sam_consensus_v3: env/lib/python3.9/site-packages/planemo-0.74.3.dist-info/METADATA comparison

comparison env/lib/python3.9/site-packages/planemo-0.74.3.dist-info/METADATA @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

author	shellac
date	Mon, 22 Mar 2021 18:12:50 +0000
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+:4f3585e2f14b
+Metadata-Version: 2.1
+Name: planemo
+Version: 0.74.3
+Summary: Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
+Home-page: https://github.com/galaxyproject/planemo
+Author: Galaxy Project and Community
+Author-email: jmchilton@gmail.com
+License: AFL
+Keywords: planemo
+Platform: UNKNOWN
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Environment :: Console
+Classifier: License :: OSI Approved :: Academic Free License (AFL)
+Classifier: Operating System :: POSIX
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Code Generators
+Classifier: Topic :: Software Development :: Testing
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Description-Content-Type: text/x-rst
+Requires-Dist: allure-python-commons
+Requires-Dist: BeautifulSoup4
+Requires-Dist: bioblend (>=0.14.0)
+Requires-Dist: Click
+Requires-Dist: configparser
+Requires-Dist: cwltool (>=1.0.20191225192155)
+Requires-Dist: docutils
+Requires-Dist: ephemeris (>=0.10.3)
+Requires-Dist: galaxy-containers
+Requires-Dist: galaxy-tool-util (>=21.1.0.dev4)
+Requires-Dist: galaxy-util (>=20.5.0)
+Requires-Dist: glob2
+Requires-Dist: gxformat2 (>=0.12.0)
+Requires-Dist: jinja2
+Requires-Dist: lxml
+Requires-Dist: oyaml
+Requires-Dist: pyaml
+Requires-Dist: pyyaml
+Requires-Dist: six (>=1.7.0)
+Requires-Dist: virtualenv
+Requires-Dist: tabulate
+.. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png
+:alt: Planemo Logo
+:align: center
+:figwidth: 100%
+:target: https://github.com/galaxyproject/planemo
+Command-line utilities to assist in developing Galaxy_ and `Common Workflow Language`_ artifacts -
+including tools, workflows, and training materials.
+.. image:: https://readthedocs.org/projects/planemo/badge/?version=latest
+:target: http://planemo.readthedocs.io/en/latest/?badge=latest
+:alt: Documentation Status
+.. image:: https://badge.fury.io/py/planemo.svg
+:target: https://pypi.python.org/pypi/planemo/
+:alt: Planemo on the Python Package Index (PyPI)
+.. image:: https://github.com/galaxyproject/planemo/workflows/Python%20CI/badge.svg
+:target: https://github.com/galaxyproject/planemo/actions?query=workflow%3A%22Python+CI%22
+.. image:: https://travis-ci.org/galaxyproject/planemo.png?branch=master
+:target: https://travis-ci.org/galaxyproject/planemo
+:alt: Build Status
+* Free software: Academic Free License version 3.0
+* Documentation: https://planemo.readthedocs.io.
+* Code: https://github.com/galaxyproject/planemo
+Quick Start
+-----------
+-----------------
+Obtaining
+-----------------
+For a traditional Python installation of Planemo, first set up a virtualenv
+for ``planemo`` (this example creates a new one in ``.venv``) and then
+install with ``pip``. Planemo requires pip 7.0 or newer.
+::
+$ virtualenv .venv; . .venv/bin/activate
+$ pip install "pip>=7" # Upgrade pip if needed.
+$ pip install planemo
+For information on updating Planemo, installing the latest development release,
+or installing Planemo via `Bioconda <https://github.com/bioconda/bioconda-recipes>`__
+- checkout the `installation <http://planemo.readthedocs.io/en/latest/installation.html>`__
+documentation.
+Planemo is also available as a `virtual appliance
+<https://planemo.readthedocs.io/en/latest/appliance.html>`_ bundled
+with a preconfigured Galaxy server and set up for Galaxy_ and
+`Common Workflow Language`_ tool development.
+You can choose from open virtualization format (OVA_, .ova) or Docker_
+appliances.
+-----------------
+Basics - Galaxy
+-----------------
+This quick start will assume you have a directory with one or more Galaxy
+tool XML files. If no such directory is available, one can be quickly created for
+demonstrating ``planemo`` as follows ``project_init --template=demo mytools; cd mytools``.
+Planemo can check tool XML files for common problems and best
+practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
+(also aliased as ``l``).
+::
+$ planemo lint
+Like many ``planemo`` commands - by default this will search the
+current directory and use all tool files it finds. It can be explicitly
+passed a path to tool files or a directory of tool files.
+::
+$ planemo l randomlines.xml
+The ``lint`` command takes in additional options related to
+reporting levels, exit code, etc. These options are described
+in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
+or (like with all commands) can be accessed by passing ``--help`` to it.
+::
+$ planemo l --help
+Usage: planemo lint [OPTIONS] TOOL_PATH
+Once tools are syntactically correct - it is time to test. The ``test``
+`command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__
+can be used to test a tool or a directory of tools.
+::
+	$ planemo test --galaxy_root=../galaxy randomlines.xml
+If no ``--galaxy_root`` is defined, Planemo will download and configure
+a disposable Galaxy instance for testing.
+Planemo will create a HTML output report in the current directory named
+``tool_test_output.html`` (override with ``--test_output``). See an
+`example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_
+of such a report for Tophat.
+Once tools have been linted and tested - the tools can be viewed in a
+Galaxy interface using the ``serve`` (``s``) `command
+<http://planemo.readthedocs.org/en/latest/commands.html#serve-command>`__.
+::
+	$ planemo serve
+Like ``test``, ``serve`` requires a Galaxy root and one can be
+explicitly specified with ``--galaxy_root`` or installed dynamically
+with ``--install_galaxy``.
+For more information on building Galaxy tools in general please check out
+`Building Galaxy Tools Using Planemo`_.
+For more information on developing Galaxy workflows with Planemo checkout
+`best practices for Galaxy Workflows`_ and the description of Planemo's
+`test format`_. For information on developing Galaxy training materials
+checkout the `contributing documentation <https://training.galaxyproject.org/training-material/topics/contributing/>`__
+on training.galaxyproject.org.
+----------------------------------
+Basics - Common Workflow Language
+----------------------------------
+This quick start will assume you have a directory with one or more `Common Workflow
+Language`_ YAML files. If no such directory is available, one can be quickly created for
+demonstrating ``planemo`` as follows ``planemo project_init --template=seqtk_complete_cwl mytools; cd mytools``.
+Planemo can check tools YAML files for common problems and best
+practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
+(also aliased as ``l``).
+::
+$ planemo lint
+Like many ``planemo`` commands - by default this will search the
+current directory and use all tool files it finds. It can be explicitly
+passed a path to tool files or a directory of tool files.
+::
+$ planemo l seqtk_seq.cwl
+The ``lint`` command takes in additional options related to
+reporting levels, exit code, etc. These options are described
+in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
+or (like with all commands) can be accessed by passing ``--help`` to it.
+::
+$ planemo l --help
+Usage: planemo lint [OPTIONS] TOOL_PATH
+Once tools are syntactically correct - it is time to test. The ``test``
+`command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__
+can be used to test a CWL tool, workflow, or a directories thereof.
+::
+$ planemo test --engine cwltool seqtk_seq.cwl
+Planemo will create a HTML output report in the current directory named
+``tool_test_output.html``. Check out the file ``seqtk_seq_tests.yml`` for
+an example of Planemo test for a CWL tool. A test consists of any number of
+jobs (with input descriptions) and corresponding output assertions.
+Checkout the `Commmon Workflow User Guide`_ for more information on developing
+CWL tools in general and  `Building Common Workflow Language Tools`_ for more
+information on using Planemo to develop CWL tools.
+---------
+Tool Shed
+---------
+Planemo can help you publish tools to the Galaxy Tool Shed.
+Check out `Publishing to the Tool Shed`_ for more information.
+------
+Conda
+------
+Planemo can help develop tools and Conda packages in unison.
+Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda>`__ or `CWL
+<http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda-cwl>`__ version of the "Dependencies and Conda" tutorial
+for more information.
+-----------------------
+Docker and Containers
+-----------------------
+Planemo can help develop tools that run in "Best Practice" containers for
+scientific workflows. Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-containers>`__ or `CWL
+<http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers-cwl>`__ version of the "Dependencies and Containers" tutorial for more information.
+.. _Galaxy: http://galaxyproject.org/
+.. _GitHub: https://github.com/
+.. _Conda: http://conda.pydata.org/
+.. _Docker: https://www.docker.com/
+.. _Vagrant: https://www.vagrantup.com/
+.. _Travis CI: http://travis-ci.org/
+.. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam
+.. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc
+.. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html
+.. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html
+.. _Common Workflow Language: https://www.commonwl.org/
+.. _Commmon Workflow User Guide: http://www.commonwl.org/user_guide/
+.. _Building Common Workflow Language Tools: http://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html
+.. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format
+.. _test format: https://planemo.readthedocs.io/en/latest/test_format.html
+.. _best practices for Galaxy Workflows: https://planemo.readthedocs.io/en/latest/best_practices_workflows.html
+History
+-------
+.. to_doc
+---------------------
+0.74.3 2020-02-25)
+---------------------
+* Load both cat1 versions when testing workflows `Pull Request 1146`_
+* Fix isolated virtualenv not getting activated `Pull Request 1145`_
+* Use bioblend's make_get_request for authenticated request `Pull Request 1144`_
+* Display live logs when Galaxy is run in background `Pull Request 1142`_
+---------------------
+0.74.2 (2020-02-21)
+---------------------
+* Allow testing dir of workflows `Pull Request 1095`_
+* Fix container register for gh workflow `Pull Request 1135`_, `Pull Request 1133`_
+* Don't fail URL linting if blocked by CloudFlare `Pull Request 1134`_
+1133`_
+* Allow planemo run to stage exisiting datasets and relative paths (thanks to `@simonbray`_).
+`Pull Request 1128`_
+---------------------
+0.74.1 (2020-01-03)
+---------------------
+* Fix ``ci_find_tools`` and ``ci_find_repos`` commands. `Pull Request 1127`_
+---------------------
+0.74.0 (2020-12-30)
+---------------------
+* Allow running Galaxy workflow tests against externally defined workflows.
+`Pull Request 1126`_, `Pull Request 1125`_,
+`Pull Request 1123`_
+* Require Python ``tabulate`` package for the ``list_invocations`` command.
+`Pull Request 1124`_
+---------------------
+0.73.0 (2020-12-28)
+---------------------
+* Integrate important features from gxwf_ for running workflows - including
+building up profile commands for creating aliases, allowing referencing workflows
+by external IDs, and listing invocations (thanks to `@simonbray`_).
+`Pull Request 1076`_
+* Documentation for using ``planemo run`` to execute workflows (thanks to `@simonbray`_).
+`Pull Request 1102`_
+* Add ``workflow_upload`` command for publishing each workflow of a repository with many
+workflows to their own standalone repository.
+`Pull Request 1091`_
+* Update github commands to authenticate with a token rather than
+username/password (thanks to `@simonbray`_).
+`Pull Request 1083`_
+* Document "advanced" tool test debugging (thanks to `@bernt-matthias`_).
+`Pull Request 1108`_
+* Various fixes for workflow commands - including ``workflow_convert``,
+``workflow_lint``, ``workflow_job_init``, and ``workflow_test_init``
+(thanks to `@simonbray`_).
+`Pull Request 1101`_, `Pull Request 1118`_, `Pull Request 1121`_,
+`Pull Request 1116`_, `Pull Request 1064`_
+* Allow outputting test results as Allure_ framework results.
+`Pull Request 1115`_
+* Fix ``run_tests.sh`` invocation `Pull Request 1099`_
+* Tiny typo in debugging output (thanks to `@abretaud`_). `Pull Request 1066`_
+* Fix typo in 'planemo test' help text for --skip_venv (thanks to
+`@peterjc`_).
+`Pull Request 1068`_
+* Fixes for CLI when ``external_galaxy`` is used as the engine (thanks to
+`@simonbray`_).
+`Pull Request 1072`_
+* Updating base image to 20.05 for training topics
+(thanks to `@bedroesb`_).
+`Pull Request 1074`_
+* Changes to update_test_data testing mode (thanks to `@simonbray`_).
+`Pull Request 1079`_
+* Fix docker options when filling ``job_conf.xml`` template.
+`Pull Request 1086`_
+* Explicit tests for Galaxy 20.09. `Pull Request 1093`_
+* Minor fix for ``ci_find_repos`` command. `Pull Request 1094`_
+* Fix a couple of Cheetah_ urls in Galaxy tool documentation (thanks to `@martenson`_).
+`Pull Request 1096`_
+* Fix doc link from a redirect loop to a section (thanks to `@martenson`_).
+`Pull Request 1110`_
+* Clarify ``tutorial.md`` usage of citations (thanks to `@blankenberg`_).
+`Pull Request 1114`_
+* Fix ``ZeroDivisionError`` when no tests are executed (thanks to `@simonbray`_).
+`Pull Request 1120`_
+---------------------
+0.72.0 (2020-08-04)
+---------------------
+* More documentation/support around running workflows including new command
+to initialize workflow jobs ``workflow_init_job``.
+`Pull Request 1052`_
+* Workflow tests and documentation for tagging inputs. `Pull Request 1058`_
+* Various documentation improvements.
+`Pull Request 1061`_, `Pull Request 1062`_
+* Add mypy type checking. `Pull Request 1060`_
+* Progress decoupling Planemo's core from click & CLI interactions.
+`Pull Request 1059`_
+* Tests for workflow testing script. `Pull Request 821`_
+---------------------
+0.71.0 (2020-08-03)
+---------------------
+* Drop Python 2 support. `Pull Request 1026`_
+* Rev Galaxy dependencies - including bumping bioblend to 0.14.0, galaxy-tool-util,
+and unpinning cwltool (last of these thanks to thanks to `@TMiguelT`_).
