CONTRIBUTING.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
docs/Makefile
docs/appliance.rst
docs/commands.rst
docs/conf.py
docs/configuration.rst
docs/contributing.rst
docs/developing.rst
docs/history.rst
docs/index.rst
docs/installation.rst
docs/make.bat
docs/modules.rst
docs/planemo.commands.rst
docs/planemo.reports.rst
docs/planemo.rst
docs/planemo.shed2tap.rst
docs/planemo_ext.galaxy.eggs.rst
docs/planemo_ext.galaxy.jobs.metrics.collectl.rst
docs/planemo_ext.galaxy.jobs.metrics.instrumenters.rst
docs/planemo_ext.galaxy.jobs.metrics.rst
docs/planemo_ext.galaxy.jobs.rst
docs/planemo_ext.galaxy.objectstore.rst
docs/planemo_ext.galaxy.rst
docs/planemo_ext.galaxy.tools.deps.resolvers.rst
docs/planemo_ext.galaxy.tools.deps.rst
docs/planemo_ext.galaxy.tools.linters.rst
docs/planemo_ext.galaxy.tools.rst
docs/planemo_ext.galaxy.util.rst
docs/planemo_ext.rst
docs/readme.rst
docs/writing.rst
docs/commands/brew.rst
docs/commands/brew_env.rst
docs/commands/brew_init.rst
docs/commands/config_init.rst
docs/commands/docker_build.rst
docs/commands/docker_shell.rst
docs/commands/lint.rst
docs/commands/normalize.rst
docs/commands/project_init.rst
docs/commands/serve.rst
docs/commands/share_test.rst
docs/commands/shed_diff.rst
docs/commands/shed_upload.rst
docs/commands/syntax.rst
docs/commands/test.rst
docs/commands/tool_factory.rst
docs/commands/tool_init.rst
docs/commands/travis_before_install.rst
docs/commands/travis_init.rst
planemo/__init__.py
planemo/cli.py
planemo/config.py
planemo/galaxy_config.py
planemo/galaxy_run.py
planemo/galaxy_serve.py
planemo/galaxy_test.py
planemo/github_util.py
planemo/io.py
planemo/options.py
planemo/shed.py
planemo/tool_builder.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_brew.py
planemo/commands/cmd_brew_env.py
planemo/commands/cmd_brew_init.py
planemo/commands/cmd_config_init.py
planemo/commands/cmd_create_gist.py
planemo/commands/cmd_docker_build.py
planemo/commands/cmd_docker_shell.py
planemo/commands/cmd_lint.py
planemo/commands/cmd_normalize.py
planemo/commands/cmd_project_init.py
planemo/commands/cmd_serve.py
planemo/commands/cmd_share_test.py
planemo/commands/cmd_shed_diff.py
planemo/commands/cmd_shed_download.py
planemo/commands/cmd_shed_upload.py
planemo/commands/cmd_syntax.py
planemo/commands/cmd_test.py
planemo/commands/cmd_tool_factory.py
planemo/commands/cmd_tool_init.py
planemo/commands/cmd_travis_before_install.py
planemo/commands/cmd_travis_init.py
planemo/reports/__init__.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/report_template.html
planemo/shed2tap/__init__.py
planemo_ext/__init__.py
planemo_ext/galaxy/__init__.py
planemo_ext/galaxy/exceptions.py
planemo_ext/galaxy/eggs/__init__.py
planemo_ext/galaxy/tools/__init__.py
planemo_ext/galaxy/tools/lint.py
planemo_ext/galaxy/tools/loader.py
planemo_ext/galaxy/tools/loader_directory.py
planemo_ext/galaxy/tools/deps/__init__.py
planemo_ext/galaxy/tools/deps/brew_exts.py
planemo_ext/galaxy/tools/deps/brew_util.py
planemo_ext/galaxy/tools/deps/commands.py
planemo_ext/galaxy/tools/deps/containers.py
planemo_ext/galaxy/tools/deps/dependencies.py
planemo_ext/galaxy/tools/deps/docker_util.py
planemo_ext/galaxy/tools/deps/dockerfiles.py
planemo_ext/galaxy/tools/deps/requirements.py
planemo_ext/galaxy/tools/deps/resolvers/__init__.py
planemo_ext/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
planemo_ext/galaxy/tools/deps/resolvers/galaxy_packages.py
planemo_ext/galaxy/tools/deps/resolvers/homebrew.py
planemo_ext/galaxy/tools/deps/resolvers/modules.py
planemo_ext/galaxy/tools/deps/resolvers/resolver_mixins.py
planemo_ext/galaxy/tools/deps/resolvers/tool_shed_packages.py
planemo_ext/galaxy/tools/linters/__init__.py
planemo_ext/galaxy/tools/linters/citations.py
planemo_ext/galaxy/tools/linters/command.py
planemo_ext/galaxy/tools/linters/help.py
planemo_ext/galaxy/tools/linters/inputs.py
planemo_ext/galaxy/tools/linters/outputs.py
planemo_ext/galaxy/tools/linters/tests.py
planemo_ext/galaxy/tools/linters/top_level.py
planemo_ext/galaxy/util/__init__.py
planemo_ext/galaxy/util/bunch.py
planemo_ext/galaxy/util/directory_hash.py
planemo_ext/galaxy/util/odict.py
planemo_ext/galaxy/util/plugin_config.py
planemo_ext/galaxy/util/sleeper.py
planemo_ext/galaxy/util/submodules.py
tests/__init__.py
tests/test_planemo.py