxy.tool_util.verify.asserts.xml
    galaxy.tool_util.verify.interactor
    galaxy.tool_util.verify.script
    galaxy.tool_util.verify.test_data
    galaxy.tool_util.verify.wait
    galaxy.tools
    galaxy.tools.actions
    galaxy.tools.actions.data_manager
    galaxy.tools.actions.data_source
    galaxy.tools.actions.history_imp_exp
    galaxy.tools.actions.metadata
    galaxy.tools.actions.model_operations
    galaxy.tools.actions.upload
    galaxy.tools.actions.upload_common
    galaxy.tools.biotools
    galaxy.tools.cache
    galaxy.tools.data
    galaxy.tools.data_fetch
    galaxy.tools.data_manager
    galaxy.tools.data_manager.manager
    galaxy.tools.error_reports
    galaxy.tools.error_reports.plugins
    galaxy.tools.error_reports.plugins.base_git
    galaxy.tools.error_reports.plugins.email
    galaxy.tools.error_reports.plugins.github
    galaxy.tools.error_reports.plugins.gitlab
    galaxy.tools.error_reports.plugins.influxdb
    galaxy.tools.error_reports.plugins.json
    galaxy.tools.error_reports.plugins.sentry
    galaxy.tools.errors
    galaxy.tools.evaluation
    galaxy.tools.exception_handling
    galaxy.tools.execute
    galaxy.tools.expressions
    galaxy.tools.expressions.evaluation
    galaxy.tools.expressions.script
    galaxy.tools.expressions.util
    galaxy.tools.filters
    galaxy.tools.imp_exp
    galaxy.tools.imp_exp.export_history
    galaxy.tools.imp_exp.unpack_tar_gz_archive
    galaxy.tools.parameters
    galaxy.tools.parameters.basic
    galaxy.tools.parameters.dataset_matcher
    galaxy.tools.parameters.dynamic_options
    galaxy.tools.parameters.grouping
    galaxy.tools.parameters.history_query
    galaxy.tools.parameters.input_translation
    galaxy.tools.parameters.meta
    galaxy.tools.parameters.sanitize
    galaxy.tools.parameters.validation
    galaxy.tools.parameters.wrapped
    galaxy.tools.parameters.wrapped_json
    galaxy.tools.recommendations
    galaxy.tools.remote_tool_eval
    galaxy.tools.repositories
    galaxy.tools.search
    galaxy.tools.special_tools
    galaxy.tools.test
    galaxy.tools.util
    galaxy.tools.util.galaxyops
    galaxy.tools.util.maf_utilities
    galaxy.tools.wrappers
    galaxy.tours
    galaxy.tours.validate
    galaxy.util
    galaxy.util.aliaspickler
    galaxy.util.bool_expressions
    galaxy.util.bunch
    galaxy.util.bytesize
    galaxy.util.checkers
    galaxy.util.commands
    galaxy.util.compression_utils
    galaxy.util.custom_logging
    galaxy.util.custom_logging.fluent_log
    galaxy.util.dbkeys
    galaxy.util.dictifiable
    galaxy.util.dynamic
    galaxy.util.expressions
    galaxy.util.facts
    galaxy.util.filelock
    galaxy.util.form_builder
    galaxy.util.hash_util
    galaxy.util.heartbeat
    galaxy.util.image_util
    galaxy.util.inflection
    galaxy.util.json
    galaxy.util.jstree
    galaxy.util.lazy_process
    galaxy.util.monitors
    galaxy.util.odict
    galaxy.util.oset
    galaxy.util.path
    galaxy.util.path.ntpath
    galaxy.util.path.posixpath
    galaxy.util.permutations
    galaxy.util.plugin_config
    galaxy.util.properties
    galaxy.util.renamed_temporary_file
    galaxy.util.resources
    galaxy.util.rules_dsl
    galaxy.util.sanitize_html
    galaxy.util.script
    galaxy.util.search
    galaxy.util.simplegraph
    galaxy.util.sleeper
    galaxy.util.sockets
    galaxy.util.specs
    galaxy.util.sqlite
    galaxy.util.submodules
    galaxy.util.task
    galaxy.util.template
    galaxy.util.tool_shed