+`Pull Request 1038`_, `Pull Request 1034`_
+* Workflow linting, best practices, and tooling to assist in following them.
+`Pull Request 1028`_, `Pull Request 1049`_, `Pull Request 1051`_
+`Pull Request 1044`_
+* Substantial rewrites to Galaxy workflow input staging - including allow nested
+collection and composite inputs to Galaxy for ``run`` and ``test``.
+`Pull Request 900`_, `Pull Request 1029`_
+* Remove assorted older, likely unused commands. `Pull Request 1043`_
+* Update installation.rst (thanks to `@mblue9`_). `Pull Request 1032`_
+* Automatic PyPI upload on tag using GitHub Actions.
+`Pull Request 994`_
+* Fix quay repository presence check for single target builds.
+`Pull Request 993`_
+* More fine grained options for ``--shed_install`` (thanks to `@AndreasSko`_).
+`Pull Request 1001`_
+* Change default Python version for Galaxy (thanks to `@bernt-matthias`_).
+`Pull Request 1021`_
+* Sort tests by id when merging (thanks to `@bernt-matthias`_).
+`Pull Request 1022`_
+* Add ``--group_tools`` option to ``ci_find_tools``
+(thanks to `@bernt-matthias`_).
+`Pull Request 1008`_
+* Add shared data library path to the data upload box for training material
+(thanks to `@shiltemann`_).
+`Pull Request 1013`_
+* Add support for tool versions to tutorial template generator (thanks to
+`@shiltemann`_). `Pull Request 1041`_
+* Only copy test files if they don't exist. `Pull Request 1037`_
+* Improvements to loading stock tools for workflow testing and serving (
+add new stock tools to list and check subworkflows).
+`Pull Request 1031`_
+* Fix link for composite data type docs (thanks to `@bernt-matthias`_).
+`Pull Request 1020`_
+* Do not use ``gi._make_url()`` internal BioBlend method.
+* Switch CWL examples to use https://schema.org/version/latest/schema.rdf
+(thanks to `@mr-c`_).
+`Pull Request 1015`_
+* Fix docs not to claim Galaxy can't run on Python 3.
+`Pull Request 1023`_
+* Improved abstractions around target Galaxy instance. `Pull Request 1046`_
+* Add empty refgenie config for tests (thanks to `@blankenberg`_).
+`Pull Request 1025`_
+* Substantial reworking of testing infrastructure.
+`Pull Request 1024`_, `Pull Request 1003`_,
+`Pull Request 1011`_, `Pull Request 1006`_,
+`Pull Request 1040`_, `Pull Request 1036`_,
+`Pull Request 1042`_
+---------------------
+0.70.0 (2020-01-29)
+---------------------
+* Temporarily add galaxy-util requirement `Pull Request 991`_
+* Make symlinks in tool tree work for planemo test `Pull Request 988`_
+* Reduce use of ``shell=True`` in subprocesses `Pull Request 989`_
+* Drop planemo database seed option `Pull Request 985`_
+* Don't execute ``untar_to()`` subprocesses through the shell `Pull Request  984`_
+* Allow setting database_connection for planemo test runs `Pull Request 986`_
+* Fix copy-paste mistakes `Pull Request 983`_
+* Add planemo list_repos command `Pull Request 982`_
+* Make container_register build files with headers and include base_image `Pull Request 980`_
+* Replace deprecated galaxy-lib requirement with galaxy-tool-util `Pull  Request 978`_
+* Close all opened files (thanks to `@bernt-matthias`_). `Pull Request 979`_
+* Build single requirement container, log if requirement not in best-practice channels `Pull Request 977`_
+* Use tojson jinja2 filter instead of json.dumps `Pull Request 975`_
+* Add merge_test_reports command `Pull Request 974`_
+* Implement github workflow and fix profile commands if psql unavailable `Pull Request 976`_
+* Fix planemo lint --biocontainers if no build number in container `Pull Request 972`_
+* Update a training command (thanks to `@hexylena`_). `Pull Request 973`_
+* Allow passing through GALAXY_VIRTUAL_ENV variable to venv setup `Pull Request 971`_
+* Correct help text (thanks to `@hexylena`_). `Pull Request 970`_
+* Remove unneeded html5lib requirement `Pull Request 968`_
+---------------------
+0.62.1 (2019-10-14)
+---------------------
+* Init & update submodules when installing and creating packages. Stop
+distributing eggs (thanks to `@nsoranzo`_). 1ab8530_
+---------------------
+0.62.0 (2019-10-11)
+---------------------
+* Use ``unicodify()`` on exceptions and subprocess outputs (thanks to
+`@nsoranzo`_) `Pull Request 944`_
+* Do not override ``None`` with empty string (thanks to `@ic4f`_). `Pull Request
+950`_
+* Update Docker template for training material generation (thanks to
+`@bedroesb`_). `Pull Request 958`_
+* Add support for suite of repos with different owners (thanks to `@nsoranzo`_).
+`Pull Request 959`_
+* Link for collection details updated in the docs (thanks to `@martin-raden`_).
+`Pull Request 963`_
+* Move most tests to Python 3.7, drop Python 3.4 (thanks to `@nsoranzo`_).
+`Pull Request 964`_
+* Remove confusing warning `Pull Request 966`_
+---------------------
+0.61.0 (2019-07-08)
+---------------------
+* Training - fix empty repeat + some formatting (thanks to `@bebatut`_). `Pull
+Request 926`_
+* Training - add bibliography to tutorial template (thanks to `@shiltemann`_).
+`Pull Request 938`_
+* Training - support new class definition for input in workflow step (thanks to
+`@bebatut`_). `Pull Request 943`_
+* Various tool tutorial fixes ahead of GCC 2019 (thanks to `@nsoranzo`_).
+`Pull Request 940`_
+* Return validation error if doi is empty (thanks to `@nsoranzo`_).
+`Pull Request 937`_
+---------------------
+0.60.0 (2019-05-31)
+---------------------
+* Return validation error if doi is empty `Pull Request 937`_
+* Add junit as test reporter (thanks to `@selten`_). `Pull Request 935`_
+* Update galaxy.xsd for new python 3 compatibility attribute (thanks to `@martenson`_). `Pull Request
+931`_
+* Documentation: add a little warning for <param ... multiple="true"> (thanks to
+`@bernt-matthias`_). `Pull Request 930`_
+---------------------
+0.59.0 (2019-05-09)
+---------------------
+* Add ability to test data manager tools (thanks to `@mvdbeek`_).
+`Pull Request 912`_
+* Update Training for new requirement definition (thanks to `@bebatut`_).
+`Pull Request 913`_
+* Drop amqp workaround (thanks to `@mvdbeek`_). `Pull Request 917`_
+* Use ``yaml.safe_load()`` instead of deprecated ``load()`` (thanks to `@nsoranzo`_).
+`Pull Request 921`_
+* Allow converting ``tool_test_report.json`` to xunit (thanks to `@mvdbeek`_).
+`Pull Request 918`_
+* Fix error if testcase.data.job does not exist (thanks to `@mvdbeek`_).
+`Pull Request 924`_
+* Fix deprecated ``getchildren()`` (thanks to `@nsoranzo`_).
+`Pull Request 925`_
+---------------------
+0.58.2 (2019-03-01)
+---------------------
+* Fix display of tool ids in planemo html report (thanks to `@mvdbeek`_).
+`Pull Request 908`_
+* Single quotes for file names (thanks to `@bernt-matthias`_). `Pull Request
+909`_
+* Fix doc linting (thanks to `@mvdbeek`_). `Pull Request 910`_
+* Update TS categories (thanks to `@nsoranzo`_). 07dc6e0_
+* Close tag in doc help, to help with copy&paste (thanks to `@blankenberg`_).
+`Pull Request 914`_
+* Update the tool XSD file (thanks to `@bgruening`_). `Pull Request 915`_
+---------------------
+0.58.1 (2019-01-03)
+---------------------
+* Update galaxy-lib requirement to 18.9.2 to add Python 3.7 support (thanks to
+`@nsoranzo`_). `Pull Request 906`_
+* Fix command run by `planemo test --skip_venv` (thanks to `@nsoranzo`_).
+`Pull Request 907`_
+---------------------
+0.58.0 (2019-01-01)
+---------------------
+* Remove deprecated ``sudo: false`` from .travis.yml (thanks to `@nsoranzo`_).
+`Pull Request 902`_
+* Do not skip Galaxy client build for ``planemo serve``. Install Galaxy when the
+directory specified with ``--galaxy_root`` does not exist or is empty. (thanks
+to `@nsoranzo`_). `Pull Request 895`_, `Issue 845`_
+---------------------
+0.57.1 (2018-11-23)
+---------------------
+* Fix username validation for shed linting (thanks to `@martenson`_).
+`Pull Request 899`_, `Issue 898`_
+---------------------
+0.57.0 (2018-11-19)
+---------------------
+* Allow ``workflow_convert`` to convert a native ``.ga`` workflows to format 2 (yaml).
+`Pull Request 896`_
+* New command (``workflow_edit``) to open workflow in a synchronized graphical editor.
+`Pull Request 894`_
+* Conda tutorial fixes (thanks to `@nsoranzo`_). `Pull Request 876`_
+* Enable ``--conda_use_local`` option for ``planemo test`` (thanks to
+`@nsoranzo`_). `Pull Request 876`_
+* When testing, skip workflow outputs that do not have a `label` set (thanks to
+`@bgruening`_). `Pull Request 893`_
+* Add ``__repr__`` for ``TestCase`` to improve debugging Planemo
+(thanks to `@bgruening`_). `Pull Request 892`_
+* Increase IO polling interval over time (thanks to `@martenson`_).
+`Pull Request 891`_
+* Sync galaxy xsd and fix tests (thanks to `@mvdbeek`_).
+`Pull Request 889`_
+* Linting fix for ``W605`` (thanks to `@martenson`_). `Pull Request 888`_
+* Add icon for repeat parameters in training (thanks to `@bebatut`_).
+`Pull Request 887`_
+---------------------
+0.56.0 (2018-10-30)
+---------------------
+* Allow selection of Python version when starting managed Galaxy
+(thanks to `@mvdbeek`_). `Pull Request 874`_
+* Change the channel priority of conda (again). (thanks to `@bgruening`_).
+`Pull Request 867`_
+* Some small english corrections (thanks to `@hexylena`_). `Pull Request 868`_
+* Print the list of excluded paths when running ``ci_find_repos``
+(thanks to `@nsoranzo`_). `Pull Request 877`_
+* Improved XSD lint reporting. `Pull Request 871`_
+* Fix Planemo writing a file called ``gx_venv_None``. `Pull Request 870`_
+* Update cwltool and galaxy-lib dependencies for Python 3.7 (thanks to
+`@nsoranzo`_). `Pull Request 864`_
+* Fix to make workflow testing more robust.
+`Pull Request 882`_
+---------------------
+0.55.0 (2018-09-12)
+---------------------
+* Add commands to create Galaxy training materials (thanks to `@bebatut`_).
+`Pull Request 861`_
+* Fix `planemo test` when TEMP env variable contain spaces (thanks to
+`@nsoranzo`_).
+`Pull Request 851`_
+* Support testing a completely remote galaxy instance (thanks to `@hexylena`_).
+`Pull Request 856`_
+* Allow naming history from command line (thanks to `@hexylena`_).
+`Pull Request 860`_
+* Sync galaxy.xsd from galaxy repo (thanks to `@nsoranzo`_).
+`Pull Request 866`_
+* Fix ServeTestCase.test_shed_serve test (thanks to `@nsoranzo`). bad810a_
+---------------------
+0.54.0 (2018-06-06)
+---------------------
+* Better support for testings against different versions of Galaxy efficiently and robustly.
+`Pull Request 849`_
+* New database version (thanks to `@bgruening`_).
+`Pull Request 847`_
+* Hyperlink DOIs against preferred resolver (thanks to `@katrinleinweber`_).
+`Pull Request 850`_
+* Tests for collection inputs to workflows. `Pull Request 843`_
+* Bring in Ephemeris sleep function - hopefully makes serve tests a bit more robust.
+b12b117_
+* More tutorial testing, tutorial updates.
+016b923_, 324c776_, 2002b49_
+* More isolated ``test_shed_upload.py`` tests. 72d2ca7_
+* Add filetype support for workflow test inputs (thanks to `@bgruening`_).
+`Pull Request 842`_
+* Add ``--no_shed_install`` option, to prevent shed installs as part of workflow testing.
+`Pull Request 841`_
+* Small docs fix (thanks to `@hexylena`_). `Pull Request 848`_
+---------------------
+0.53.0 (2018-05-22)
+---------------------
+* Make Planemo testing easier for CWL tools and workflows in various ways and update
+tutorials to reflect these simplifications. `Pull Request 837`_
+* Test and fix running workflow tests against externally managed Galaxy servers.
+`Pull Request 833`_, `Pull Request 836`_
+* Allow using URIs for inputs of workflow test. `Pull Request 840`_
+* Slide Galaxy testing window to include 18.05 and drop 17.09. `Pull Request 838`_
+---------------------
+0.52.0 (2018-05-20)
+---------------------
+* Allow optional disabling of Galaxy single user mode. `Pull Request 835`_
+* Fix for path pasting options during workflow testing. `Pull Request 834`_
+---------------------
+0.51.0 (2018-05-19)
+---------------------
+* Fix essentially all Conda_ and BioContainers_ related functionality to allow parity between
+CWL_ and existing Galaxy functionality - fixes and enhances many commands including ``lint``,
+``conda_install``, ``conda_env``, ``test``, ``run``, and ``mull``.
+`Pull Request 828`_
+* Add two new tutorials for `Conda
+<http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda>`__
+and `Container
+<http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers>`__
+development with CWL tools that mirrors the existing tutorials for Galaxy tools - including new
+CWL exercises, answers, and example project templates.
