LICENCE.txt
README.md
setup.py
galaxy2janis/__init__.py
galaxy2janis/aliases.py
galaxy2janis/cli.py
galaxy2janis/run.py
galaxy2janis/tool_mode.py
galaxy2janis/workflow_mode.py
galaxy2janis.egg-info/PKG-INFO
galaxy2janis.egg-info/SOURCES.txt
galaxy2janis.egg-info/dependency_links.txt
galaxy2janis.egg-info/entry_points.txt
galaxy2janis.egg-info/requires.txt
galaxy2janis.egg-info/top_level.txt
galaxy2janis/containers/Container.py
galaxy2janis/containers/ContainerCache.py
galaxy2janis/containers/__init__.py
galaxy2janis/containers/fetch.py
galaxy2janis/containers/fetching/ContainerReqFetcher.py
galaxy2janis/containers/fetching/Fetcher.py
galaxy2janis/containers/fetching/GA4GHFetcher.py
galaxy2janis/containers/fetching/QuayIOFetcher.py
galaxy2janis/containers/fetching/__init__.py
galaxy2janis/containers/fetching/presets.py
galaxy2janis/containers/fetching/utils.py
galaxy2janis/containers/selection/VersionMatcher.py
galaxy2janis/containers/selection/__init__.py
galaxy2janis/containers/selection/selection.py
galaxy2janis/data/container_url_cache.json
galaxy2janis/data/galaxy_config.yaml
galaxy2janis/data/galaxy_janis_types.yaml
galaxy2janis/data/logging_config.yaml
galaxy2janis/data/wrappers.json
galaxy2janis/datatypes/JanisDatatype.py
galaxy2janis/datatypes/__init__.py
galaxy2janis/datatypes/conversion.py
galaxy2janis/datatypes/core.py
galaxy2janis/datatypes/galaxy.py
galaxy2janis/datatypes/main.py
galaxy2janis/datatypes/register.py
galaxy2janis/datatypes/strategies.py
galaxy2janis/entities/__init__.py
galaxy2janis/entities/protocols.py
galaxy2janis/entities/tool/Tool.py
galaxy2janis/entities/tool/ToolFactory.py
galaxy2janis/entities/tool/__init__.py
galaxy2janis/entities/tool/generate.py
galaxy2janis/entities/tool/outputs.py
galaxy2janis/entities/workflow/__init__.py
galaxy2janis/entities/workflow/input.py
galaxy2janis/entities/workflow/metadata.py
galaxy2janis/entities/workflow/workflow.py
galaxy2janis/entities/workflow/registers/StepInputRegister.py
galaxy2janis/entities/workflow/registers/StepOutputRegister.py
galaxy2janis/entities/workflow/registers/__init__.py
galaxy2janis/entities/workflow/step/__init__.py
galaxy2janis/entities/workflow/step/inputs.py
galaxy2janis/entities/workflow/step/metadata.py
galaxy2janis/entities/workflow/step/outputs.py
galaxy2janis/entities/workflow/step/step.py
galaxy2janis/expressions/__init__.py
galaxy2janis/expressions/checks.py
galaxy2janis/expressions/matches.py
galaxy2janis/expressions/patterns.py
galaxy2janis/fileio/__init__.py
galaxy2janis/fileio/initialisation.py
galaxy2janis/fileio/write.py
galaxy2janis/fileio/formats/DefaultFormat.py
galaxy2janis/fileio/formats/Format.py
galaxy2janis/fileio/formats/SubworkflowFormat.py
galaxy2janis/fileio/formats/__init__.py
galaxy2janis/fileio/text/TextRender.py
galaxy2janis/fileio/text/__init__.py
galaxy2janis/fileio/text/formatting.py
galaxy2janis/fileio/text/ordering.py
galaxy2janis/fileio/text/tool/ConfigfileText.py
galaxy2janis/fileio/text/tool/ToolInputSectionText.py
galaxy2janis/fileio/text/tool/ToolInputText.py
galaxy2janis/fileio/text/tool/ToolOutputSectionText.py
galaxy2janis/fileio/text/tool/ToolOutputText.py
galaxy2janis/fileio/text/tool/ToolText.py
galaxy2janis/fileio/text/tool/UnstranslatedText.py
galaxy2janis/fileio/text/tool/__init__.py
galaxy2janis/fileio/text/workflow/ConfigText.py
galaxy2janis/fileio/text/workflow/InputsText.py
galaxy2janis/fileio/text/workflow/StepText.py
galaxy2janis/fileio/text/workflow/WorkflowInputText.py
galaxy2janis/fileio/text/workflow/WorkflowOutputText.py
