CODE_OF_CONDUCT.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.rst
dev-requirements.txt
pyproject.toml
requirements.txt
setup.cfg
setup.py
planemo/__init__.py
planemo/autoupdate.py
planemo/bioblend.py
planemo/ci.py
planemo/cli.py
planemo/conda.py
planemo/config.py
planemo/context.py
planemo/deps.py
planemo/docker.py
planemo/exit_codes.py
planemo/git.py
planemo/github_util.py
planemo/glob.py
planemo/io.py
planemo/lint.py
planemo/mulled.py
planemo/network_util.py
planemo/options.py
planemo/runnable.py
planemo/runnable_resolve.py
planemo/shed_lint.py
planemo/templates.py
planemo/tool_builder.py
planemo/tool_lint.py
planemo/tools.py
planemo/virtualenv.py
planemo/workflow_lint.py
planemo.egg-info/PKG-INFO
planemo.egg-info/SOURCES.txt
planemo.egg-info/dependency_links.txt
planemo.egg-info/entry_points.txt
planemo.egg-info/not-zip-safe
planemo.egg-info/requires.txt
planemo.egg-info/top_level.txt
planemo/commands/__init__.py
planemo/commands/cmd_autoupdate.py
planemo/commands/cmd_ci_find_repos.py
planemo/commands/cmd_ci_find_tools.py
planemo/commands/cmd_clone.py
planemo/commands/cmd_conda_build.py
planemo/commands/cmd_conda_env.py
planemo/commands/cmd_conda_init.py
planemo/commands/cmd_conda_install.py
planemo/commands/cmd_conda_search.py
planemo/commands/cmd_config_init.py
planemo/commands/cmd_container_register.py
planemo/commands/cmd_create_alias.py
planemo/commands/cmd_create_gist.py
planemo/commands/cmd_database_create.py
planemo/commands/cmd_database_delete.py
planemo/commands/cmd_database_list.py
planemo/commands/cmd_delete_alias.py
planemo/commands/cmd_docker_build.py
planemo/commands/cmd_docker_shell.py
planemo/commands/cmd_dockstore_init.py
planemo/commands/cmd_docs.py
planemo/commands/cmd_lint.py
planemo/commands/cmd_list_alias.py
planemo/commands/cmd_list_invocations.py
planemo/commands/cmd_list_repos.py
planemo/commands/cmd_merge_test_reports.py
planemo/commands/cmd_mull.py
planemo/commands/cmd_mulled_init.py
planemo/commands/cmd_normalize.py
planemo/commands/cmd_open.py
planemo/commands/cmd_profile_create.py
planemo/commands/cmd_profile_delete.py
planemo/commands/cmd_profile_list.py
planemo/commands/cmd_project_init.py
planemo/commands/cmd_pull_request.py
planemo/commands/cmd_rerun.py
planemo/commands/cmd_run.py
planemo/commands/cmd_serve.py
planemo/commands/cmd_share_test.py
planemo/commands/cmd_shed_build.py
planemo/commands/cmd_shed_create.py
planemo/commands/cmd_shed_diff.py
planemo/commands/cmd_shed_download.py
planemo/commands/cmd_shed_init.py
planemo/commands/cmd_shed_lint.py
planemo/commands/cmd_shed_serve.py
planemo/commands/cmd_shed_test.py
planemo/commands/cmd_shed_update.py
planemo/commands/cmd_shed_upload.py
planemo/commands/cmd_syntax.py
planemo/commands/cmd_test.py
planemo/commands/cmd_test_reports.py
planemo/commands/cmd_tool_init.py
planemo/commands/cmd_training_fill_data_library.py
planemo/commands/cmd_training_generate_from_wf.py
planemo/commands/cmd_training_init.py
planemo/commands/cmd_upload_data.py
planemo/commands/cmd_workflow_convert.py
planemo/commands/cmd_workflow_edit.py
planemo/commands/cmd_workflow_job_init.py
planemo/commands/cmd_workflow_lint.py
planemo/commands/cmd_workflow_test_init.py
planemo/commands/cmd_workflow_upload.py
planemo/cwl/__init__.py
planemo/cwl/run.py
planemo/cwl/toil.py
planemo/database/__init__.py
planemo/database/factory.py
planemo/database/interface.py
planemo/database/postgres.py
planemo/database/postgres_docker.py
planemo/engine/__init__.py
planemo/engine/cwltool.py
planemo/engine/factory.py
planemo/engine/galaxy.py
planemo/engine/interface.py
planemo/engine/test.py
planemo/engine/toil.py
planemo/galaxy/__init__.py
planemo/galaxy/activity.py
planemo/galaxy/api.py
planemo/galaxy/config.py
planemo/galaxy/distro_tools.py
planemo/galaxy/ephemeris_sleep.py
planemo/galaxy/profiles.py
planemo/galaxy/run.py
planemo/galaxy/serve.py
planemo/galaxy/workflows.py
planemo/galaxy/test/__init__.py
planemo/galaxy/test/actions.py
planemo/galaxy/test/structures.py
planemo/linters/__init__.py
planemo/linters/biocontainer_registered.py
planemo/linters/conda_requirements.py
planemo/linters/doi.py
planemo/linters/urls.py
planemo/linters/xsd.py
planemo/reports/__init__.py
planemo/reports/allure.py
planemo/reports/bootstrap.min.css
planemo/reports/bootstrap.min.js
planemo/reports/build_report.py
planemo/reports/custom.css
planemo/reports/custom.js
planemo/reports/jquery.min.js
planemo/reports/macros.tmpl
planemo/reports/markdown-it.min.js
planemo/reports/report_html.tpl
planemo/reports/report_junit.tpl
planemo/reports/report_markdown.tpl
planemo/reports/report_text.tpl
planemo/reports/report_xunit.tpl
planemo/reports/xunit.tpl
planemo/reports/xunit_handler.py
planemo/scripts/planemo-completion.sh
planemo/shed/__init__.py
planemo/shed/diff.py
planemo/shed/interface.py
planemo/shed2tap/__init__.py
planemo/shed2tap/base.py
planemo/test/__init__.py
planemo/test/_check_output.py
planemo/test/data.py
planemo/test/results.py
planemo/training/__init__.py
planemo/training/tool_input.py
planemo/training/topic.py
planemo/training/tutorial.py
planemo/training/utils.py
planemo/xml/__init__.py
planemo/xml/diff.py
planemo/xml/validation.py
planemo/xml/xsd/repository_dependencies.xsd
planemo/xml/xsd/tool_dependencies.xsd