+347c622_
+* Improve the CWL generated by the ``tool_init`` command to properly deal with
+``SoftwareRequirement`` s and generate more idiomatic CWL.
+`Pull Request 820`_, a5c72e3_
+* Add new engine type (``--engine toil``) for testing and running CWL_ tools (requires
+manually installing Toil_ with ``pip install toil`` in Planemo's environment).
+`Pull Request 831`_
+* Add `documentation <http://planemo.readthedocs.io/en/latest/test_format.html>`__
+for the Galaxy Workflow and CWL_ test format files (includes information on configuring
+various test engines).
+`Pull Request 832`_
+* Better default logging config for CWL development. `Pull Request 830`_
+* Various fixes for the ``conda_search`` command. `Pull Request 826`_
+* Fix test coverage configuration. `Pull Request 822`_
+* Reorganize .travis.yml for clarity. `Pull Request 829`_
+* More isolated, robust unit tests that use git_.
+`Pull Request 827`_, `Pull Request 818`_
+* Fix default list of best-practice Conda channels. `Pull Request 825`_
+* Refactor tests to speed up quick tests - fewer buggy URLs fetched in "quick" mode.
+`Pull Request 823`_
+* Fix upload configuration of workflow testing to default (overrideable) external Galaxies
+to not use path pasting.
+`Pull Request 816`_
+* Fix test number parsing for workflow tests. `Pull Request 817`_
+---------------------
+0.50.1 (2018-05-11)
+---------------------
+* Fix the process of waiting on Galaxy to boot up for the Docker Galaxy container ``--engine``.
+---------------------
+0.50.0 (2018-05-10)
+---------------------
+* Fixes and small CLI tweaks to get the Docker Galaxy container working as an ``--engine`` for the
+run, serve, and test commands.
+---------------------
+0.49.2 (2018-05-09)
+---------------------
+* Various small fixes for new external Galaxy engine type.
+---------------------
+0.49.1 (2018-05-06)
+---------------------
+* Fix PyPI_ README rendering for 0.49.0 release changes.
+---------------------
+0.49.0 (2018-05-06)
+---------------------
+* Implement external Galaxy engine. `Pull Request 781`_
+* Restructure serve testing code for reuse. `Pull Request 795`_
+* Improve test report handling for JSON generated via galaxy-lib testing
+script. `Pull Request 799`_
+* Improve how various branches of Galaxy are tested. `Pull Request 800`_
+* Added documentation for ``GALAXY_MEMORY_MB`` (thanks to `@bernt-matthias`_).
+`Pull Request 801`_
+* Log tool config in verbose logging mode. `Pull Request 802`_
+* Replace ``r`` channel with ``conda-forge`` (thanks to `@bgruening`_).
+`Pull Request 805`_
+* Sync ``galaxy.xsd`` with latest Galaxy updates (thanks to `@nsoranzo`_).
+`Pull Request 806`_
+* Use ``requests.get()`` when validating http URLs (thanks to `@nsoranzo`_).
+`Pull Request 809`_
+* Do not consider tools with "deprecated" in the path (thanks to
+`@bgruening`_). `Pull Request 810`_
+* Automatically load tools shipped with Galaxy when testing, running, or serving
+workflows that reference these tools. `Pull Request 790`_
+* Revise README and touch up documentation in general. `Pull Request 787`_
+* Various small changes to testing and test framework. `Pull Request 792`_
+* Various Python 3 fixes. 8cfe9e9_, 41f7df1_
+* Fixes for Galaxy 18.0X releases.
+`Pull Request 803`_, dc443d6_
+---------------------
+0.48.0 (2018-02-28)
+---------------------
+* Run all CI tests against Python 3 (thanks to `@nsoranzo`_).
+`Pull Request 768`_ and `Pull Request 774`_
+* Python 3 fix - subprocess with ``universal_newlines=True``
+(thanks to `@peterjc`_).
+`Pull Request 764`_
+* Record CWL_ conformance test results using JUnit xml
+(thanks to `@mr-c`_).
+`Pull Request 756`_
+* Restore run test case for simple Galaxy tools.
+`Pull Request 769`_
+* Enhancements to Galaxy profiles and workflow testing.
+`Pull Request 773`_
+* Fix resolving & installing shed repositories from workflows for ``test``
+and ``run`` commands.
+`Pull Request 776`_
+* Implement planemo command to convert format 2 workflows into .ga workflows.
+`Pull Request 771`_
+* Add a native Galaxy workflow (.ga) testing test.
+`Pull Request 770`_
+* Drop Brew support but add more detailed install instructions.
+`Pull Request 761`_
+* Clean up CWL_ conformance test execution. `Pull Request 753`_
+* Assorted small CWL_ and deamon serve fixes. `Pull Request 759`_
+---------------------
+0.47.0 (2017-11-18)
+---------------------
+* Update to the latest Galaxy tool XSD  (thanks to `@nsoranzo`_).
+`Pull Request 747`_
+* Re-fix problem when shed_update would fail if nothing to update
+(thanks to `@nsoranzo`_). `Pull Request 747`_
+* Update instructions for installation via conda (thanks to `@nsoranzo`_) .
+`Pull Request 743`_
+* Bug fix for MacOS `chmod` doesn't support `--recursive` flag.
+(thanks to `@dfornika`_). `Pull Request 739`_
+* Bug fix to also `socket.error` when linting URLs
+(thanks to `@nsoranzo`_). `Pull Request 738`_
+* Disable broken tests. `Pull Request 745`_
+---------------------
+0.46.1 (2017-09-26)
+---------------------
+* Rev to latest versions of bioblend_ and `galaxy-lib`_ for various fixes
+related to CWL_.
+---------------------
+0.46.0 (2017-09-15)
+---------------------
+* Change behavior of ``--docker`` flag, for a few releases it would require
+Galaxy use a container for every non-upload tool. This breaks various
+conversion tools for instance and so was reverted.
+`Pull Request 733`_
+* Add 'Accept' header when linting doc URLs (thanks to `@nsoranzo`_).
+`Pull Request 725`_
+* Fix `--conda_auto_install` help (thanks to `@nsoranzo`_).
+`Pull Request 727`_
+* Incremental progress toward CWL support via Galaxy.
+`Pull Request 729`_, `Pull Request 732`_
+* Update galaxy-lib to latest version to fix various issues.
+`Pull Request 730`_
+* Fix lint detected problems with documentation.
+`Pull Request 731`_
+---------------------
+0.45.0 (2017-09-06)
+---------------------
+* Update to the latest `galaxy-lib`_ for Conda fixes. (thanks `@nsoranzo`_)
+and updated CWL_ utilities.  `Pull Request 716`_, `Pull Request 723`_
+* Update Conda_ channel order to sync with Bioconda_
+(thanks to `@nsoranzo`_). `Pull Request 715`_
+* Experimental support running CWL_ workflows through the CWL_ fork of Galaxy.
+* Mention ``planemo command --help`` in main help
+(thanks to `@peterjc`_). `Pull Request 709`_
+* Bugfix handle ``None`` requirement versions when registering containers
+(thanks to `@bgruening`_). `Pull Request 704`_
+* Bugfix for dependencies by pinning ruamel.yaml version
+(thanks to `@mvdbeek`_). `Pull Request 720`_
+---------------------
+0.44.0 (2017-06-22)
+---------------------
+* Fix and improve Galaxy root option specification options.
+`Pull Request 701`_, 8a608e0_
+* Update `planemo mull` to use a default action of `build-and-test` since
+`build` no longer cleans up itself. ecc1bc2_
+* Add a command to pre-install Involucro_.
+`Pull Request 702`_
+---------------------
+0.43.0 (2017-06-22)
+---------------------
+* Remove stdio from generated tools - just use exit_code for everything.
+91b6fa0_
+* Implement some ad-hoc documentation tests. `Pull Request 699`_
+* A large number of small enhancements and fixes for the documentation and
+example projects.
+---------------------
+0.42.1 (2017-06-16)
+---------------------
+* Fix Readme typos (thanks to `@manabuishii`_) 904d77a_
+* Fix `container_register` to create pull requests against the newly finalized home of the
+multi-package-containers registry repository.
+9636682_
+* Fix `use_global_config` and `use_env_var` for options with unspecified defaults.
+475104c_
+---------------------
+0.42.0 (2017-06-15)
+---------------------
+* Conda/Container documentation and option naming improvements. `Pull Request
+684`_
+* Sync `galaxy.xsd` with latest upstream Galaxy updates (thanks to `@nsoranzo`_).
+`Pull Request 687`_
+* Fix `ci_find_repos` command to not filter repos whose only modifications where
+in subdirs (thanks to `@nsoranzo`_).
+`Pull Request 688`_
+* Update `container_register` for mulled version 2 and repository name changes.
+`Pull Request 689`_
+* Better pull request messages for the `container_register` command.
+`Pull Request 690`_
+---------------------
+0.41.0 (2017-06-05)
+---------------------
+* Fix ``shed_update`` not fail if there is nothing to update
+(thanks to `@nsoranzo`_). `Issue 494`_, `Pull Request 680`_
+* Conda documentation and option naming improvements.
+`Pull Request 683`_
+* Implement ``container_register`` for tool repositories.
+`Pull Request 675`_
+* Fix ``hub`` binary installation for Mac OS X.
+`Pull Request 682`_
+---------------------
+0.40.1 (2017-05-03)
+---------------------
+* Fix data manager configuration to not conflict with original Galaxy at
+``galaxy_root`` (thanks to `@nsoranzo`_). `Pull Request 662`_
+* Fix ``filter_paths()`` to not partial match paths when filtering shed repositories
+(thanks to `@nsoranzo`_). `Pull Request 665`_
+* Fix description when creating ``.shed.yml`` files (thanks to `@RJMW`_).
+`Pull Request 664`_
+---------------------
+0.40.0 (2017-03-16)
+---------------------
+* Implement instructions and project template for GA4GH Tool Execution
+Challenge Phase 1. 84c4a73_
+* Eliminate Conda hack forcing ``/tmp`` as temp directory. b4ae44d_
+* Run dependency script tests in isolated directories. 32f41c9_
+* Fix OS X bug in ``planemo run`` by reworking it to wait using urllib instead of sockets.
+3129216_
+---------------------
+0.39.0 (2017-03-15)
+---------------------
+* Implement documentation and examples for Conda-based dependency development (under
+"Advanced" topics).
+`Pull Request 642`_, `Pull Request 643`_
+* Implement documentation and examples for container-based dependency development (under
+"Advanced" topics).
+0a1abfe_
+* Implement a ``planemo conda_search`` command for searching best practice channels
+from the command line.
+`Pull Request 642`_
+* Allow Planemo to work with locally built Conda packages using the ``--conda_use_local``
+command.
+`Pull Request 643`_, `Issue 620`_
+* Implement an ``open`` (or just ``o``) command to quickly open the last test results
+(or any file if supplied). `Pull Request 641`_
+* Linting improvements and fixes due to `galaxy-lib`_ update.
+* WARN on test output names not found or not matching.
+* INFO correct information about stdio if profile version is found.
+* WARN if profile version is incorrect.
+* INFO profile version
+* Fix ``assert_command`` not detected as a valid test (fixes  `Issue 260`_).
+* Have ``lint --conda_requirements`` check that at least one actual requirement is found.
+6638caa_
+* Allow ``conda_install`` to work with packages as well as just tools.
+8faf661_
+* Add ``--global`` option to conda_install to install requirements into global Conda setup
+instead of using an environment.
+8faf661_
+* Implement ``planemo lint --biocontainer`` that checks that a tool has an available BioContainer
+registered.
+0a1abfe_
+* Add more options and more documentation to the ``planemo mull`` command.
+0a1abfe_
+* Hack around a bug in Conda 4.2 that makes it so ``planemo mull`` doesn't work out of the box on
+Mac OS X.
+0a1abfe_
+* Allow URIs to be used instead of paths for a couple operations. ce0dc4e_
+* Implement non-strict CWL parsing option. 4c0f100_
+* Fixes for changes to cwltool_ and general CWL-relate functionality.
+3c95b7b_, 06bcf19_, 525de8f_, 9867e56_, 9ab4a0d_
+* Eliminate deprecated XML-based abstraction from ``planemo.tools``. 04238d3_
+* Fix ``MANIFEST.in`` entry that was migrated to galaxy-lib. ced5ce2_
+* Various fixes for the command ``conda_env``. `Pull Request 640`_
+* Improved command help - both formatting and content. `Pull Request 639`_
+* Implement a ``--no_dependency_resolution`` option disabling conda dependency
+resolver.
+`Pull Request 635`_, `Issue 633`_
+* Tests for new linting logic. `Pull Request 638`_
+* Fix bug where tool IDs needs to be lowercase for the shed (thanks to
+`@bgruening`_).
+`Pull Request 649`_
+* Update seqtk version targetted by intro docs. e343b67_
+* Various other Conda usability improvements. `Pull Request 634`_
+---------------------
+0.38.1 (2017-02-06)
+---------------------
+* Fix bug with ``shed_lint --urls`` introduced in 0.38.0.
+84ebc1f_
+---------------------
+0.38.0 (2017-02-06)
+---------------------
+* Trim down the default amount of logging during testing.
+`Pull Request 629`_, `Issue 515`_
+* Improved log messages during shed operations. 08c067c_
+* Update tool XSD against latest Galaxy.
+fca4183_, 03c9658_
+* Fix bug where ``shed_lint --tools`` for a suite lints the same tools multiple
+times.
+`Issue 564`_, `Pull Request 628`_
+---------------------
+0.37.0 (2017-01-25)
+---------------------
+* Update to the latest `galaxy-lib`_ release. This means new installs start with
+Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes many
+Conda_ related bugs.
+* Change defaults so that Conda automatically initializes and performs tool installs
+by default from within the spawned Galaxy server. The trio of flags
+``--conda_dependency_resolution``, ``--conda_auto_install``, and ``--conda_auto_init``
+are effectively enabled by default now. 4595953_
+* Use the Galaxy cached dependency manager by default (thanks to `@abretaud`_).
