Python Module Index

g | t
 
g
galaxy
    galaxy.actions
    galaxy.actions.admin
    galaxy.actions.library
    galaxy.app
    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.config
    galaxy.config.script
    galaxy.config_watchers
    galaxy.containers
    galaxy.containers.docker
    galaxy.containers.docker_decorators
    galaxy.containers.docker_model
    galaxy.containers.docker_swarm
    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.bedgraph_to_array_tree_converter
    galaxy.datatypes.converters.bgzip
    galaxy.datatypes.converters.cram_to_bam
    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_coverage
    galaxy.datatypes.converters.interval_to_fli
    galaxy.datatypes.converters.interval_to_interval_index_converter
    galaxy.datatypes.converters.interval_to_tabix_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.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.sam_to_bam
    galaxy.datatypes.converters.tabular_csv
    galaxy.datatypes.converters.tabular_to_dbnsfp
    galaxy.datatypes.converters.vcf_to_interval_index_converter
    galaxy.datatypes.converters.vcf_to_vcf_bgzip
    galaxy.datatypes.converters.wiggle_to_array_tree_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.genetics
    galaxy.datatypes.gis
    galaxy.datatypes.graph
    galaxy.datatypes.images
    galaxy.datatypes.interval
    galaxy.datatypes.isa
    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.qualityscore
    galaxy.datatypes.registry
    galaxy.datatypes.sequence
    galaxy.datatypes.sniff
    galaxy.datatypes.spaln
    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.eggs
    galaxy.exceptions
    galaxy.exceptions.error_codes
    galaxy.forms
    galaxy.forms.forms
    galaxy.job_execution
    galaxy.job_execution.datasets
    galaxy.job_execution.output_collect
    galaxy.job_metrics
    galaxy.job_metrics.collectl
    galaxy.job_metrics.collectl.cli
    galaxy.job_metrics.collectl.processes
    galaxy.job_metrics.collectl.stats
    galaxy.job_metrics.collectl.subsystems
    galaxy.job_metrics.formatting
    galaxy.job_metrics.instrumenters
    galaxy.job_metrics.instrumenters.cgroup
    galaxy.job_metrics.instrumenters.collectl
    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.jobs
    galaxy.jobs.actions
    galaxy.jobs.actions.post
    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.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.pykube_util
    galaxy.jobs.runners.util.sudo
    galaxy.jobs.splitters
    galaxy.jobs.splitters.basic
    galaxy.jobs.splitters.multi
    galaxy.jobs.stock_rules
    galaxy.jobs.transfer_manager
    galaxy.main
    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.containers
    galaxy.managers.context
    galaxy.managers.datasets
    galaxy.managers.deletable
    galaxy.managers.folders
    galaxy.managers.hdas
    galaxy.managers.hdcas
    galaxy.managers.histories
    galaxy.managers.history_contents
    galaxy.managers.jobs
    galaxy.managers.lddas
    galaxy.managers.libraries
    galaxy.managers.library_datasets
    galaxy.managers.pages
    galaxy.managers.ratable
    galaxy.managers.rbac_secured
    galaxy.managers.roles
    galaxy.managers.secured
    galaxy.managers.sharable
    galaxy.managers.taggable
    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.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.item_attrs
    galaxy.model.mapping
    galaxy.model.metadata
    galaxy.model.migrate
    galaxy.model.migrate.check
    galaxy.model.migrate.versions
    galaxy.model.migrate.versions.0001_initial_tables
    galaxy.model.migrate.versions.0002_metadata_file_table
    galaxy.model.migrate.versions.0003_security_and_libraries
    galaxy.model.migrate.versions.0004_indexes_and_defaults
    galaxy.model.migrate.versions.0005_cleanup_datasets_fix
    galaxy.model.migrate.versions.0006_change_qual_datatype
    galaxy.model.migrate.versions.0007_sharing_histories
    galaxy.model.migrate.versions.0008_galaxy_forms
    galaxy.model.migrate.versions.0009_request_table
    galaxy.model.migrate.versions.0010_hda_display_at_authz_table
    galaxy.model.migrate.versions.0011_v0010_mysql_index_fix
    galaxy.model.migrate.versions.0012_user_address
    galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms
    galaxy.model.migrate.versions.0014_pages
    galaxy.model.migrate.versions.0015_tagging
    galaxy.model.migrate.versions.0016_v0015_mysql_index_fix
    galaxy.model.migrate.versions.0017_library_item_indexes
    galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags
    galaxy.model.migrate.versions.0019_request_library_folder
    galaxy.model.migrate.versions.0020_library_upload_job
    galaxy.model.migrate.versions.0021_user_prefs
    galaxy.model.migrate.versions.0022_visualization_tables
    galaxy.model.migrate.versions.0023_page_published_and_deleted_columns
    galaxy.model.migrate.versions.0024_page_slug_unique_constraint