galaxy2janis/fileio/text/workflow/WorkflowText.py
galaxy2janis/fileio/text/workflow/__init__.py
galaxy2janis/gx/__init__.py
galaxy2janis/gx/command/Command.py
galaxy2janis/gx/command/__init__.py
galaxy2janis/gx/command/annotation.py
galaxy2janis/gx/command/factory.py
galaxy2janis/gx/command/generate.py
galaxy2janis/gx/command/cmdstr/CommandString.py
galaxy2janis/gx/command/cmdstr/DynamicCommandStatement.py
galaxy2janis/gx/command/cmdstr/MainStatementInferrer.py
galaxy2janis/gx/command/cmdstr/RealisedTokenValues.py
galaxy2janis/gx/command/cmdstr/__init__.py
galaxy2janis/gx/command/cmdstr/constructs.py
galaxy2janis/gx/command/cmdstr/generate.py
galaxy2janis/gx/command/cmdstr/utils.py
galaxy2janis/gx/command/components/CommandComponent.py
galaxy2janis/gx/command/components/ValueRecord.py
galaxy2janis/gx/command/components/__init__.py
galaxy2janis/gx/command/components/factory.py
galaxy2janis/gx/command/components/inputs/Flag.py
galaxy2janis/gx/command/components/inputs/InputComponent.py
galaxy2janis/gx/command/components/inputs/Option.py
galaxy2janis/gx/command/components/inputs/Positional.py
galaxy2janis/gx/command/components/inputs/__init__.py
galaxy2janis/gx/command/components/inputs/utils.py
galaxy2janis/gx/command/components/linux/Tee.py
galaxy2janis/gx/command/components/linux/__init__.py
galaxy2janis/gx/command/components/linux/streams.py
galaxy2janis/gx/command/components/outputs/InputOutput.py
galaxy2janis/gx/command/components/outputs/OutputComponent.py
galaxy2janis/gx/command/components/outputs/RedirectOutput.py
galaxy2janis/gx/command/components/outputs/WildcardOutput.py
galaxy2janis/gx/command/components/outputs/__init__.py
galaxy2janis/gx/command/epath/Annotator.py
galaxy2janis/gx/command/epath/ComponentOrderingStrategy.py
galaxy2janis/gx/command/epath/ExecutionPath.py
galaxy2janis/gx/command/epath/ExecutionPathAnnotator.py
galaxy2janis/gx/command/epath/__init__.py
galaxy2janis/gx/command/epath/utils.py
galaxy2janis/gx/command/tokens/__init__.py
galaxy2janis/gx/command/tokens/factory.py
galaxy2janis/gx/command/tokens/prioritisation.py
galaxy2janis/gx/command/tokens/token.py
galaxy2janis/gx/command/tokens/utils.py
galaxy2janis/gx/configfiles/Configfile.py
galaxy2janis/gx/configfiles/__init__.py
galaxy2janis/gx/gxtool/TestRegister.py
galaxy2janis/gx/gxtool/ToolXMLMetadata.py
galaxy2janis/gx/gxtool/XMLToolDefinition.py
galaxy2janis/gx/gxtool/__init__.py
galaxy2janis/gx/gxtool/citations.py
galaxy2janis/gx/gxtool/load.py
galaxy2janis/gx/gxtool/requirements.py
galaxy2janis/gx/gxtool/tests.py
galaxy2janis/gx/gxtool/param/InputParam.py
galaxy2janis/gx/gxtool/param/OutputParam.py
galaxy2janis/gx/gxtool/param/Param.py
galaxy2janis/gx/gxtool/param/ParamRegister.py
galaxy2janis/gx/gxtool/param/__init__.py
galaxy2janis/gx/gxtool/parsing/ParamFlattener.py
galaxy2janis/gx/gxtool/parsing/__init__.py
galaxy2janis/gx/gxtool/parsing/inputs.py
galaxy2janis/gx/gxtool/parsing/outputs.py
galaxy2janis/gx/gxtool/parsing/tests/TestFactory.py
galaxy2janis/gx/gxtool/parsing/tests/__init__.py
galaxy2janis/gx/gxtool/parsing/tests/checks.py
galaxy2janis/gx/gxtool/parsing/tests/custom_ops.py
galaxy2janis/gx/gxtool/parsing/tests/custom_preprocessors.py
galaxy2janis/gx/gxtool/parsing/tests/mapper.py
galaxy2janis/gx/gxtool/text/__init__.py
galaxy2janis/gx/gxtool/text/load.py
galaxy2janis/gx/gxtool/text/utils.py
galaxy2janis/gx/gxtool/text/cheetah/__init__.py
galaxy2janis/gx/gxtool/text/cheetah/blocks.py
galaxy2janis/gx/gxtool/text/cheetah/evaluation.py
galaxy2janis/gx/gxtool/text/simplification/__init__.py