+`Pull Request 612`_
+* Test Conda dependency resolution for more versions of Galaxy including the forthcoming
+release of 17.01.
+* Update to the latest Galaxy tool XSD for various tool linting fixes. 32acd68_
+* Fix pip ignores for ``bioconda_scripts`` (thanks to `@nturaga`_)
+`Pull Request 614`_
+---------------------
+0.36.1 (2016-12-12)
+---------------------
+* Fix move error when using ``project_init``.
+`Issue 388`_, `Pull Request 610`_
+* Improved integration testing for ``test`` command. `Pull Request 609`_
+* Update CWL links to v1.0 (thanks to `@mr-c`_).
+`Pull Request 608`_
+---------------------
+0.36.0 (2016-12-11)
+---------------------
+* Bring in latest tool XSD file from Galaxy (thanks to `@peterjc`_).
+`Pull Request 605`_
+* PEP8 fixes for various linting problems
+(thanks to `@peterjc`_).
+`Pull Request 606`_
+* Update tool syntax URL to new URL (thanks to `@mvdbeek`_).
+`Pull Request 602`_
+---------------------
+0.35.0 (2016-11-14)
+---------------------
+* Native support for building bioconductor tools and recipes
+(thanks to `@nturaga`_). `Pull Request 570`_
+* Fixes for running Galaxy via docker-galaxy-stable (thanks to
+`@bgruening`_). 50d3c4a_
+* Import order linting fixes (thanks to `@bgruening`_).
+---------------------
+0.34.1 (2016-10-12)
+---------------------
+* Mimic web browser to validate user help URLs fixing `Issue 578`_
+(thanks to `@peterjc`_). `Pull Request 591`_
+* Fix for Bioconda recipes depending on ``conda-forge`` (thanks to `@nsoranzo`_).
+`Pull Request 590`_
+---------------------
+0.34.0 (2016-10-05)
+---------------------
+* Implement ``mull`` command to build containers for tools based on Conda_
+recipes matching requirement definitions. 08cef54_
+* Implement ``--mulled_containers`` flag on ``test``, ``serve``, and ``run``
+commands to run tools in "mulled" containers. Galaxy will first search
+locally cache containers (such as ones built with ``mull``), then search
+the mulled namespace of `quay.io`_, and finally build one on-demand if
+needed using `galaxy-lib`_ and Involucro_ developed by `@thriqon`_.
+* Implement ``--conda_requirements`` flag on ``lint`` command to ensure requirements
+can be resolved in best practice channels. 9da8387_
+* Allow ``conda_install`` command over multiple tool paths. 2e4e5fc_
+* Update pip_ as part of setting virtual environment in ``Makefile`` target.
+19b2ee9_
+* Add script to auto-update Bioconda_ recipe for Planemo and open a pull request.
+f0da66f_
+---------------------
+0.33.2 (2016-09-28)
+---------------------
+* Fix HISTORY.rst link problem that prevented correct display of content on PyPI_.
+---------------------
+0.33.1 (2016-09-28)
+---------------------
+* Fix ``lint --urls`` false positives by being more restrictive with what is considered a URL
+(fixed by `@hexylena`_ after detailed report from `@peterjc`_).
+`Issue 573`_, `Pull Request 579`_
+---------------------
+0.33.0 (2016-09-23)
+---------------------
+* Enable XSD validation of tools by default (restore old behavior with
+``planemo lint --no_xsd``). 1ef05d2_
+* Implement a ``conda_lint`` command to lint Conda_ recipes based
+on `anaconda-verify`_. 6a6f164_
+* Implement ``clone`` and ``pull_request`` commands to ease PRs
+(with documentation fixes from `@martenson`_).
+e925ba1_, ea5324f_
+* Update `galaxy.xsd`_ to allow version_command's to have an interpreter
+attribute. 7cca2e4_
+* Apply improvement from `@nsoranzo`_ for Planemo's use of
+`git diff <https://git-scm.com/docs/git-diff>`__.
+6f91719_
+* Pull in downstream refactoring of ``tool_init`` code from `@nturaga`_'s
+Bioconductor_ work. ccdd2d5_
+* Update to latest `Tool Factory`_ code from `tools-iuc`_. ca88b0c_
+* Small code cleanups. b6d8294_, d6da3a8_
+* Fixup docs in ``planemo.xml.validation``.
+* Allow skipping newly required lxml_ dependency in `setup.py`_. 34538de_
+---------------------
+0.32.0 (2016-09-16)
+---------------------
+* Enhance ``planemo lint --xsd`` to use a fairly complete and newly official XSD
+definition. `Pull Request 566`_
+* Migrate and update documentation related to tool XML macros and handling
+multiple outputs from the Galaxy wiki (with help from `@bgruening`_, `@mvdbeek`_,
+and `@nsoranzo`_). `Pull Request 559`_
+* Documentation fixes (thanks to `@ramezrawas`_). `Pull Request 561`_
+* Do not fail URL linting in case of too many requests (thanks to `@nsoranzo`_).
+`Pull Request 565`_
+---------------------
+0.31.0 (2016-09-06)
+---------------------
+* Implement new commands to ``ci_find_repos`` and ``ci_find_tools`` to ease
+CI scripting.
+`Pull Request 555`_
+---------------------
+0.30.2 (2016-09-01)
+---------------------
+* Fix another problem with Conda_ prefix handling when using
+``--conda_dependency_resolution``. f7b6c7e_
+---------------------
+0.30.1 (2016-09-01)
+---------------------
+* Fix a problem with Conda_ prefix handling when using
+``--conda_dependency_resolution``. f7b6c7e_
+* Fix for quote problem in ``update_planemo_recipe.bash``. 6c03de8_
+* Fix to restore linting of ``tests/`` directory and fix import order throughout
+module. ef4b9f4_
+---------------------
+0.30.0 (2016-09-01)
+---------------------
+* Update to the latest `galaxy-lib`_ release and change Conda_ semantics to match
+recent updates to Galaxy. For the most robust Conda_ usage - use planemo 0.30+
+with Galaxy 16.07 or master.
+07d94bd_
+* Implement the ``--conda_auto_init`` flag for ``conda_install``. ca19910_
+* Allow the environment variable ``PLANEMO_CONDA_PREFIX`` to set a default
+for ``--conda_prefix``.
+24008ab_
+* Fixup documentation regarding installs and Conda_. ce44e87_
+* Fix and lint Python module import order throughout project.
+`Pull Request 550`_
+* Use ``cp`` rather than symlink to ``$DOWNLOAD_CACHE`` in the
+``dependency_script`` command (thanks to `@peterjc`_).  c2204b3_
+* Fixes for the Homebrew recipe updater. c262b6d_
+---------------------
+0.29.1 (2016-08-19)
+---------------------
+* Improved handling of Python 2.7 specific dependencies.
+---------------------
+0.29.0 (2016-08-19)
+---------------------
+* Look for sha256sum checksums during shed_lint (thanks to `@peterjc`_).
+`Pull Request 539`_
+* An assortment fixes and enhancements to the ``dependency_script`` command
+(thanks to `@peterjc`_). `Pull Request 541`_, `Pull Request 545`_
+* Fix shed_build to respect exclude: in .shed.yml (thanks to `@nsoranzo`_).
+`Pull Request 540`_
+* Fix linting of tool URLs (thanks to `@nsoranzo`_). `Pull Request 546`_
+---------------------
+0.28.0 (2016-08-17)
+---------------------
+* Fixes for bioblend_ v0.8.0 (thanks to `@nsoranzo`_). 9fdf490_
+* Enable shed repo type update (thanks to `@nsoranzo`_). 3ceaa40_
+* Create suite repositories with repository_suite_definition type by default
+(thanks to `@nsoranzo`_).
+057f4f0_
+* Include ``shed_lint`` in script run by ``travis_init`` (thanks to `@peterjc`_).
+`Pull Request 528`_
+* Minor polish to the ``travis_init`` command (thanks to `@peterjc`_).
+`Pull Request 512`_
+* Update pip_ and setuptools on TravisCI; fix travis_init (thanks to `@peterjc`_).
+`Pull Request 521`_
+* Shorten command one line descriptions for main help (thanks to `@peterjc`_).
+`Pull Request 510`_
+* Use ``planemo test --no_cache_galaxy`` under TravisCI (thanks to `@peterjc`_).
+`Pull Request 513`_
+* Improve and fix docs ahead of GCC 2016 (thanks to `@martenson`_).
+`Pull Request 498`_, 725b232_
+* Add description of ``expect_num_outputs`` to planemo FAQ. a066afb_
+* Revise planemo tools docs to be more explicit about collection identifiers.
+a811e65_
+* Add more docs on existing dynamic tool output features. `Pull Request 526`_
+* Fix serve command doc (thanks to `@nsoranzo`_). 8c088c6_
+* Fix `make lint-readme` (RST link errors) (thanks to `@peterjc`_).
+`Pull Request 525`_
+* Add union bedgraph example to project templates (for GCC demo example).
+d53bcd6_
+* Add Flow Cytometry Analysis, Data Export, and Constructive Solid Geometry as
+shed categories (thanks to `@bgruening`_, `@gregvonkuster`_, and `@nsoranzo`_).
+e890ab5_, 08bb354_, e2398fb_
+* Remove duplicated attribute in docs/writing/bwa-mem_v5.xml (thanks to
+Paul Stewart `@pstew`_).
+`Pull Request 507`_
+---------------------
+0.27.0 (2016-06-22)
+---------------------
+* Use ephemeris to handle syncing shed tools for workflow actions.
+1c6cfbb_
+* More planemo testing enhancements for testing artifacts that aren't
+Galaxy tools. `Pull Request 491`_
+* Implement ``docker_galaxy`` engine type. eb039c0_, `Issue 15`_
+* Enhance profiles to be Dockerized Galaxy-aware. `Pull Request 488`_
+* Add linter for DOI type citation - thanks to `@mvdbeek`_.
+`Pull Request 484`_
+---------------------
+0.26.0 (2016-05-20)
+---------------------
+* Implement ``Engine`` and ``Runnable`` abstractions - Planemo now has
+beta support for testing Galaxy workflows and CWL_ tools with Galaxy and
+any CWL_ artifact with cwltool_.
+`Pull Request 454`_, 7be1bf5_
+* Fix missing command_line in test output json. e38c436_
+* More explicit Galaxy ``job_conf.xml`` handling, fixes bugs caused by
+``galaxy_root`` having existing and incompatible ``job_conf.xml`` files
+and makes it possible to specify defaults with fixed server name. c4dfd55_
+* Introduce profile commands (``profile_create``, ``profile_delete``, and
+``profile_list``) and profile improvements (automatic postgres database
+creation support). `Pull Request 480`_, a87899b_
+* Rework Galaxy test reporting to use structured data instead of XUnit
+data. 4d29bf1_
+* Refactor Galaxy configuration toward support for running Galaxy in
+docker-galaxy-stable. `Pull Request 479`_
+---------------------
+0.25.1 (2016-05-11)
+---------------------
+* Tweak dependencies to try to fix cwltool_ related issues - such
+as `Issue 475`_.
+---------------------
+0.25.0 (2016-05-11)
+---------------------
+* Implement Galaxy "profiles" - the ability to configure
+perisistent, named environments for ``serve`` and ``test``.
+5d08b67_
+* Greatly improved ``serve`` command - make ``test-data``
+available as an FTP folder, (on 16.07) automatically log
+in an admin user, and many more options (such as those
+required for "profiles" and a ``--daemon`` mode).
+* Two fixes to ensure more consistent, dependable ``test`` output.
+`Pull Request 472`_, f3c6917_
+* Add code and documentation for linting (``lint``) and
+building (``tool_init``) CWL_ tools. a4e6958_, b0b867e_,
+4cd571c_
+* If needed for Conda_ workaround, shorten ``config_directory``
+path (thanks to `@mvdbeek`_). efc5f30_
+* Fix ``--no_cache_galaxy`` option (thanks to Gildas Le
+Corguillé). d8f2038_
+* Target draft 3 of CWL_ instead of draft 2. 775bf49_
+* Fix ``cwltool`` dependency version - upstream changes broke
+compatibility. `65b999d`_
+* Add documentation section and slides about recent Galaxy
+tool framework changes (with fix from `@remimarenco`_). 069e7ba_
+* Add IUC standards to Planemo docs. 2ae2b49_
+* Improve collection-related contents in documentation
+(thanks in part to `@martenson`_).
+fea51fc_, 13a5ae7_
+* Add documentation on ``GALAXY_SLOTS`` and running planemo
+on a cluster. 45135ff_, e0acf91_
+* Revise command-line handling framework for consistency and
+extension - allow extra options to be configured as
+defaults ``~/.planemo.yml`` including ``--job_config_file``
+and Conda_ configuration options. e769118_, 26e378e_
+* Fix ``tool_init`` commans options typos (thanks to
+Nitesh Turaga). 826d371_
+* Refactor galaxy-related modules into submodules of a new
+``planemo.galaxy`` package. 8e96864_
+* Fix error message typo (thanks to `@blankenberg`_). b1c8f1d_
+* Update documentation for recent command additions. 3f4ab44_
+* Rename option ``--galaxy_sqlite_database`` option to
+``--galaxy_database_seed`` and fix it so it actually works.
+f7554d1_
+* Add ``--extra_tools`` option to ``serve`` command. 02a08a0_
+* Update project testing to include linting documentation
+(``docs/``), Python import order, and docstrings.
+a13a120_, 6e1e726_, 95d5cba_
+---------------------
+0.24.2 (2016-04-25)
+---------------------
+* Revert "check ``.shed.yml`` owner against credentials during shed
+creation", test was incorrect and preventing uploads.