    galaxy.model.migrate.versions.0025_user_info
    galaxy.model.migrate.versions.0026_cloud_tables
    galaxy.model.migrate.versions.0027_request_events
    galaxy.model.migrate.versions.0028_external_metadata_file_override
    galaxy.model.migrate.versions.0029_user_actions
    galaxy.model.migrate.versions.0030_history_slug_column
    galaxy.model.migrate.versions.0031_community_and_workflow_tags
    galaxy.model.migrate.versions.0032_stored_workflow_slug_column
    galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows
    galaxy.model.migrate.versions.0034_page_user_share_association
    galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags
    galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables
    galaxy.model.migrate.versions.0037_samples_library
    galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables
    galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table
    galaxy.model.migrate.versions.0040_page_annotations
    galaxy.model.migrate.versions.0041_workflow_invocation
    galaxy.model.migrate.versions.0042_workflow_invocation_fix
    galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating
    galaxy.model.migrate.versions.0044_add_notify_column_to_request_table
    galaxy.model.migrate.versions.0045_request_type_permissions_table
    galaxy.model.migrate.versions.0046_post_job_actions
    galaxy.model.migrate.versions.0047_job_table_user_id_column
    galaxy.model.migrate.versions.0048_dataset_instance_state_column
    galaxy.model.migrate.versions.0049_api_keys_table
    galaxy.model.migrate.versions.0050_drop_cloud_tables
    galaxy.model.migrate.versions.0051_imported_col_for_jobs_table
    galaxy.model.migrate.versions.0052_sample_dataset_table
    galaxy.model.migrate.versions.0053_item_ratings
    galaxy.model.migrate.versions.0054_visualization_dbkey
    galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs
    galaxy.model.migrate.versions.0056_workflow_outputs
    galaxy.model.migrate.versions.0057_request_notify
    galaxy.model.migrate.versions.0058_history_import_export
    galaxy.model.migrate.versions.0059_sample_dataset_file_path
    galaxy.model.migrate.versions.0060_history_archive_import
    galaxy.model.migrate.versions.0061_tasks
    galaxy.model.migrate.versions.0062_user_openid_table
    galaxy.model.migrate.versions.0063_sequencer_table
    galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables
    galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values
    galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables
    galaxy.model.migrate.versions.0067_populate_sequencer_table
    galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services
    galaxy.model.migrate.versions.0069_rename_sequencer_form_type
    galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table
    galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample
    galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table
    galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table
    galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table
    galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table
    galaxy.model.migrate.versions.0076_fix_form_values_data_corruption
    galaxy.model.migrate.versions.0077_create_tool_tag_association_table
    galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting
    galaxy.model.migrate.versions.0079_input_library_to_job_table
    galaxy.model.migrate.versions.0080_quota_tables
    galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda
    galaxy.model.migrate.versions.0082_add_tool_shed_repository_table
    galaxy.model.migrate.versions.0083_add_prepare_files_to_task
    galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table
    galaxy.model.migrate.versions.0085_add_task_info
    galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns
    galaxy.model.migrate.versions.0087_tool_id_guid_map_table
    galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column
    galaxy.model.migrate.versions.0089_add_object_store_id_columns
    galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns
    galaxy.model.migrate.versions.0091_add_tool_version_tables
    galaxy.model.migrate.versions.0092_add_migrate_tools_table
    galaxy.model.migrate.versions.0093_add_job_params_col
    galaxy.model.migrate.versions.0094_add_job_handler_col
    galaxy.model.migrate.versions.0095_hda_subsets
    galaxy.model.migrate.versions.0096_openid_provider
    galaxy.model.migrate.versions.0097_add_ctx_rev_column
    galaxy.model.migrate.versions.0098_genome_index_tool_data_table
    galaxy.model.migrate.versions.0099_add_tool_dependency_table
    galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column
    galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column
    galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns
    galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns
    galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters
    galaxy.model.migrate.versions.0105_add_cleanup_event_table
    galaxy.model.migrate.versions.0106_add_missing_indexes
    galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task
    galaxy.model.migrate.versions.0108_add_extended_metadata
    galaxy.model.migrate.versions.0109_add_repository_dependency_tables
    galaxy.model.migrate.versions.0110_add_dataset_uuid
    galaxy.model.migrate.versions.0111_add_job_destinations
    galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables
    galaxy.model.migrate.versions.0113_update_migrate_tools_table
    galaxy.model.migrate.versions.0114_update_migrate_tools_table_again
    galaxy.model.migrate.versions.0115_longer_user_password_field
    galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col
    galaxy.model.migrate.versions.0117_add_user_activation
    galaxy.model.migrate.versions.0118_add_hda_extended_metadata
    galaxy.model.migrate.versions.0119_job_metrics
    galaxy.model.migrate.versions.0120_dataset_collections
    galaxy.model.migrate.versions.0121_workflow_uuids
    galaxy.model.migrate.versions.0122_grow_mysql_blobs
    galaxy.model.migrate.versions.0123_add_workflow_request_tables
    galaxy.model.migrate.versions.0124_job_state_history
    galaxy.model.migrate.versions.0125_workflow_step_tracking
    galaxy.model.migrate.versions.0126_password_reset
    galaxy.model.migrate.versions.0127_output_collection_adjustments
    galaxy.model.migrate.versions.0128_session_timeout
    galaxy.model.migrate.versions.0129_job_external_output_metadata_validity
    galaxy.model.migrate.versions.0130_change_pref_datatype
    galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules
    galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user
    galaxy.model.migrate.versions.0133_add_dependency_column_to_job
    galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged
    galaxy.model.migrate.versions.0135_add_library_tags
    galaxy.model.migrate.versions.0136_collection_and_workflow_state
    galaxy.model.migrate.versions.0137_add_copied_from_job_id_column
    galaxy.model.migrate.versions.0138_add_hda_version
    galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table
    galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table
    galaxy.model.migrate.versions.0141_add_oidc_tables
    galaxy.model.migrate.versions.0142_change_numeric_metric_precision
    galaxy.model.migrate.versions.0143_add_cloudauthz_tables
    galaxy.model.migrate.versions.0144_add_cleanup_event_user_table
    galaxy.model.migrate.versions.0145_add_workflow_step_input
    galaxy.model.migrate.versions.0146_workflow_paths
    galaxy.model.migrate.versions.0147_job_messages
    galaxy.model.migrate.versions.0148_add_checksum_table
    galaxy.model.migrate.versions.0149_dynamic_tools
    galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz
    galaxy.model.migrate.versions.0151_add_worker_process
    galaxy.model.migrate.versions.0152_add_metadata_file_uuid
    galaxy.model.migrate.versions.0153_add_custos_authnz_token_table
    galaxy.model.migrate.versions.0154_created_from_basename
    galaxy.model.migrate.versions.util
    galaxy.model.none_like
    galaxy.model.orm
    galaxy.model.orm.engine_factory
    galaxy.model.orm.logging_connection_proxy
    galaxy.model.orm.now
    galaxy.model.orm.scripts
    galaxy.model.search
    galaxy.model.security
    galaxy.model.store
    galaxy.model.store.build_objects
    galaxy.model.store.discover
    galaxy.model.tags
    galaxy.model.tool_shed_install
    galaxy.model.tool_shed_install.mapping
    galaxy.model.tool_shed_install.migrate
    galaxy.model.tool_shed_install.migrate.check
    galaxy.objectstore
    galaxy.objectstore.azure_blob
    galaxy.objectstore.cloud
    galaxy.objectstore.pithos
    galaxy.objectstore.pulsar
    galaxy.objectstore.rods
    galaxy.objectstore.s3
    galaxy.objectstore.s3_multipart_upload
    galaxy.openid
    galaxy.openid.openid_manager
    galaxy.openid.providers
    galaxy.queue_worker
    galaxy.queues
    galaxy.quota
    galaxy.security
    galaxy.security.idencoding
    galaxy.security.passwords
    galaxy.security.validate_user_input
    galaxy.selenium
    galaxy.selenium.cli
    galaxy.selenium.components
    galaxy.selenium.data
    galaxy.selenium.driver_factory
    galaxy.selenium.has_driver
    galaxy.selenium.navigates_galaxy
    galaxy.selenium.scripts
    galaxy.selenium.scripts.dump_tour
    galaxy.selenium.sizzle
    galaxy.selenium.smart_components
    galaxy.tool_util
    galaxy.tool_util.cwl
    galaxy.tool_util.cwl.cwltool_deps
    galaxy.tool_util.cwl.parser
    galaxy.tool_util.cwl.representation
    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.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.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_search