    galaxy.util.tool_shed.common_util
    galaxy.util.tool_shed.encoding_util
    galaxy.util.tool_shed.xml_util
    galaxy.util.tool_version
    galaxy.util.topsort
    galaxy.util.ucsc
    galaxy.util.validation
    galaxy.util.watcher
    galaxy.util.xml_macros
    galaxy.util.yaml_util
    galaxy.util.zipstream
    galaxy.version
    galaxy.visualization
    galaxy.visualization.data_providers
    galaxy.visualization.data_providers.basic
    galaxy.visualization.data_providers.cigar
    galaxy.visualization.data_providers.genome
    galaxy.visualization.data_providers.phyloviz
    galaxy.visualization.data_providers.phyloviz.baseparser
    galaxy.visualization.data_providers.phyloviz.newickparser
    galaxy.visualization.data_providers.phyloviz.nexusparser
    galaxy.visualization.data_providers.phyloviz.phyloxmlparser
    galaxy.visualization.data_providers.registry
    galaxy.visualization.genome
    galaxy.visualization.genomes
    galaxy.visualization.plugins
    galaxy.visualization.plugins.config_parser
    galaxy.visualization.plugins.plugin
    galaxy.visualization.plugins.registry
    galaxy.visualization.plugins.resource_parser
    galaxy.visualization.plugins.utils
    galaxy.visualization.tracks
    galaxy.web
    galaxy.web.form_builder
    galaxy.web.framework
    galaxy.web.framework.base
    galaxy.web.framework.decorators
    galaxy.web.framework.helpers
    galaxy.web.framework.helpers.grids
    galaxy.web.framework.helpers.tags
    galaxy.web.framework.middleware
    galaxy.web.framework.middleware.error
    galaxy.web.framework.middleware.profile
    galaxy.web.framework.middleware.remoteuser
    galaxy.web.framework.middleware.request_id
    galaxy.web.framework.middleware.sqldebug
    galaxy.web.framework.middleware.static
    galaxy.web.framework.middleware.statsd
    galaxy.web.framework.middleware.translogger
    galaxy.web.framework.middleware.xforwardedhost
    galaxy.web.legacy_framework
    galaxy.web.legacy_framework.grids
    galaxy.web.proxy
    galaxy.web.short_term_storage
    galaxy.web.statsd_client
    galaxy.web_stack
    galaxy.web_stack.gunicorn_config
    galaxy.web_stack.handlers
    galaxy.web_stack.message
    galaxy.web_stack.transport
    galaxy.webapps
    galaxy.webapps.base
    galaxy.webapps.base.api
    galaxy.webapps.base.controller
    galaxy.webapps.base.webapp
    galaxy.webapps.galaxy
    galaxy.webapps.galaxy.api
    galaxy.webapps.galaxy.api.annotations
    galaxy.webapps.galaxy.api.authenticate
    galaxy.webapps.galaxy.api.cloud
    galaxy.webapps.galaxy.api.cloudauthz
    galaxy.webapps.galaxy.api.common
    galaxy.webapps.galaxy.api.configuration
    galaxy.webapps.galaxy.api.container_resolution
    galaxy.webapps.galaxy.api.dataset_collections
    galaxy.webapps.galaxy.api.datasets
    galaxy.webapps.galaxy.api.datatypes
    galaxy.webapps.galaxy.api.display_applications
    galaxy.webapps.galaxy.api.dynamic_tools
    galaxy.webapps.galaxy.api.extended_metadata
    galaxy.webapps.galaxy.api.folder_contents
    galaxy.webapps.galaxy.api.folders
    galaxy.webapps.galaxy.api.forms
    galaxy.webapps.galaxy.api.genomes
    galaxy.webapps.galaxy.api.group_roles
    galaxy.webapps.galaxy.api.group_users
    galaxy.webapps.galaxy.api.groups
    galaxy.webapps.galaxy.api.histories
    galaxy.webapps.galaxy.api.history_contents
    galaxy.webapps.galaxy.api.item_tags
    galaxy.webapps.galaxy.api.job_files
    galaxy.webapps.galaxy.api.job_lock