+`Pull Request 425`_, `Issue 246`_
+---------------------
+0.24.1 (2016-04-08)
+---------------------
+* Fix test summary report. `Pull Request 429`_
+* Improve error reporting when running ``shed_test``. ce8e1be_
+* Improved code comments and tests for shed related functionality.
+89674cb_
+* Rev `galaxy-lib`_ dependency to 16.4.1 to fix wget usage in
+newer versions of wget. d76b489_
+---------------------
+0.24.0 (2016-03-29)
+---------------------
+* Drop support for Python 2.6. 93b7bda_
+* A variety of fixes for ``shed_update``.
+`Pull Request 428`_, `Issue 416`_
+* Fix reporting of metadata updates for invalid shed updates.
+`Pull Request 426`_, `Issue 420`_
+* Check ``.shed.yml`` owner against credentials during shed creation.
+`Pull Request 425`_, `Issue 246`_
+* Fix logic error if there is a problem with ``shed_create``. 358a42c_
+* Tool documentation improvements. 0298510_, a58a3b8_
+---------------------
+0.23.0 (2016-02-15)
+---------------------
+* Fix duplicated attributes with Conda_ resolver (thanks
+to Björn Grüning). `Pull Request 403`_
+* Upgrade to latest version of `galaxy-lib`_ for more linting.
+* Attempt to better handle conditional dependency on cwltool.
+---------------------
+0.22.2 (2016-01-14)
+---------------------
+* Fixed bug targetting forthcoming release of Galaxy 16.01.
+---------------------
+0.22.1 (2016-01-14)
+---------------------
+* Fixed problem with PyPI_ build artifacts due to submodule's not
+being initialized during previous release.
+---------------------
+0.22.0 (2016-01-13)
+---------------------
+* Add ``--skip_venv`` to support running Galaxy 16.01 inside of
+conda environments. 9f3957d_
+* Implement conda support. f99f6c1_, ad3b2f0_, 5e0b6d1_
+* Update LICENSE for Planemo to match Galaxy. 15d33c7_
+* Depend on new `galaxy-lib`_ on PyPI_ instead of previous hacks....
+`Pull Request 394`_
+* Fix egg caching against master/15.10. 6d0f502_
+* Fix bug causing shed publishing of ``.svn`` directories.
+`Issue 391`_
+* Bug fixes for Conda_ support thanks to `@bgruening`_. 63e456c_
+* Fix document issues thanks to `@einon`_.
+`Pull Request 390`_
+* Improve client for shed publishing to support newer shed backend
+being developed by `@hexylena`_. `Pull Request 394`_
+* Tool Shed ``repo_id`` change, `@hexylena`_. `Pull Request 398`_
+* Various other small changes to testing, project structure, and
+Python 3 support.
+---------------------
+0.21.1 (2015-11-29)
+---------------------
+* Fix serious regression to ``test`` command. 94097c7_
+* Small fixes to release process. 4e1377c_, 94645ed_
+---------------------
+0.21.0 (2015-11-29)
+---------------------
+* If ``virtualenv`` not on ``PATH``, have Planemo create one for Galaxy.
+5b97f2e_
+* Add documentation section on testing tools installed in an existing
+Galaxy instance. 1927168_
+* When creating a virtualenv for Galaxy, prefer Python 2.7.
+e0577e7_
+* Documentation fixes and improvements thanks to `@martenson`_.
+0f8cb10_, 01584c5_, b757791_
+* Specify a minimum ``six`` version requirement. 1c7ee5b_
+* Add script to test a planemo as a wheel. 6514ff5_, `Issue 184`_
+* Fix empty macro loading. `Issue 362`_
+* Fix an issue when you run ``shed_diff --shed_target local`` thanks
+to Gwendoline Andres and Gildas Le Corguillé at ABiMS Roscoff.
+`Pull Request 375`_
+* Fix ``shed_diff`` printing to stdout if ``-o`` isn't specified.
+f3394e7_
+* Small ``shed_diff`` improvements to XML diffing and XUnit reporting.
+af7448c_, 83e227a_
+* More logging of ``shed_diff`` results if ``--verbose`` flagged.
+9427b47_
+* Add ``test_report`` command for rebuilding reports from structured JSON.
+99ee51a_
+* Fix option bug with Click 6.0 thanks to `@bgruening`_. 2a7c792_
+* Improved error messages for test commands. fdce74c_
+* Various fixes for Python 3. 2f66fc3_, 7572e99_, 8eda729_, 764ce01_
+* Use newer travis container infrastructure for testing. 6d81a94_
+* Test case fixes. 98fdc8c_, 0e4f70a_
+---------------------
+0.20.0 (2015-11-11)
+---------------------
+* More complete I/O capturing for XUnit. 6409449_
+* Check for select parameter without options when linting tools.
+`Issue 373`_
+* Add ``--cwl_engine`` argument to ``cwl_run`` command. dd94ddc_
+* Fixes for select parameter linting. 8b31850_
+* Fix to demultiplexing repositories after tool uploads. `Issue 361`_
+* Fix to update planemo for Galaxy wheels. 25ef0d5_
+* Various fixes for Python 2.6 and Python 3.
+c1713d2_, 916f610_, c444855_
+---------------------
+0.19.0 (2015-11-03)
+---------------------
+* Initial implementation of ``cwl_run`` command that runs a
+CWL tool and job file through Galaxy. 49c5c1e_
+* Add ``--cwl`` flag to ``serve`` to experimentally serve CWL tools
+in Galaxy.
+`Pull Request 339`_
+* Implement highly experimental ``cwl_script`` command to convert
+a CWL job to a bash script. 508dce7_
+* Add name to all XUnit reports (thanks to `@hexylena`_).
+`Pull Request 343`_
+* Capture stdout and stderr for ``shed_diff`` and ``shed_update``
+XUnit reports. `Pull Request 344`_
+* More tool linting (conditionals) thanks to `@hexylena`_.
+`Pull Request 350`_
+* UTF-8 fixes when handling XUnit reports. `Pull Request 345`_
+* Add `Epigenetics` as Tool Shed category. `Pull Request 351`_
+* Merge changes to common modules shared between Galaxy, Planemo, and Pulsar (thanks to `@natefoo`_).
+`Pull Request 356`_
+* Add ``--cite_url`` to ``tool_init``. fdb1b51_
+* ``tool_init`` bug fix. f854138_
+* Fix `setup.py`_ for cwltool and bioblend_ changes. 1a157d4_
+* Add option to specify template sqlite database locally. c23569f_
+* Add example IPython notebooks to docs. c8640b6_
+---------------------
+0.18.1 (2015-10-22)
+---------------------
+* Fix issue with test reporting not being populated. 19900a6_
+---------------------
+0.18.0 (2015-10-20)
+---------------------
+* Improvements to ``docker_shell`` usability (thanks to `@kellrott`_).
+`Pull Request 334`_
+* Add docker pull attempt when missing Dockerfile (thanks to `@kellrott`_).
+`Pull Request 333`_
+* Fix bug inferring which files are tool files (thanks to `@hexylena`_).
+`Pull Request 335`_, `Issue 313`_
+* Initial work toward automating brew recipe update. 4d6f7d9_, `Issue 329`_
+---------------------
+0.17.0 (2015-10-19)
+---------------------
+* Implement basic XUnit report option for ``shed_update`` (thanks to `@martenson`_).
+`Pull Request 322`_
+* Fix issues with producing test outputs. 572e754_
+* Xunit reporting improvements - refactoring, times, diff output (thanks to `@hexylena`_).
+`Pull Request 330`_
+* Implement project governance policy and update developer code of conduct to
+match that of the Galaxy project. `Pull Request 316`_
+* Update filters for account for new ``.txt`` and ``.md`` test outputs
+(thanks to `@hexylena`_). `Pull Request 327`_
+* Add verbose logging to galaxy test output handling problems. 5d7db92_
+* Flake8 fixes (thanks to `@martenson`_). 949a36d_
+* Remove uses of deprecated ``mktemp`` Python standard library function
+(thanks to `@hexylena`_). `Pull Request 330`_
+---------------------
+0.16.0 (2015-10-07)
+---------------------
+* Adding new command ``dependency_script`` to convert Tool Shed dependencies
+into shell scripts - thanks to `@peterjc`_.
+`Pull Request 310`_, f798c7e_, `Issue 303`_
+* Implement profiles in sheds section of the ``~/.planemo.yml``.
+`Pull Request 314`_
+---------------------
+0.15.0 (2015-10-01)
+---------------------
+* Template framework for reporting including new markdown and plain
+text reporting options for testing - thanks to `@hexylena`_.
+`Pull Request 304`_
+* XUnit style reporting for ``shed_diff`` command - thanks to
+`@hexylena`_. `Pull Request 305`_
+* Add new ``shed_build`` command for building repository tarballs -
+thanks to `@kellrott`_. `Pull Request 297`_
+* Fix exit code handling for ``lint`` commands - thanks to `@mvdbeek`_.
+`Pull Request 292`_
+* Improved documentation for ``serve`` command - thanks to `@lparsons`_.
+`Pull Request 312`_
+* Tiny backward compatible Python 3 tweaks for `Tool Factory`_ - thanks
+to `@peterjc`_. dad2d9d_
+* Fixed detection of virtual environment in ``Makefile`` - thanks to
+`@lparsons`_. `Pull Request 311`_
+* Updates to Galaxy XSD - thanks to `@mr-c`_. `Pull Request 309`_
+* Allow reading shed key option from an environment variable.
+`Pull Request 307`_
+* Allow specifying host to serve Galaxy using ``-host`` - thanks in
+part to `@chambm`_. `Pull Request 301`_
+* Allow specifying defaults for ``-host`` and ``--port`` in
+``~/.planemo.yml``. `Pull Request 301`_
+* Improve ``~/.planemo.yml`` sample comments - thanks to `@martenson`_.
+`Pull Request 287`_
+* Update tool shed categories - thanks to `@bgruening`_. `Pull Request 285`_
+* Improved output readibility for ``diff`` command - thanks to `@martenson`_. `Pull Request 284`_
+---------------------
+0.14.0 (2015-08-06)
+---------------------
+* Allow ``-t`` as shorthand for ``--shed_target`` (thanks to Peter Cock).
+`Pull Request 278`_
+* Fix ``tool_init`` command to use ``from_work_dir`` only if file in command
+(thanks to bug report and initial fix outline by Gildas Le Corguillé).
+`Pull Request 277`_
+* Various documentation fixes (thanks in part to Peter Cock and Daniel
+Blankenberg). `Pull Request 256`_, `Pull Request 253`_, `Pull Request 254`_,
+`Pull Request 255`_, `Pull Request 251`_, `Issue 272`_
+---------------------
+0.13.2 (2015-07-06)
+---------------------
+* Fix project_init for missing files. cb5b906_
+* Various documentation improvements.
+---------------------
+0.13.1 (2015-07-01)
+---------------------
+* Fix for ``shed_init`` producing non-standard type hints. `Issue 243`_,
+f0610d7_
+* Fix tool linting for parameters that define an ``argument`` but not a
+``name``. `Issue 245`_, aad1eed_
+* Many doc updates including a tutorial for developing tools in a test-driven
+fashion and instructions for using the planemo appliance through Kitematic
+(with Kitematic screenshots from E. Rasche).
+---------------------
+0.13.0 (2015-06-28)
+---------------------
+* If planemo cannot find a Galaxy root, it will now automatically fetch
+one (specifing ``--galaxy_install`` will still force a fetch).
+`Pull Request 235`_
+* `Docuementation <http://planemo.readthedocs.org/en/latest/appliance.html>`__
+has been updated to reflect new and vastly improved Docker and Vagrant
+virtual appliances are now available, as well as a new VirtualBox OVA
+variant.
+* Update linting for new tool XML features (including ``detect_errors``
+and output collections). `Issue 233`_, 334f2d4_
+* Fix ``shed_test`` help text. `Issue 223`_
+* Fix code typo (thanks to Nicola Soranzo). `Pull Request 230`_
+* Improvements to algorithm used to guess if an XML file is a tool XML file.
+`Issue 231`_
+* Fix configuration file handling bug. `Issue 240`_
+---------------------
+0.12.2 (2015-05-23)
+---------------------
+* Fix ``shed_test`` and ``shed_serve`` for test and local tool sheds.
+f3cafaa_
+---------------------
+0.12.1 (2015-05-21)
+---------------------
+* Fix to ensure the tab completion script is in the Python source tarball
+(required for setting up tab-completion for Homebrew). 6b4e7a6_
+---------------------
+0.12.0 (2015-05-21)
+---------------------
+* Implement a ``--failed`` flag for the ``test`` command to rerun
+previously faied tests. `Pull Request 210`_
+* Implement ``shed_update`` to upload contents and update repository
+metadata. `Pull Request 216`_
+* Implement ``shed_test`` and ``shed_serve`` commands to test and view
+published artifacts in the Tool Shed. `Pull Request 213`_, `Issue 176`_
+* Add shell tab-completion script. 37dcc07_
+* Many more commands allow specifing multiple tool and/or repository targets.
+`Issue 150`_
+* Add -m as alias for --message in planemo shed_upload (thanks to
+Peter Cock). `Pull Request 200`_
+* Add ``--ensure_metadata`` option to ``shed_lint`` to ensure ``.shed.yml``
+files contain many repository. `Pull Request 215`_
+* More developer documentation, additional ``make`` targets including ones
+for setting up git pre-commit hooks. cc8abb6_, `Issue 209`_
+* Small README improvement (thanks to Martin Čech) b53006d_
+* Fixes for shed operation error handling (thanks to Martin Čech).
+`Pull Request 203`_,  `Pull Request 206`_
+* Fix for "smart" ``shed_diff`` not in the repository root directory
+(thanks to Peter Cock). `Pull Request 207`_, `Issue 205`_
+* Recursive ``shed_diff`` with directories not yet in Tool Shed.
