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.tool_shed
    galaxy.webapps.tool_shed.api
    galaxy.webapps.tool_shed.api.authenticate
    galaxy.webapps.tool_shed.api.categories
    galaxy.webapps.tool_shed.api.configuration
    galaxy.webapps.tool_shed.api.groups
    galaxy.webapps.tool_shed.api.repositories
    galaxy.webapps.tool_shed.api.repository_revisions
    galaxy.webapps.tool_shed.api.tools
    galaxy.webapps.tool_shed.api.users
    galaxy.webapps.tool_shed.app
    galaxy.webapps.tool_shed.buildapp
    galaxy.webapps.tool_shed.config
    galaxy.webapps.tool_shed.controllers
    galaxy.webapps.tool_shed.controllers.admin
    galaxy.webapps.tool_shed.controllers.groups
    galaxy.webapps.tool_shed.controllers.hg
    galaxy.webapps.tool_shed.controllers.repository
    galaxy.webapps.tool_shed.controllers.repository_review
    galaxy.webapps.tool_shed.controllers.upload
    galaxy.webapps.tool_shed.controllers.user
    galaxy.webapps.tool_shed.framework
    galaxy.webapps.tool_shed.framework.middleware
    galaxy.webapps.tool_shed.framework.middleware.remoteuser
    galaxy.webapps.tool_shed.model
    galaxy.webapps.tool_shed.model.mapping
    galaxy.webapps.tool_shed.model.migrate
    galaxy.webapps.tool_shed.model.migrate.check
    galaxy.webapps.tool_shed.model.migrate.versions
    galaxy.webapps.tool_shed.model.migrate.versions.0001_initial_tables
    galaxy.webapps.tool_shed.model.migrate.versions.0002_add_tool_suite_column
    galaxy.webapps.tool_shed.model.migrate.versions.0003_review_and_review_association_tables
    galaxy.webapps.tool_shed.model.migrate.versions.0004_repository_tables
    galaxy.webapps.tool_shed.model.migrate.versions.0005_drop_tool_related_tables
    galaxy.webapps.tool_shed.model.migrate.versions.0006_add_email_alerts_column
    galaxy.webapps.tool_shed.model.migrate.versions.0007_add_long_description_times_downloaded_columns
    galaxy.webapps.tool_shed.model.migrate.versions.0008_add_repository_metadata_table
    galaxy.webapps.tool_shed.model.migrate.versions.0009_add_malicious_column
    galaxy.webapps.tool_shed.model.migrate.versions.0010_add_new_repo_alert_column
    galaxy.webapps.tool_shed.model.migrate.versions.0011_add_tool_versions_column
    galaxy.webapps.tool_shed.model.migrate.versions.0012_add_downloadable_column
    galaxy.webapps.tool_shed.model.migrate.versions.0013_add_review_tables
    galaxy.webapps.tool_shed.model.migrate.versions.0014_add_deprecated_column
    galaxy.webapps.tool_shed.model.migrate.versions.0015_add_api_keys_table
    galaxy.webapps.tool_shed.model.migrate.versions.0016_add_do_not_test_tools_functionally_correct_errors_columns
    galaxy.webapps.tool_shed.model.migrate.versions.0017_add_galaxy_utility_columns_to_repository_metadata_table
    galaxy.webapps.tool_shed.model.migrate.versions.0018_add_repository_metadata_flag_columns
    galaxy.webapps.tool_shed.model.migrate.versions.0019_add_skip_tool_test_table_and_test_install_error_column
    galaxy.webapps.tool_shed.model.migrate.versions.0020_add_repository_type_column
    galaxy.webapps.tool_shed.model.migrate.versions.0021_change_repository_type_value
    galaxy.webapps.tool_shed.model.migrate.versions.0022_add_repository_admin_roles
    galaxy.webapps.tool_shed.model.migrate.versions.0023_add_repository_url_and_hompeage_url
    galaxy.webapps.tool_shed.model.migrate.versions.0024_password_reset
    galaxy.webapps.tool_shed.model.migrate.versions.0025_session_timeout
    galaxy.webapps.tool_shed.model.migrate.versions.0026_add_numeric_revision_column
    galaxy.webapps.tool_shed.search
    galaxy.webapps.tool_shed.search.repo_search
    galaxy.webapps.tool_shed.search.tool_search
    galaxy.webapps.tool_shed.security
    galaxy.webapps.tool_shed.util
    galaxy.webapps.tool_shed.util.hgweb_config
    galaxy.webapps.tool_shed.util.ratings_util
    galaxy.webapps.tool_shed.util.shed_statistics
    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.capsule
    tool_shed.capsule.capsule_manager
    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.datatypes
    tool_shed.galaxy_install.datatypes.custom_datatype_manager
    tool_shed.galaxy_install.dependency_display
    tool_shed.galaxy_install.grids
    tool_shed.galaxy_install.grids.admin_toolshed_grids
    tool_shed.galaxy_install.install_manager
    tool_shed.galaxy_install.installed_repository_manager
    tool_shed.galaxy_install.metadata
    tool_shed.galaxy_install.metadata.installed_repository_metadata_manager
    tool_shed.galaxy_install.migrate
    tool_shed.galaxy_install.migrate.check
    tool_shed.galaxy_install.migrate.common
    tool_shed.galaxy_install.migrate.versions
    tool_shed.galaxy_install.migrate.versions.0001_tools
    tool_shed.galaxy_install.migrate.versions.0002_tools
    tool_shed.galaxy_install.migrate.versions.0003_tools
    tool_shed.galaxy_install.migrate.versions.0004_tools
    tool_shed.galaxy_install.migrate.versions.0005_tools
    tool_shed.galaxy_install.migrate.versions.0006_tools
    tool_shed.galaxy_install.migrate.versions.0007_tools
    tool_shed.galaxy_install.migrate.versions.0008_tools
    tool_shed.galaxy_install.migrate.versions.0009_tools
    tool_shed.galaxy_install.migrate.versions.0010_tools
    tool_shed.galaxy_install.migrate.versions.0011_tools
    tool_shed.galaxy_install.migrate.versions.0012_tools
    tool_shed.galaxy_install.repair_repository_manager
    tool_shed.galaxy_install.repository_dependencies
    tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager
    tool_shed.galaxy_install.tool_dependencies
    tool_shed.galaxy_install.tool_dependencies.env_manager
    tool_shed.galaxy_install.tool_dependencies.recipe
    tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader
    tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder
    tool_shed.galaxy_install.tool_dependencies.recipe.install_environment
    tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager
    tool_shed.galaxy_install.tool_dependencies.recipe.step_handler
    tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler
    tool_shed.galaxy_install.tool_migration_manager
    tool_shed.galaxy_install.tools
    tool_shed.galaxy_install.tools.data_manager
    tool_shed.galaxy_install.tools.tool_panel_manager
    tool_shed.galaxy_install.update_repository_manager
    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.tool_shed_registry
    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.workflow_util
    tool_shed.util.xml_util
    tool_shed.utility_containers
    tool_shed.utility_containers.utility_container_manager