    galaxy.webapps.galaxy.api.job_ports
    galaxy.webapps.galaxy.api.jobs
    galaxy.webapps.galaxy.api.libraries
    galaxy.webapps.galaxy.api.library_contents
    galaxy.webapps.galaxy.api.library_datasets
    galaxy.webapps.galaxy.api.licenses
    galaxy.webapps.galaxy.api.metrics
    galaxy.webapps.galaxy.api.page_revisions
    galaxy.webapps.galaxy.api.pages
    galaxy.webapps.galaxy.api.plugins
    galaxy.webapps.galaxy.api.provenance
    galaxy.webapps.galaxy.api.quotas
    galaxy.webapps.galaxy.api.remote_files
    galaxy.webapps.galaxy.api.roles
    galaxy.webapps.galaxy.api.sanitize_allow
    galaxy.webapps.galaxy.api.search
    galaxy.webapps.galaxy.api.short_term_storage
    galaxy.webapps.galaxy.api.tags
    galaxy.webapps.galaxy.api.tasks
    galaxy.webapps.galaxy.api.tool_data
    galaxy.webapps.galaxy.api.tool_dependencies
    galaxy.webapps.galaxy.api.tool_entry_points
    galaxy.webapps.galaxy.api.tool_shed_repositories
    galaxy.webapps.galaxy.api.tools
    galaxy.webapps.galaxy.api.toolshed
    galaxy.webapps.galaxy.api.tours
    galaxy.webapps.galaxy.api.trs_consumer
    galaxy.webapps.galaxy.api.trs_search
    galaxy.webapps.galaxy.api.uploads
    galaxy.webapps.galaxy.api.users
    galaxy.webapps.galaxy.api.visualizations
    galaxy.webapps.galaxy.api.webhooks
    galaxy.webapps.galaxy.api.workflows
    galaxy.webapps.galaxy.buildapp
    galaxy.webapps.galaxy.controllers
    galaxy.webapps.galaxy.controllers.admin
    galaxy.webapps.galaxy.controllers.admin_toolshed
    galaxy.webapps.galaxy.controllers.async
    galaxy.webapps.galaxy.controllers.authnz
    galaxy.webapps.galaxy.controllers.data_manager
    galaxy.webapps.galaxy.controllers.dataset
    galaxy.webapps.galaxy.controllers.error
    galaxy.webapps.galaxy.controllers.forms
    galaxy.webapps.galaxy.controllers.history
    galaxy.webapps.galaxy.controllers.page
    galaxy.webapps.galaxy.controllers.root
    galaxy.webapps.galaxy.controllers.shed_tool_static
    galaxy.webapps.galaxy.controllers.tag
    galaxy.webapps.galaxy.controllers.tool_runner
    galaxy.webapps.galaxy.controllers.user
    galaxy.webapps.galaxy.controllers.userskeys
    galaxy.webapps.galaxy.controllers.visualization
    galaxy.webapps.galaxy.controllers.workflow
    galaxy.webapps.galaxy.fast_app
    galaxy.webapps.galaxy.fast_factory
    galaxy.webapps.galaxy.services
    galaxy.webapps.galaxy.services.authenticate
    galaxy.webapps.galaxy.services.base
    galaxy.webapps.galaxy.services.dataset_collections
    galaxy.webapps.galaxy.services.datasets
    galaxy.webapps.galaxy.services.histories
    galaxy.webapps.galaxy.services.history_contents
    galaxy.webapps.galaxy.services.invocations
    galaxy.webapps.galaxy.services.jobs
    galaxy.webapps.galaxy.services.libraries
    galaxy.webapps.galaxy.services.library_folder_contents
    galaxy.webapps.galaxy.services.library_folders
    galaxy.webapps.galaxy.services.pages
    galaxy.webapps.galaxy.services.quotas
    galaxy.webapps.galaxy.services.sharable
    galaxy.webapps.galaxy.services.tools
    galaxy.webapps.galaxy.services.users
    galaxy.webapps.galaxy.services.visualizations
    galaxy.webapps.galaxy.services.workflows
    galaxy.webapps.galaxy.workers
    galaxy.webapps.openapi
    galaxy.webapps.openapi.utils
    galaxy.webapps.reports
    galaxy.webapps.reports.api
    galaxy.webapps.reports.app
    galaxy.webapps.reports.buildapp
    galaxy.webapps.reports.config
    galaxy.webapps.reports.controllers