+`Pull Request 208`_
+* Improve error handling and reporting for problematic ``--shed_target``
+values. `Issue 217`_
+* Fix typos in lint messages. `Issue 211`_
+---------------------
+0.11.1 (2015-05-12)
+---------------------
+* Fix default behavior for ``planemo lint`` to use current directory if
+explicit paths are not supplied. 1e3668a_
+---------------------
+0.11.0 (2015-05-12)
+---------------------
+* More compact syntax for defining multiple custom inclusions in ``.shed.yml``
+files - thanks to Peter Cock. `Issue 180`_, `Pull Request 185`_,
+`Pull Request 196`_
+* Prevent ambigous destinations when defining custom inclusions in
+``.shed.yml``- thanks to Peter Cock. `Pull Request 186`_
+* ``lint`` now warns if tool ids contain whitespace. `Pull Request 190`_
+* Handle empty tar-balls gracefully on older Python versions - thanks
+to Peter Cock. `Pull Request 187`_
+* Tweak quoting in ``cp`` command - thanks to Peter Cock. 6bcf699_
+* Fix regression causing testing to no longer produce "pretty" test
+results under certain circumstances. `Issue 188`_
+* Fix for recursive ``shed_diff`` folder naming. `Issue 192`_
+* Fix output definitions to ``tool_init`` command. `Issue 189`_
+---------------------
+0.10.0 (2015-05-06)
+---------------------
+* Extend ``shed_lint`` to check for valid actions in tool_dependencies.xml
+files. 8117e03_
+* Extend ``shed_lint`` to check for required files based on repository type.
+`Issue 156`_
+* Ignore common editor backup files during ``shed_upload``. `Issue 179`_
+* Fix missing file when installing from source via PyPI_. `Issue 181`_
+* Fix ``lint`` to verify ``data`` inputs specify a ``format`` attribute.
+8117e03_
+* Docstring fix thanks to `@peterjc`_. fe7ad46_
+---------------------
+0.9.0 (2015-05-03)
+---------------------
+* Add new logo to the README thanks to `@petrkadlec`_ from `puradesign.cz
+<http://puradesign.cz/en>`__ and `@carlfeberhard`_ from the Galaxy Project.
+`Issue 108`_
+* Implement smarter ``shed_diff`` command - it now produces a meaningful
+exit codes and doesn't report differences if these correspond to attributes
+that will be automatically populated by the Tool Shed. `Issue 167`_
+* Use new smarter ``shed_diff`` code to implement a new ``--check_diff``
+option for ``shed_upload`` - to check for meaningful differences before
+updating repositories. `Issue 168`_
+* Record git commit hash during ``shed_upload`` if the ``.shed.yml`` is
+located in a git repository. `Issue 170`_
+* Allow ``shed_`` operations to operate on git URLs directly. `Issue 169`_
+* Fail if missing file inclusion statements encountered during ``.shed.yml``
+repository resolution - bug reported by `@peterjc`_. `Issue 158`_
+* Improved exception handling for tool shed operations including new
+``--fail_fast`` command-line option. * `Issue 114`_, `Pull Request 173`_
+* Implement more validation when using the ``shed_init`` command. 1cd0e2d_
+* Add ``-r/--recursive`` option to ``shed_download`` and ``shed_diff``
+commands and allow these commands to work with ``.shed.yml`` files defining
+multipe repositories. 40a1f57_
+* Add ``--port`` option to the ``serve`` and ``tool_factory`` commands.
+15804be_
+* Fix problem introduced with `setup.py`_ during the 0.9.0 development cycle
+- thanks to `@peterjc`_. `Pull Request 171`_
+* Fix clone bug introduced during 0.9.0 development cycle - thanks to
+`@bgruening`_. `Pull Request 175`_
+---------------------
+0.8.4 (2015-04-30)
+---------------------
+* Fix for Travis CI testing picking up invalid tests (reported by `@takadonet`_). `Issue 161`_
+* Fix tar ordering for consistency (always sort by name) - thanks to `@peterjc`_.  `Pull Request 164`_, `Issue 159`_
+* Fix exception handling related to tool shed operations - thanks to `@peterjc`_. `Pull Request 155`_, b86fe1f_
+---------------------
+0.8.3 (2015-04-29)
+---------------------
+* Fix bug where ``shed_lint`` was not respecting the ``-r/--recursive`` flag.
+9ff0d2d_
+* Fix bug where planemo was producing tar files incompatible with the Tool
+Shed for package and suite repositories. a2ee135_
+---------------------
+0.8.2 (2015-04-29)
+---------------------
+* Fix bug with ``config_init`` command thanks to `@bgruening`_. `Pull Request 151`_
+* Fix unnessecary ``lint`` warning about ``parallelism`` tag reported by
+`@peterjc`_. 9bf1eab_
+---------------------
+0.8.1 (2015-04-28)
+---------------------
+* Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.
+---------------------
+0.8.0 (2015-04-27)
+---------------------
+* Implement the new ``shed_lint`` command that verifies various aspects of tool
+shed repositories - including XSD_ validation of ``repository_dependencies.xml``
+and ``tool_dependencies.xml`` files, best practices for README files, and the
+contents of ``.shed.yml`` files. This requires the lxml_ library to be available
+to Planemo or the application xmllint_ to be on its ``PATH``. `Pull Request 130`_
+`Issue 89`_ `Issue 91`_ 912df02_ d26929e_ 36ac6d8_
+* Option to enable experimental XSD_ based validation of tools when ``lint``
+is executed with the new ``--xsd`` flag. This validation occurs against the
+unofficial `Galaxy Tool XSD project <https://github.com/JeanFred/Galaxy-XSD>`__
+maintained by `@JeanFred`_. This requires the lxml_ library to be
+available to Planemo or the application xmllint_ to be on its ``PATH``.
+`Pull Request 130`_ 912df02_
+* Allow skipping specific linters when using the ``lint`` command using the new
+``--skip`` option. 26e3cdb_
+* Implement sophisticated options in ``.shed.yml`` to map a directory to many,
+custom Tool Shed repositories during shed operaitons such ``shed_upload``
+including automatically mapping tools to their own directories and automatically
+building suites repositories. `Pull Request 143`_
+* Make ``shed_upload`` more intelligent when building tar files so that package
+and suite repositories may have README files in source control and they will
+just be filtered out during upload. 53edd99_
+* Implement a new ``shed_init`` command that will help bootstrap ``.shed.yml``
+files in the specified directory. cc1a447_
+* Extend ``shed_init`` to automatically build a ``repository_rependencies.xml``
+file corresponding to a Galaxy workflow (``.ga`` file). `Issue 118`_ 988de1d_
+* In addition to a single file or directory, allow ``lint`` to be passed multiple
+files. 343902d_ `Issue 139`_
+* Add ``-r/--recursive`` option to ``shed_create`` and ``lint`` commands. 63cd431_
+01f2af9_
+* Improved output formatting and option to write diffs to a file for the
+``shed_diff`` command. 965511d_
+* Fix lint problem when using new Galaxy testing features such as expecting
+job failures and verifing job output. `Issue 138`_
+* Fix typo in ``test`` help thanks to first time contributor `@pvanheus`_.
+`Pull Request 129`_ 1982076_
+* Fix NPE on empty ``help`` element when linting tools. `Issue 124`_
+* Fix ``lint`` warnings when ``configfiles`` are defined in a tool. 1a85493_
+* Fix for empty ``.shed.yml`` files. b7d9e96_
+* Fix the ``test`` command for newer versions of nose_. 33294d2_
+* Update help content and documentation to be clear ``normalize`` should not
+be used to update the contents of tool files at this time. 08de8de_
+* Warn on unknown ``command`` attributes when linting tools (anything but
+``interpreter``). 4f61025_
+* Various design, documentation (including new documentation on Tool Shed
+`publishing <http://planemo.readthedocs.org/en/latest/publishing.html>`__),
+and testing related improvements (test coverage has risen from 65% to over
+80% during this release cycle).
+---------------------
+0.7.0 (2015-04-13)
+---------------------
+* Implement `shed_create` command to create Tool Shed repositories from
+``.shed.yml`` files (thanks to E. Rasche). `Pull Request 101`_
+* Allow automatic creation of missing repositories  during ``shed_upload``
+with the new ``--force_repository_creation`` flag (thanks to E. Rasche).
+`Pull Request 102`_
+* Allow specifying files to exclude in ``.shed.yml`` when creating tar files
+for ``shed_upload`` (thanks to Björn Grüning). `Pull Request 99`_
+* Resolve symbolic links when building Tool Shed tar files with
+``shed_upload`` (thanks to Dave Bouvier). `Pull Request 104`_
+* Add a `Contributor Code of Conduct
+<https://planemo.readthedocs.org/en/latest/conduct.html>`__.
+`Pull Request 113`_
+* Omit ``tool_test_output.json`` from Tool Shed tar file created with
+``shed_upload`` (thanks to Dave Bouvier). `Pull Request 111`_
+* Update required version of bioblend_ to ``0.5.3``. Fixed `Issue 88`_.
+* Initial work on implementing tests cases for Tool Shed functionality.
+182fe57_
+* Fix incorrect link in HTML test report (thanks to Martin Čech). 4c71299_
+* Download Galaxy from the new, official Github repository. 7c69bf6_
+* Update travis_test to install stable planemo from PyPI_. 39fedd2_
+* Enable caching on ``--install_galaxy`` by default (disable with
+``--no_cache_galaxy``). d755fe7_
+---------------------
+0.6.0 (2015-03-16)
+---------------------
+* Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc...
+* Fix ``tool_init`` to quote file names (thanks to Peter Cock).  `Pull Request 98`_.
+* Allow ignoring file patterns in ``.shed.yml`` (thanks to Björn Grüning). `Pull Request 99`_
+* Add ``--macros`` flag to ``tool_init`` command to generate a macro file as part of tool generation. ec6e30f_
+* Add linting of tag order for tool XML files. 4823c5e_
+* Add linting of ``stdio`` tags in tool XML files. 8207026_
+* More tests, much higher test coverage. 0bd4ff0_
+---------------------
+0.5.0 (2015-02-22)
+---------------------
+* Implement ``--version`` option. `Issue 78`_
+* Implement ``--no_cleanup`` option for ``test`` and ``serve`` commands to
+persist temp files. 2e41e0a_
+* Fix bug that left temp files undeleted. `Issue 80`_
+* More improvements to release process. fba3874_
+---------------------
+0.4.2 (2015-02-21)
+---------------------
+* Fix `setup.py`_ for installing non-Python data from PyPI_ (required newer
+for ``tool_factory`` command and reStructuredText linting). Thanks to
+Damion Dooley for the bug report. `Issue 83`_
+---------------------
+0.4.1 (2015-02-16)
+---------------------
+* Fix README.rst so it renders properly on PyPI_.
+---------------------
+0.4.0 (2015-02-16)
+---------------------
+* Implement ``tool_init`` command for bootstrapping creation of new
+tools (with `tutorial <http://planemo.readthedocs.org/en/latest/writing.html>`_.) 78f8274_
+* Implement ``normalize`` command for reorganizing tool XML and macro
+debugging. e8c1d45_
+* Implement ``tool_factory`` command to spin up Galaxy pre-configured the
+`Tool Factory`_. 9e746b4_
+* Added basic linting of ``command`` blocks. b8d90ab_
+* Improved linting of ``help`` blocks, including verifying valid
+`reStructuredText`. 411a8da_
+* Fix bug related to ``serve`` command not killing Galaxy properly when complete. 53a6766_
+* Have ``serve`` command display tools at the top level instead of in shallow sections. badc25f_
+* Add additional dependencies to ``setup.py`` more functionality works out
+of the box. 85b9614_
+* Fix terrible error message related to bioblend_ being unavailable.
+`Issue 70`_
+* Various smaller documentation and project structure improvements.
+---------------------
+0.3.1 (2015-02-15)
+---------------------
+* Fixes to get PyPI_ workflow working properly.
+---------------------
+0.3.0 (2015-02-13)
+---------------------
+* Add option (``-r``) to the ``shed_upload`` command to recursively upload
+subdirectories (thanks to E. Rasche). `Pull Request 68`_
+* Fix diff formatting in test reports (thanks to E. Rasche).
+`Pull Request 63`_
+* Grab updated test database to speed up testing (thanks to approach from
+E. Rasche and Dannon Baker). `Issue 61`_, dff4f33_
+* Fix test data command-line argument name (was ``test-data`` now it is
+``test_data``). 834bfb2_
+* Use ``tool_data_table_conf.xml.sample`` file if
+``tool_data_table_conf.xml.test`` is unavailable. Should allow some
+new tools to be tested without modifying Galaxy's global
+``tool_data_table_conf.xml`` file. ac4f828_
+---------------------
+0.2.0 (2015-01-13)
+---------------------
+* Improvements to way Planemo loads its own copy of Galaxy modules to prevent
+various conflicts when launching Galaxy from Planemo. `Pull Request 56`_
+* Allow setting various test output options in ``~/.planemo.yml`` and disabling
+JSON output. 21bb463_
+* More experimental Brew and Tool Shed options that should not be considered
+part of Planemo's stable API. See bit.ly/gxbrew1 for more details.
+* Fix ``project_init`` for BSD tar (thanks to Nitesh Turaga for the bug
+report.) a4110a8_
+* Documentation fixes for tool linting command (thanks to Nicola Soranzo).
+`Pull Request 51`_
+---------------------
+0.1.0 (2014-12-16)
+---------------------
+* Moved repository URL to https://github.com/galaxyproject/planemo.