    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.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.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.util
    galaxy.tool_util.parser.xml
    galaxy.tool_util.parser.yaml
    galaxy.tool_util.provided_metadata
    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.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.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.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.repositories
    galaxy.tools.search
    galaxy.tools.special_tools
    galaxy.tools.test
    galaxy.tools.toolbox
    galaxy.tools.toolbox.base
    galaxy.tools.toolbox.filters
    galaxy.tools.toolbox.integrated_panel
    galaxy.tools.toolbox.lineages
    galaxy.tools.toolbox.lineages.factory
    galaxy.tools.toolbox.lineages.interface
    galaxy.tools.toolbox.panel
    galaxy.tools.toolbox.parser
    galaxy.tools.toolbox.tags
    galaxy.tools.toolbox.watcher
    galaxy.tools.util
    galaxy.tools.util.galaxyops
    galaxy.tools.util.maf_utilities
    galaxy.tools.wrappers
    galaxy.tours
    galaxy.util
    galaxy.util.aliaspickler
    galaxy.util.bunch
    galaxy.util.bytesize
    galaxy.util.checkers
    galaxy.util.compression_utils
    galaxy.util.dbkeys
    galaxy.util.dictifiable
    galaxy.util.expressions
    galaxy.util.facts
    galaxy.util.filelock
    galaxy.util.form_builder
    galaxy.util.getargspec
    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.logging
    galaxy.util.logging.fluent_log
    galaxy.util.monitors
    galaxy.util.object_wrapper
    galaxy.util.odict
    galaxy.util.oset
    galaxy.util.pastescript
    galaxy.util.pastescript.loadwsgi
    galaxy.util.pastescript.serve
    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.rules_dsl
    galaxy.util.sanitize_html
    galaxy.util.script
    galaxy.util.simplegraph
    galaxy.util.sleeper
    galaxy.util.sockets
    galaxy.util.specs
    galaxy.util.sqlite
    galaxy.util.streamball
    galaxy.util.submodules
    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.web_compat
    galaxy.util.xml_macros
    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.interactive_environments
    galaxy.visualization.plugins.plugin
    galaxy.visualization.plugins.registry
    galaxy.visualization.plugins.resource_parser
    galaxy.visualization.plugins.utils
    galaxy.visualization.tracks
    galaxy.web
    galaxy.web.buildapp
    galaxy.web.form_builder
    galaxy.web.formatting
    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.batch
    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.sentry
    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.framework.webapp
    galaxy.web.params
    galaxy.web.proxy
    galaxy.web_stack
    galaxy.web_stack.handlers
    galaxy.web_stack.message
    galaxy.web_stack.transport
    galaxy.webapps
    galaxy.webapps.base
    galaxy.webapps.base.controller
    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.configuration
    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.jobs
    galaxy.webapps.galaxy.api.libraries
    galaxy.webapps.galaxy.api.library_contents
    galaxy.webapps.galaxy.api.library_datasets
    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.search
    galaxy.webapps.galaxy.api.tool_data
    galaxy.webapps.galaxy.api.tool_dependencies
    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.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.interactive_environments
    galaxy.webapps.galaxy.controllers.library
    galaxy.webapps.galaxy.controllers.openid
    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.reports
    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.framework
    galaxy.webapps.reports.framework.grids
    galaxy.webapps.util
    galaxy.webhooks
    galaxy.work
    galaxy.work.context
    galaxy.workflow
    galaxy.workflow.extract
    galaxy.workflow.modules
    galaxy.workflow.render
    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_ext
    galaxy_ext.expressions
    galaxy_ext.expressions.handle_job
    galaxy_ext.metadata
    galaxy_ext.metadata.set_metadata
 
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.galaxy_install.dependency_display
    tool_shed.galaxy_install.grids
    tool_shed.galaxy_install.grids.admin_toolshed_grids
    tool_shed.galaxy_install.utility_containers
    tool_shed.grids
    tool_shed.grids.admin_grids
    tool_shed.grids.repository_grid_filter_manager
    tool_shed.grids.repository_grids
    tool_shed.grids.repository_review_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.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.metadata_util
    tool_shed.util.readme_util
    tool_shed.util.repository_content_util
    tool_shed.util.repository_util
    tool_shed.util.review_util
    tool_shed.util.search_util
    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.app
    tool_shed.webapp.buildapp
    tool_shed.webapp.config