    galaxy.webapps.reports.controllers.history
    galaxy.webapps.reports.controllers.home
    galaxy.webapps.reports.controllers.jobs
    galaxy.webapps.reports.controllers.query
    galaxy.webapps.reports.controllers.root
    galaxy.webapps.reports.controllers.system
    galaxy.webapps.reports.controllers.tools
    galaxy.webapps.reports.controllers.users
    galaxy.webapps.reports.controllers.workflows
    galaxy.webapps.reports.fast_app
    galaxy.webapps.reports.fast_factory
    galaxy.webapps.util
    galaxy.webhooks
    galaxy.work
    galaxy.work.context
    galaxy.workflow
    galaxy.workflow.extract
    galaxy.workflow.modules
    galaxy.workflow.refactor
    galaxy.workflow.refactor.execute
    galaxy.workflow.refactor.schema
    galaxy.workflow.render
    galaxy.workflow.reports
    galaxy.workflow.reports.generators
    galaxy.workflow.reports.generators.markdown
    galaxy.workflow.resources
    galaxy.workflow.run
    galaxy.workflow.run_request
    galaxy.workflow.schedulers
    galaxy.workflow.schedulers.core
    galaxy.workflow.scheduling_manager
    galaxy.workflow.steps
    galaxy.workflow.trs_proxy
galaxy_ext
    galaxy_ext.container_monitor
    galaxy_ext.container_monitor.monitor
    galaxy_ext.expressions
    galaxy_ext.expressions.handle_job
    galaxy_ext.metadata
    galaxy_ext.metadata.set_metadata
galaxy_test
    galaxy_test.api
    galaxy_test.api.cwl
    galaxy_test.api.sharable
    galaxy_test.api.test_authenticate
    galaxy_test.api.test_configuration
    galaxy_test.api.test_dataset_collections
    galaxy_test.api.test_datasets
    galaxy_test.api.test_datatypes
    galaxy_test.api.test_display_applications
    galaxy_test.api.test_folder_contents
    galaxy_test.api.test_folders
    galaxy_test.api.test_framework
    galaxy_test.api.test_group_roles
    galaxy_test.api.test_group_users
    galaxy_test.api.test_groups
    galaxy_test.api.test_histories
    galaxy_test.api.test_history_contents
    galaxy_test.api.test_history_contents_provenance
    galaxy_test.api.test_jobs
    galaxy_test.api.test_libraries
    galaxy_test.api.test_licenses
    galaxy_test.api.test_page_revisions
    galaxy_test.api.test_pages
    galaxy_test.api.test_roles
    galaxy_test.api.test_search
    galaxy_test.api.test_tool_data
    galaxy_test.api.test_tools
    galaxy_test.api.test_tools_upload
    galaxy_test.api.test_tours
    galaxy_test.api.test_users
    galaxy_test.api.test_visualizations
    galaxy_test.api.test_webhooks
    galaxy_test.api.test_workflow_extraction
    galaxy_test.api.test_workflows
    galaxy_test.api.test_workflows_cwl
    galaxy_test.api.test_workflows_from_yaml
    galaxy_test.base
    galaxy_test.base.api
    galaxy_test.base.api_asserts
    galaxy_test.base.api_util
    galaxy_test.base.constants
    galaxy_test.base.env
    galaxy_test.base.interactor
    galaxy_test.base.populators
    galaxy_test.base.rules_test_data
    galaxy_test.base.testcase
    galaxy_test.base.workflow_fixtures
    galaxy_test.conftest
    galaxy_test.driver
    galaxy_test.driver.driver_util
    galaxy_test.driver.integration_setup
    galaxy_test.driver.integration_util
    galaxy_test.driver.test_logging
    galaxy_test.driver.testcase
    galaxy_test.performance
    galaxy_test.performance.test_workflow_framework_performance
    galaxy_test.selenium
    galaxy_test.selenium.conftest
    galaxy_test.selenium.framework
    galaxy_test.selenium.jupyter
    galaxy_test.selenium.jupyter_context