+* Support for publishing to the Tool Shed. `Pull Request 6`_
+* Support for producing diffs (``shed_diff``) between local repositories and
+the Tool Shed (based on scripts by Peter Cock). `Pull Request 33`_
+* Use tool's local test data when available - add option for configuring
+``test-data`` target. `Pull Request 1`_
+* Support for testing tool features dependent on cached data. 44de95c_
+* Support for generating XUnit tool test reports. 82e8b1f_
+* Prettier HTML reports for tool tests. 05cc9f4_
+* Implement ``share_test`` command for embedding test result links in pull
+requests. `Pull Request 40`_
+* Fix for properly resolving links during Tool Shed publishing (thanks to Dave
+Bouvier). `Pull Request 29`_
+* Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061_
+* Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan
+Blankenberg). a2c13e4_
+* Automate more of Travis CI testing so the scripts added to tool repository
+can be smaller. 20a8680_
+* Documentation fixes for Travis CI (thanks to Peter Cock). `Pull Request 22`_,
+`Pull Request 23`_
+* Various documentation fixes (thanks to Martin Čech). 36f7cb1_, b9232e5_
+* Various smaller fixes for Docker support, tool linting, and documentation.
+---------------------
+0.0.1 (2014-10-04)
+---------------------
+* Initial work on the project - commands for testing, linting, serving Galaxy
+tools - and more experimental features involving Docker and Homebrew. 7d07782_
+.. github_links
+.. _Pull Request 1146: https://github.com/galaxyproject/planemo/pull/1146
+.. _Pull Request 1145: https://github.com/galaxyproject/planemo/pull/1145
+.. _Pull Request 1144: https://github.com/galaxyproject/planemo/pull/1144
+.. _Pull Request 1142: https://github.com/galaxyproject/planemo/pull/1142
+.. _Pull Request 1095: https://github.com/galaxyproject/planemo/pull/1095
+.. _Pull Request 1135: https://github.com/galaxyproject/planemo/pull/1135
+.. _Pull Request 1134: https://github.com/galaxyproject/planemo/pull/1134
+.. _Pull Request 1133: https://github.com/galaxyproject/planemo/pull/1133
+.. _Pull Request 1128: https://github.com/galaxyproject/planemo/pull/1128
+.. _Pull Request 1127: https://github.com/galaxyproject/planemo/pull/1127
+.. _Pull Request 1126: https://github.com/galaxyproject/planemo/pull/1126
+.. _Pull Request 1125: https://github.com/galaxyproject/planemo/pull/1125
+.. _Pull Request 1124: https://github.com/galaxyproject/planemo/pull/1124
+.. _Pull Request 1123: https://github.com/galaxyproject/planemo/pull/1123
+.. _Pull Request 1064: https://github.com/galaxyproject/planemo/pull/1064
+.. _Pull Request 1066: https://github.com/galaxyproject/planemo/pull/1066
+.. _Pull Request 1068: https://github.com/galaxyproject/planemo/pull/1068
+.. _Pull Request 1072: https://github.com/galaxyproject/planemo/pull/1072
+.. _Pull Request 1074: https://github.com/galaxyproject/planemo/pull/1074
+.. _Pull Request 1076: https://github.com/galaxyproject/planemo/pull/1076
+.. _Pull Request 1079: https://github.com/galaxyproject/planemo/pull/1079
+.. _Pull Request 1083: https://github.com/galaxyproject/planemo/pull/1083
+.. _Pull Request 1086: https://github.com/galaxyproject/planemo/pull/1086
+.. _Pull Request 1091: https://github.com/galaxyproject/planemo/pull/1091
+.. _Pull Request 1093: https://github.com/galaxyproject/planemo/pull/1093
+.. _Pull Request 1094: https://github.com/galaxyproject/planemo/pull/1094
+.. _Pull Request 1096: https://github.com/galaxyproject/planemo/pull/1096
+.. _Pull Request 1099: https://github.com/galaxyproject/planemo/pull/1099
+.. _Pull Request 1101: https://github.com/galaxyproject/planemo/pull/1101
+.. _Pull Request 1102: https://github.com/galaxyproject/planemo/pull/1102
+.. _Pull Request 1108: https://github.com/galaxyproject/planemo/pull/1108
+.. _Pull Request 1110: https://github.com/galaxyproject/planemo/pull/1110
+.. _Pull Request 1114: https://github.com/galaxyproject/planemo/pull/1114
+.. _Pull Request 1115: https://github.com/galaxyproject/planemo/pull/1115
+.. _Pull Request 1116: https://github.com/galaxyproject/planemo/pull/1116
+.. _Pull Request 1118: https://github.com/galaxyproject/planemo/pull/1118
+.. _Pull Request 1120: https://github.com/galaxyproject/planemo/pull/1120
+.. _Pull Request 1121: https://github.com/galaxyproject/planemo/pull/1121
+.. _Pull Request 821: https://github.com/galaxyproject/planemo/pull/821
+.. _Pull Request 1052: https://github.com/galaxyproject/planemo/pull/1052
+.. _Pull Request 1061: https://github.com/galaxyproject/planemo/pull/1061
+.. _Pull Request 1062: https://github.com/galaxyproject/planemo/pull/1062
+.. _Pull Request 1060: https://github.com/galaxyproject/planemo/pull/1060
+.. _Pull Request 1059: https://github.com/galaxyproject/planemo/pull/1059
+.. _Pull Request 1058: https://github.com/galaxyproject/planemo/pull/1058
+.. _Pull Request 1051: https://github.com/galaxyproject/planemo/pull/1051
+.. _Pull Request 1049: https://github.com/galaxyproject/planemo/pull/1049
+.. _Pull Request 1046: https://github.com/galaxyproject/planemo/pull/1046
+.. _Pull Request 1044: https://github.com/galaxyproject/planemo/pull/1044
+.. _Pull Request 1043: https://github.com/galaxyproject/planemo/pull/1043
+.. _Pull Request 1042: https://github.com/galaxyproject/planemo/pull/1042
+.. _Pull Request 1041: https://github.com/galaxyproject/planemo/pull/1041
+.. _Pull Request 1040: https://github.com/galaxyproject/planemo/pull/1040
+.. _Pull Request 1038: https://github.com/galaxyproject/planemo/pull/1038
+.. _Pull Request 1037: https://github.com/galaxyproject/planemo/pull/1037
+.. _Pull Request 1036: https://github.com/galaxyproject/planemo/pull/1036
+.. _Pull Request 1034: https://github.com/galaxyproject/planemo/pull/1034
+.. _Pull Request 1032: https://github.com/galaxyproject/planemo/pull/1032
+.. _Pull Request 1029: https://github.com/galaxyproject/planemo/pull/1029
+.. _Pull Request 1028: https://github.com/galaxyproject/planemo/pull/1028
+.. _Pull Request 1031: https://github.com/galaxyproject/planemo/pull/1031
+.. _Pull Request 1026: https://github.com/galaxyproject/planemo/pull/1026
+.. _Pull Request 994: https://github.com/galaxyproject/planemo/pull/994
+.. _Pull Request 993: https://github.com/galaxyproject/planemo/pull/993
+.. _Pull Request 1001: https://github.com/galaxyproject/planemo/pull/1001
+.. _Pull Request 1003: https://github.com/galaxyproject/planemo/pull/1003
+.. _Pull Request 900: https://github.com/galaxyproject/planemo/pull/900
+.. _Pull Request 1008: https://github.com/galaxyproject/planemo/pull/1008
+.. _Pull Request 1006: https://github.com/galaxyproject/planemo/pull/1006
+.. _Pull Request 1011: https://github.com/galaxyproject/planemo/pull/1011
+.. _Pull Request 1017: https://github.com/galaxyproject/planemo/pull/1017
+.. _Pull Request 1015: https://github.com/galaxyproject/planemo/pull/1015
+.. _Pull Request 1013: https://github.com/galaxyproject/planemo/pull/1013
+.. _Pull Request 1020: https://github.com/galaxyproject/planemo/pull/1020
+.. _Pull Request 1021: https://github.com/galaxyproject/planemo/pull/1021
+.. _Pull Request 1022: https://github.com/galaxyproject/planemo/pull/1022
+.. _Pull Request 1023: https://github.com/galaxyproject/planemo/pull/1023
+.. _Pull Request 1025: https://github.com/galaxyproject/planemo/pull/1025
+.. _Pull Request 1024: https://github.com/galaxyproject/planemo/pull/1024
+.. _Pull Request 991: https://github.com/galaxyproject/planemo/pull/991
+.. _Pull Request 988: https://github.com/galaxyproject/planemo/pull/988
+.. _Pull Request 989: https://github.com/galaxyproject/planemo/pull/989
+.. _Pull Request 985: https://github.com/galaxyproject/planemo/pull/985
+.. _Pull Request 984: https://github.com/galaxyproject/planemo/pull/984
+.. _Pull Request 986: https://github.com/galaxyproject/planemo/pull/986
+.. _Pull Request 983: https://github.com/galaxyproject/planemo/pull/983
+.. _Pull Request 982: https://github.com/galaxyproject/planemo/pull/982
+.. _Pull Request 980: https://github.com/galaxyproject/planemo/pull/980
+.. _Pull Request 978: https://github.com/galaxyproject/planemo/pull/978
+.. _Pull Request 979: https://github.com/galaxyproject/planemo/pull/979
+.. _Pull Request 977: https://github.com/galaxyproject/planemo/pull/977
+.. _Pull Request 975: https://github.com/galaxyproject/planemo/pull/975
+.. _Pull Request 974: https://github.com/galaxyproject/planemo/pull/974
+.. _Pull Request 976: https://github.com/galaxyproject/planemo/pull/976
+.. _Pull Request 972: https://github.com/galaxyproject/planemo/pull/972
+.. _Pull Request 973: https://github.com/galaxyproject/planemo/pull/973
+.. _Pull Request 971: https://github.com/galaxyproject/planemo/pull/971
+.. _Pull Request 970: https://github.com/galaxyproject/planemo/pull/970
+.. _Pull Request 968: https://github.com/galaxyproject/planemo/pull/968
+.. _1ab8530: https://github.com/galaxyproject/planemo/commit/1ab8530
+.. _Pull Request 966: https://github.com/galaxyproject/planemo/pull/966
+.. _Pull Request 964: https://github.com/galaxyproject/planemo/pull/964
+.. _Pull Request 963: https://github.com/galaxyproject/planemo/pull/963
+.. _Pull Request 959: https://github.com/galaxyproject/planemo/pull/959
+.. _Pull Request 958: https://github.com/galaxyproject/planemo/pull/958
+.. _Pull Request 950: https://github.com/galaxyproject/planemo/pull/950
+.. _Pull Request 944: https://github.com/galaxyproject/planemo/pull/944
+.. _Pull Request 926: https://github.com/galaxyproject/planemo/pull/926
+.. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937
+.. _Pull Request 938: https://github.com/galaxyproject/planemo/pull/938
+.. _Pull Request 943: https://github.com/galaxyproject/planemo/pull/943
+.. _Pull Request 940: https://github.com/galaxyproject/planemo/pull/940
+.. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937
+.. _Pull Request 935: https://github.com/galaxyproject/planemo/pull/935
+.. _Pull Request 931: https://github.com/galaxyproject/planemo/pull/931
+.. _Pull Request 930: https://github.com/galaxyproject/planemo/pull/930
+.. _Pull Request 913: https://github.com/galaxyproject/planemo/pull/913
+.. _Pull Request 917: https://github.com/galaxyproject/planemo/pull/917
+.. _Pull Request 921: https://github.com/galaxyproject/planemo/pull/921
+.. _Pull Request 918: https://github.com/galaxyproject/planemo/pull/918
+.. _Pull Request 924: https://github.com/galaxyproject/planemo/pull/924
+.. _Pull Request 925: https://github.com/galaxyproject/planemo/pull/925
+.. _Pull Request 912: https://github.com/galaxyproject/planemo/pull/912
+.. _Pull Request 915: https://github.com/galaxyproject/planemo/pull/915
+.. _Pull Request 914: https://github.com/galaxyproject/planemo/pull/914
+.. _07dc6e0: https://github.com/galaxyproject/planemo/commit/07dc6e0
+.. _Pull Request 910: https://github.com/galaxyproject/planemo/pull/910
+.. _Pull Request 909: https://github.com/galaxyproject/planemo/pull/909
+.. _Pull Request 908: https://github.com/galaxyproject/planemo/pull/908
+.. _Pull Request 907: https://github.com/galaxyproject/planemo/pull/907
+.. _Pull Request 906: https://github.com/galaxyproject/planemo/pull/906
+.. _Pull Request 902: https://github.com/galaxyproject/planemo/pull/902
+.. _Pull Request 895: https://github.com/galaxyproject/planemo/pull/895
+.. _Issue 845: https://github.com/galaxyproject/planemo/issues/845
+.. _Issue 898: https://github.com/galaxyproject/planemo/issues/898
+.. _Pull Request 899: https://github.com/galaxyproject/planemo/pull/899
+.. _Pull Request 896: https://github.com/galaxyproject/planemo/pull/896
+.. _Pull Request 894: https://github.com/galaxyproject/planemo/pull/894
+.. _Pull Request 876: https://github.com/galaxyproject/planemo/pull/876
+.. _Pull Request 893: https://github.com/galaxyproject/planemo/pull/893
+.. _Pull Request 892: https://github.com/galaxyproject/planemo/pull/892
+.. _Pull Request 891: https://github.com/galaxyproject/planemo/pull/891
+.. _Pull Request 889: https://github.com/galaxyproject/planemo/pull/889
+.. _Pull Request 888: https://github.com/galaxyproject/planemo/pull/888
+.. _Pull Request 887: https://github.com/galaxyproject/planemo/pull/887
+.. _Pull Request 882: https://github.com/galaxyproject/planemo/pull/882
+.. _Pull Request 877: https://github.com/galaxyproject/planemo/pull/877
+.. _Pull Request 874: https://github.com/galaxyproject/planemo/pull/874