galaxy2janis/gx/gxtool/text/simplification/aliases.py
galaxy2janis/gx/gxtool/text/simplification/filters.py
galaxy2janis/gx/gxtool/text/simplification/simplify.py
galaxy2janis/gx/gxworkflow/__init__.py
galaxy2janis/gx/gxworkflow/connections/__init__.py
galaxy2janis/gx/gxworkflow/connections/scatter.py
galaxy2janis/gx/gxworkflow/parsing/__init__.py
galaxy2janis/gx/gxworkflow/parsing/inputs.py
galaxy2janis/gx/gxworkflow/parsing/metadata.py
galaxy2janis/gx/gxworkflow/parsing/step.py
galaxy2janis/gx/gxworkflow/parsing/tool_state/__init__.py
galaxy2janis/gx/gxworkflow/parsing/tool_state/expand.py
galaxy2janis/gx/gxworkflow/parsing/tool_state/flatten.py
galaxy2janis/gx/gxworkflow/parsing/tool_state/load.py
galaxy2janis/gx/gxworkflow/parsing/tool_state/resolve.py
galaxy2janis/gx/gxworkflow/parsing/tool_state/standardisation.py
galaxy2janis/gx/gxworkflow/parsing/tool_step/__init__.py
galaxy2janis/gx/gxworkflow/parsing/tool_step/metadata.py
galaxy2janis/gx/gxworkflow/parsing/tool_step/outputs.py
galaxy2janis/gx/gxworkflow/parsing/tool_step/prepost.py
galaxy2janis/gx/gxworkflow/parsing/tool_step/tool.py
galaxy2janis/gx/gxworkflow/updates/__init__.py
galaxy2janis/gx/gxworkflow/updates/arrays.py
galaxy2janis/gx/gxworkflow/updates/datatypes.py
galaxy2janis/gx/gxworkflow/updates/main.py
galaxy2janis/gx/gxworkflow/updates/optionality.py
galaxy2janis/gx/gxworkflow/values/__init__.py
galaxy2janis/gx/gxworkflow/values/connection.py
galaxy2janis/gx/gxworkflow/values/default.py
galaxy2janis/gx/gxworkflow/values/factory.py
galaxy2janis/gx/gxworkflow/values/runtime.py
galaxy2janis/gx/gxworkflow/values/scripts.py
galaxy2janis/gx/gxworkflow/values/static.py
galaxy2janis/gx/gxworkflow/values/utils.py
galaxy2janis/gx/interaction/__init__.py
galaxy2janis/gx/interaction/mock.py
galaxy2janis/gx/interaction/tools.py
galaxy2janis/gx/wrappers/__init__.py
galaxy2janis/gx/wrappers/downloads/__init__.py
galaxy2janis/gx/wrappers/downloads/cache.py
galaxy2janis/gx/wrappers/downloads/wrappers.py
galaxy2janis/gx/wrappers/requests/__init__.py
galaxy2janis/gx/wrappers/requests/versions.py
galaxy2janis/gx/wrappers/scraping/__init__.py
galaxy2janis/gx/wrappers/scraping/repositories.py
galaxy2janis/gx/wrappers/scraping/revisions.py
galaxy2janis/gx/wrappers/scraping/scraping.py
galaxy2janis/gx/wrappers/scraping/single.py
galaxy2janis/gx/wrappers/scraping/utils.py
galaxy2janis/gx/wrappers/scraping/wrappers.py
galaxy2janis/gx/wrappers/wrappers/Wrapper.py
galaxy2janis/gx/wrappers/wrappers/WrapperCache.py
galaxy2janis/gx/wrappers/wrappers/__init__.py
galaxy2janis/logs/__init__.py
galaxy2janis/logs/logging.py
galaxy2janis/mapping/__init__.py
galaxy2janis/mapping/galaxy.py
galaxy2janis/messages/__init__.py
galaxy2janis/messages/logs.py
galaxy2janis/messages/messages.py
galaxy2janis/paths/__init__.py
galaxy2janis/runtime/__init__.py
galaxy2janis/runtime/dates.py
galaxy2janis/runtime/exceptions.py
galaxy2janis/settings/__init__.py
galaxy2janis/settings/general.py
galaxy2janis/settings/tool.py
galaxy2janis/settings/workflow.py
galaxy2janis/startup/__init__.py
galaxy2janis/startup/general.py
galaxy2janis/startup/tool.py
galaxy2janis/startup/workflow.py
galaxy2janis/tags/__init__.py
galaxy2janis/tags/groups.py
galaxy2janis/tags/manager.py
galaxy2janis/tags/rules.py
galaxy2janis/tags/strategies.py
galaxy2janis/utils/__init__.py
galaxy2janis/utils/galaxy.py
galaxy2janis/utils/general.py
test/test_aliases.py
test/test_cheetah.py
test/test_containers.py
test/test_datatypes.py
test/test_regex.py
test/test_tags.py