    galaxy_test.selenium.test_admin_app
    galaxy_test.selenium.test_anon_history
    galaxy_test.selenium.test_change_password
    galaxy_test.selenium.test_collection_builders
    galaxy_test.selenium.test_collection_edit
    galaxy_test.selenium.test_custom_builds
    galaxy_test.selenium.test_data_source_tools
    galaxy_test.selenium.test_dataset_metadata_download
    galaxy_test.selenium.test_histories_list
    galaxy_test.selenium.test_history_copy_elements
    galaxy_test.selenium.test_history_dataset_state
    galaxy_test.selenium.test_history_multi_view
    galaxy_test.selenium.test_history_options
    galaxy_test.selenium.test_history_panel
    galaxy_test.selenium.test_history_panel_collections
    galaxy_test.selenium.test_history_sharing
    galaxy_test.selenium.test_invocation_grid
    galaxy_test.selenium.test_library_contents
    galaxy_test.selenium.test_library_landing
    galaxy_test.selenium.test_library_to_collections
    galaxy_test.selenium.test_login
    galaxy_test.selenium.test_navigates_galaxy
    galaxy_test.selenium.test_pages
    galaxy_test.selenium.test_personal_information
    galaxy_test.selenium.test_registration
    galaxy_test.selenium.test_sign_out
    galaxy_test.selenium.test_sizzle_loading
    galaxy_test.selenium.test_stock_tours
    galaxy_test.selenium.test_tool_describing_tours
    galaxy_test.selenium.test_tool_form
    galaxy_test.selenium.test_uploads
    galaxy_test.selenium.test_workflow_editor
    galaxy_test.selenium.test_workflow_invocation_details
    galaxy_test.selenium.test_workflow_management
    galaxy_test.selenium.test_workflow_run
    galaxy_test.selenium.test_workflow_sharing
 
t
tool_shed
    tool_shed.dependencies
    tool_shed.dependencies.attribute_handlers
    tool_shed.dependencies.repository
    tool_shed.dependencies.repository.relation_builder
    tool_shed.dependencies.tool
    tool_shed.dependencies.tool.tag_attribute_handler
    tool_shed.galaxy_install
    tool_shed.grids
    tool_shed.grids.admin_grids
    tool_shed.grids.repository_grid_filter_manager
    tool_shed.grids.repository_grids
    tool_shed.grids.util
    tool_shed.managers
    tool_shed.managers.groups
    tool_shed.managers.repositories
    tool_shed.metadata
    tool_shed.metadata.metadata_generator
    tool_shed.metadata.repository_metadata_manager
    tool_shed.repository_registry
    tool_shed.repository_types
    tool_shed.repository_types.metadata
    tool_shed.repository_types.registry
    tool_shed.repository_types.repository_suite_definition
    tool_shed.repository_types.tool_dependency_definition
    tool_shed.repository_types.unrestricted
    tool_shed.repository_types.util
    tool_shed.test
    tool_shed.test.base
    tool_shed.test.base.common
    tool_shed.test.base.test_db_util
    tool_shed.test.base.twilltestcase
    tool_shed.test.functional
    tool_shed.test.functional.test_0000_basic_repository_features
    tool_shed.test.functional.test_0010_repository_with_tool_dependencies
    tool_shed.test.functional.test_0020_basic_repository_dependencies
    tool_shed.test.functional.test_0030_repository_dependency_revisions
    tool_shed.test.functional.test_0040_repository_circular_dependencies
    tool_shed.test.functional.test_0050_circular_dependencies_4_levels
    tool_shed.test.functional.test_0070_invalid_tool
    tool_shed.test.functional.test_0080_advanced_circular_dependencies
    tool_shed.test.functional.test_0090_tool_search
    tool_shed.test.functional.test_0100_complex_repository_dependencies
    tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies
    tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners
    tool_shed.test.functional.test_0140_tool_help_images
    tool_shed.test.functional.test_0150_prior_installation_required
    tool_shed.test.functional.test_0160_circular_prior_installation_required
    tool_shed.test.functional.test_0170_complex_prior_installation_required
    tool_shed.test.functional.test_0300_reset_all_metadata
    tool_shed.test.functional.test_0310_hg_api_features
    tool_shed.test.functional.test_0420_citable_urls_for_repositories
    tool_shed.test.functional.test_0430_browse_utilities
    tool_shed.test.functional.test_0440_deleting_dependency_definitions
    tool_shed.test.functional.test_0460_upload_to_repository
    tool_shed.test.functional.test_0470_tool_dependency_repository_type
    tool_shed.test.functional.test_0480_tool_dependency_xml_verification
    tool_shed.test.functional.test_0530_repository_admin_feature
    tool_shed.test.functional.test_0540_get_all_metadata_from_api
    tool_shed.test.functional.test_0550_metadata_updated_dependencies
    tool_shed.test.functional.test_1000_install_basic_repository
    tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies
    tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies
    tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions
    tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies
    tool_shed.test.functional.test_1050_circular_dependencies_4_levels
    tool_shed.test.functional.test_1070_invalid_tool
    tool_shed.test.functional.test_1080_advanced_circular_dependency_installation
    tool_shed.test.functional.test_1090_repository_dependency_handling
    tool_shed.test.functional.test_1100_install_updated_repository_dependencies
    tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies
    tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency
    tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners
    tool_shed.test.functional.test_1160_tool_help_images
    tool_shed.test.functional.test_1170_prior_installation_required
    tool_shed.test.functional.test_1180_circular_prior_installation_required
    tool_shed.test.functional.test_1190_complex_prior_installation_required
    tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository
    tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies
    tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions
    tool_shed.test.functional.test_1300_reset_all_metadata
    tool_shed.test.functional.test_1410_update_manager
    tool_shed.test.functional.test_1430_repair_installed_repository
    tool_shed.test.functional.test_1460_data_managers
    tool_shed.test.functional.test_1470_updating_installed_repositories
    tool_shed.tools
    tool_shed.tools.data_table_manager
    tool_shed.tools.tool_validator
    tool_shed.tools.tool_version_manager
    tool_shed.util
    tool_shed.util.admin_util
    tool_shed.util.basic_util
    tool_shed.util.commit_util
    tool_shed.util.common_util
    tool_shed.util.container_util
    tool_shed.util.encoding_util
    tool_shed.util.hg_util
    tool_shed.util.hgweb_config
    tool_shed.util.metadata_util
    tool_shed.util.readme_util
    tool_shed.util.repository_content_util
    tool_shed.util.repository_util
    tool_shed.util.search_util
    tool_shed.util.shed_index
    tool_shed.util.shed_util_common
    tool_shed.util.tool_dependency_util
    tool_shed.util.tool_util
    tool_shed.util.web_util
    tool_shed.util.xml_util
    tool_shed.utility_containers
    tool_shed.utility_containers.utility_container_manager
    tool_shed.webapp
    tool_shed.webapp.api
    tool_shed.webapp.api.authenticate
    tool_shed.webapp.api.categories
    tool_shed.webapp.api.configuration
    tool_shed.webapp.api.groups
    tool_shed.webapp.api.repositories
    tool_shed.webapp.api.repository_revisions
    tool_shed.webapp.api.tools
    tool_shed.webapp.api.users
    tool_shed.webapp.app
    tool_shed.webapp.buildapp
    tool_shed.webapp.config
    tool_shed.webapp.controllers
    tool_shed.webapp.controllers.admin
    tool_shed.webapp.controllers.groups
    tool_shed.webapp.controllers.hg
    tool_shed.webapp.controllers.repository
    tool_shed.webapp.controllers.upload
    tool_shed.webapp.controllers.user
    tool_shed.webapp.fast_app
    tool_shed.webapp.fast_factory
    tool_shed.webapp.framework
    tool_shed.webapp.framework.decorators
    tool_shed.webapp.framework.middleware
    tool_shed.webapp.framework.middleware.remoteuser
    tool_shed.webapp.model
    tool_shed.webapp.model.mapping
    tool_shed.webapp.model.migrate
    tool_shed.webapp.model.migrate.check
    tool_shed.webapp.model.migrate.versions
    tool_shed.webapp.model.migrate.versions.0001_initial_tables
    tool_shed.webapp.model.migrate.versions.0002_add_tool_suite_column
    tool_shed.webapp.model.migrate.versions.0003_review_and_review_association_tables
    tool_shed.webapp.model.migrate.versions.0004_repository_tables
    tool_shed.webapp.model.migrate.versions.0005_drop_tool_related_tables
    tool_shed.webapp.model.migrate.versions.0006_add_email_alerts_column
    tool_shed.webapp.model.migrate.versions.0007_add_long_description_times_downloaded_columns
    tool_shed.webapp.model.migrate.versions.0008_add_repository_metadata_table
    tool_shed.webapp.model.migrate.versions.0009_add_malicious_column
    tool_shed.webapp.model.migrate.versions.0010_add_new_repo_alert_column
    tool_shed.webapp.model.migrate.versions.0011_add_tool_versions_column
    tool_shed.webapp.model.migrate.versions.0012_add_downloadable_column
    tool_shed.webapp.model.migrate.versions.0013_add_review_tables
    tool_shed.webapp.model.migrate.versions.0014_add_deprecated_column
    tool_shed.webapp.model.migrate.versions.0015_add_api_keys_table
    tool_shed.webapp.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns
    tool_shed.webapp.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table
    tool_shed.webapp.model.migrate.versions.0018_add_repository_metadata_flag_columns
    tool_shed.webapp.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column
    tool_shed.webapp.model.migrate.versions.0020_add_repository_type_column
    tool_shed.webapp.model.migrate.versions.0021_change_repository_type_value
    tool_shed.webapp.model.migrate.versions.0022_add_repository_admin_roles
    tool_shed.webapp.model.migrate.versions.0023_add_repository_url_and_hompeage_url
    tool_shed.webapp.model.migrate.versions.0024_password_reset
    tool_shed.webapp.model.migrate.versions.0025_session_timeout
    tool_shed.webapp.model.migrate.versions.0026_add_numeric_revision_column
    tool_shed.webapp.search
    tool_shed.webapp.search.repo_search
    tool_shed.webapp.search.tool_search
    tool_shed.webapp.security
    tool_shed.webapp.util
    tool_shed.webapp.util.ratings_util
    tool_shed.webapp.util.shed_statistics