+.. _Pull Request 871: https://github.com/galaxyproject/planemo/pull/871
+.. _Pull Request 870: https://github.com/galaxyproject/planemo/pull/870
+.. _Pull Request 864: https://github.com/galaxyproject/planemo/pull/864
+.. _Pull Request 867: https://github.com/galaxyproject/planemo/pull/867
+.. _Pull Request 868: https://github.com/galaxyproject/planemo/pull/868
+.. _bad810a: https://github.com/galaxyproject/planemo/commit/bad810a
+.. _Pull Request 851: https://github.com/galaxyproject/planemo/pull/851
+.. _Pull Request 856: https://github.com/galaxyproject/planemo/pull/856
+.. _Pull Request 860: https://github.com/galaxyproject/planemo/pull/860
+.. _Pull Request 866: https://github.com/galaxyproject/planemo/pull/866
+.. _Pull Request 861: https://github.com/galaxyproject/planemo/pull/861
+.. _324c776: https://github.com/galaxyproject/planemo/commit/324c776
+.. _72d2ca7: https://github.com/galaxyproject/planemo/commit/72d2ca7
+.. _b12b117: https://github.com/galaxyproject/planemo/commit/b12b117
+.. _016b923: https://github.com/galaxyproject/planemo/commit/016b923
+.. _2002b49: https://github.com/galaxyproject/planemo/commit/2002b49
+.. _Pull Request 843: https://github.com/galaxyproject/planemo/pull/843
+.. _Pull Request 842: https://github.com/galaxyproject/planemo/pull/842
+.. _Pull Request 841: https://github.com/galaxyproject/planemo/pull/841
+.. _Pull Request 847: https://github.com/galaxyproject/planemo/pull/847
+.. _Pull Request 848: https://github.com/galaxyproject/planemo/pull/848
+.. _Pull Request 849: https://github.com/galaxyproject/planemo/pull/849
+.. _Pull Request 850: https://github.com/galaxyproject/planemo/pull/850
+.. _Pull Request 836: https://github.com/galaxyproject/planemo/pull/836
+.. _Pull Request 833: https://github.com/galaxyproject/planemo/pull/833
+.. _Pull Request 837: https://github.com/galaxyproject/planemo/pull/837
+.. _Pull Request 840: https://github.com/galaxyproject/planemo/pull/840
+.. _Pull Request 838: https://github.com/galaxyproject/planemo/pull/838
+.. _Pull Request 834: https://github.com/galaxyproject/planemo/pull/834
+.. _Pull Request 835: https://github.com/galaxyproject/planemo/pull/835
+.. _347c622: https://github.com/galaxyproject/planemo/commit/347c622
+.. _Pull Request 832: https://github.com/galaxyproject/planemo/pull/832
+.. _Pull Request 831: https://github.com/galaxyproject/planemo/pull/831
+.. _Pull Request 830: https://github.com/galaxyproject/planemo/pull/830
+.. _Pull Request 829: https://github.com/galaxyproject/planemo/pull/829
+.. _Pull Request 828: https://github.com/galaxyproject/planemo/pull/828
+.. _Pull Request 826: https://github.com/galaxyproject/planemo/pull/826
+.. _Pull Request 827: https://github.com/galaxyproject/planemo/pull/827
+.. _Pull Request 825: https://github.com/galaxyproject/planemo/pull/825
+.. _Pull Request 820: https://github.com/galaxyproject/planemo/pull/820
+.. _Pull Request 823: https://github.com/galaxyproject/planemo/pull/823
+.. _Pull Request 822: https://github.com/galaxyproject/planemo/pull/822
+.. _a5c72e3: https://github.com/galaxyproject/planemo/commit/a5c72e3
+.. _Pull Request 818: https://github.com/galaxyproject/planemo/pull/818
+.. _Pull Request 816: https://github.com/galaxyproject/planemo/pull/816
+.. _Pull Request 817: https://github.com/galaxyproject/planemo/pull/817
+.. _Pull Request 795: https://github.com/galaxyproject/planemo/pull/795
+.. _Pull Request 799: https://github.com/galaxyproject/planemo/pull/799
+.. _Pull Request 800: https://github.com/galaxyproject/planemo/pull/800
+.. _Pull Request 781: https://github.com/galaxyproject/planemo/pull/781
+.. _Pull Request 801: https://github.com/galaxyproject/planemo/pull/801
+.. _Pull Request 802: https://github.com/galaxyproject/planemo/pull/802
+.. _Pull Request 803: https://github.com/galaxyproject/planemo/pull/803
+.. _Pull Request 805: https://github.com/galaxyproject/planemo/pull/805
+.. _Pull Request 806: https://github.com/galaxyproject/planemo/pull/806
+.. _Pull Request 809: https://github.com/galaxyproject/planemo/pull/809
+.. _Pull Request 810: https://github.com/galaxyproject/planemo/pull/810
+.. _Pull Request 787: https://github.com/galaxyproject/planemo/pull/787
+.. _Pull Request 792: https://github.com/galaxyproject/planemo/pull/792
+.. _dc443d6: https://github.com/galaxyproject/planemo/commit/dc443d6
+.. _8cfe9e9: https://github.com/galaxyproject/planemo/commit/8cfe9e9
+.. _41f7df1: https://github.com/galaxyproject/planemo/commit/41f7df1
+.. _Pull Request 790: https://github.com/galaxyproject/planemo/pull/790
+.. _Pull Request 776: https://github.com/galaxyproject/planemo/pull/776
+.. _Pull Request 774: https://github.com/galaxyproject/planemo/pull/774
+.. _Pull Request 773: https://github.com/galaxyproject/planemo/pull/773
+.. _Pull Request 771: https://github.com/galaxyproject/planemo/pull/771
+.. _Pull Request 770: https://github.com/galaxyproject/planemo/pull/770
+.. _Pull Request 769: https://github.com/galaxyproject/planemo/pull/769
+.. _Pull Request 768: https://github.com/galaxyproject/planemo/pull/768
+.. _Pull Request 764: https://github.com/galaxyproject/planemo/pull/764
+.. _Pull Request 761: https://github.com/galaxyproject/planemo/pull/761
+.. _Pull Request 759: https://github.com/galaxyproject/planemo/pull/759
+.. _Pull Request 756: https://github.com/galaxyproject/planemo/pull/756
+.. _Pull Request 753: https://github.com/galaxyproject/planemo/pull/753
+.. _Pull Request 747: https://github.com/galaxyproject/planemo/pull/747
+.. _Pull Request 745: https://github.com/galaxyproject/planemo/pull/745
+.. _Pull Request 743: https://github.com/galaxyproject/planemo/pull/743
+.. _Pull Request 739: https://github.com/galaxyproject/planemo/pull/739
+.. _Pull Request 738: https://github.com/galaxyproject/planemo/pull/738
+.. _Pull Request 725: https://github.com/galaxyproject/planemo/pull/725
+.. _Pull Request 727: https://github.com/galaxyproject/planemo/pull/727
+.. _Pull Request 729: https://github.com/galaxyproject/planemo/pull/729
+.. _Pull Request 730: https://github.com/galaxyproject/planemo/pull/730
+.. _Pull Request 731: https://github.com/galaxyproject/planemo/pull/731
+.. _Pull Request 733: https://github.com/galaxyproject/planemo/pull/733
+.. _Pull Request 732: https://github.com/galaxyproject/planemo/pull/732
+.. _Pull Request 704: https://github.com/galaxyproject/planemo/pull/704
+.. _Pull Request 709: https://github.com/galaxyproject/planemo/pull/709
+.. _Pull Request 715: https://github.com/galaxyproject/planemo/pull/715
+.. _Pull Request 716: https://github.com/galaxyproject/planemo/pull/716
+.. _Pull Request 720: https://github.com/galaxyproject/planemo/pull/720
+.. _Pull Request 723: https://github.com/galaxyproject/planemo/pull/723
+.. _8a608e0: https://github.com/galaxyproject/planemo/commit/8a608e0
+.. _ecc1bc2: https://github.com/galaxyproject/planemo/commit/ecc1bc2
+.. _Pull Request 702: https://github.com/galaxyproject/planemo/pull/702
+.. _Pull Request 701: https://github.com/galaxyproject/planemo/pull/701
+.. _Pull Request 699: https://github.com/galaxyproject/planemo/pull/699
+.. _91b6fa0: https://github.com/galaxyproject/planemo/commit/91b6fa0
+.. _904d77a: https://github.com/galaxyproject/planemo/commit/904d77a
+.. _9636682: https://github.com/galaxyproject/planemo/commit/9636682
+.. _475104c: https://github.com/galaxyproject/planemo/commit/475104c
+.. _Pull Request 684: https://github.com/galaxyproject/planemo/pull/684
+.. _Pull Request 687: https://github.com/galaxyproject/planemo/pull/687
+.. _Pull Request 688: https://github.com/galaxyproject/planemo/pull/688
+.. _Pull Request 689: https://github.com/galaxyproject/planemo/pull/689
+.. _Pull Request 690: https://github.com/galaxyproject/planemo/pull/690
+.. _Issue 494: https://github.com/galaxyproject/planemo/issues/494
+.. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665
+.. _Pull Request 675: https://github.com/galaxyproject/planemo/pull/675
+.. _Pull Request 680: https://github.com/galaxyproject/planemo/pull/680
+.. _Pull Request 682: https://github.com/galaxyproject/planemo/pull/682
+.. _Pull Request 683: https://github.com/galaxyproject/planemo/pull/683
+.. _Pull Request 662: https://github.com/galaxyproject/planemo/pull/662
+.. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665
+.. _Pull Request 664: https://github.com/galaxyproject/planemo/pull/664
+.. _84c4a73: https://github.com/galaxyproject/planemo/commit/84c4a73
+.. _32f41c9: https://github.com/galaxyproject/planemo/commit/32f41c9
+.. _3129216: https://github.com/galaxyproject/planemo/commit/3129216
+.. _b4ae44d: https://github.com/galaxyproject/planemo/commit/b4ae44d
+.. _3c95b7b: https://github.com/galaxyproject/planemo/commit/3c95b7b
+.. _06bcf19: https://github.com/galaxyproject/planemo/commit/06bcf19
+.. _525de8f: https://github.com/galaxyproject/planemo/commit/525de8f
+.. _9867e56: https://github.com/galaxyproject/planemo/commit/9867e56
+.. _ce0dc4e: https://github.com/galaxyproject/planemo/commit/ce0dc4e
+.. _4c0f100: https://github.com/galaxyproject/planemo/commit/4c0f100
+.. _04238d3: https://github.com/galaxyproject/planemo/commit/04238d3
+.. _ced5ce2: https://github.com/galaxyproject/planemo/commit/ced5ce2
+.. _9ab4a0d: https://github.com/galaxyproject/planemo/commit/9ab4a0d
+.. _Pull Request 640: https://github.com/galaxyproject/planemo/pull/640
+.. _0a1abfe: https://github.com/galaxyproject/planemo/commit/0a1abfe
+.. _Pull Request 649: https://github.com/galaxyproject/planemo/pull/649
+.. _Issue 620: https://github.com/galaxyproject/planemo/issues/620
+.. _Pull Request 643: https://github.com/galaxyproject/planemo/pull/643
+.. _Pull Request 642: https://github.com/galaxyproject/planemo/pull/642
+.. _Pull Request 641: https://github.com/galaxyproject/planemo/pull/641
+.. _Pull Request 639: https://github.com/galaxyproject/planemo/pull/639
+.. _Pull Request 635: https://github.com/galaxyproject/planemo/pull/635
+.. _Issue 633: https://github.com/galaxyproject/planemo/issues/633
+.. _Issue 260: https://github.com/galaxyproject/planemo/issues/260
+.. _Pull Request 638: https://github.com/galaxyproject/planemo/pull/638
+.. _6638caa: https://github.com/galaxyproject/planemo/commit/6638caa
+.. _8faf661: https://github.com/galaxyproject/planemo/commit/8faf661
+.. _e343b67: https://github.com/galaxyproject/planemo/commit/e343b67
+.. _Pull Request 634: https://github.com/galaxyproject/planemo/pull/634
+.. _84ebc1f: https://github.com/galaxyproject/planemo/commit/84ebc1f
+.. _03c9658: https://github.com/galaxyproject/planemo/commit/03c9658
+.. _08c067c: https://github.com/galaxyproject/planemo/commit/08c067c
+.. _fca4183: https://github.com/galaxyproject/planemo/commit/fca4183
+.. _Issue 564: https://github.com/galaxyproject/planemo/issues/564
+.. _Pull Request 628: https://github.com/galaxyproject/planemo/pull/628
+.. _Issue 515: https://github.com/galaxyproject/planemo/issues/515
+.. _Pull Request 629: https://github.com/galaxyproject/planemo/pull/629
+.. _Pull Request 614: https://github.com/galaxyproject/planemo/pull/614
+.. _32acd68: https://github.com/galaxyproject/planemo/commit/32acd68
+.. _4595953: https://github.com/galaxyproject/planemo/commit/4595953
+.. _Pull Request 612: https://github.com/galaxyproject/planemo/pull/612
+.. _Issue 388: https://github.com/galaxyproject/planemo/issues/388
+.. _Pull Request 610: https://github.com/galaxyproject/planemo/pull/610
+.. _Pull Request 609: https://github.com/galaxyproject/planemo/pull/609
+.. _Pull Request 608: https://github.com/galaxyproject/planemo/pull/608
+.. _Pull Request 605: https://github.com/galaxyproject/planemo/pull/605
+.. _Pull Request 606: https://github.com/galaxyproject/planemo/pull/606
+.. _Pull Request 602: https://github.com/galaxyproject/planemo/pull/602
+.. _Pull Request 570: https://github.com/galaxyproject/planemo/pull/570
+.. _9228416: https://github.com/galaxyproject/planemo/commit/9228416
+.. _50d3c4a: https://github.com/galaxyproject/planemo/commit/50d3c4a
+.. _Issue 578: https://github.com/galaxyproject/planemo/issues/578
+.. _Pull Request 591: https://github.com/galaxyproject/planemo/pull/591
+.. _Pull Request 590: https://github.com/galaxyproject/planemo/pull/590
+.. _f0da66f: https://github.com/galaxyproject/planemo/commit/f0da66f
+.. _19b2ee9: https://github.com/galaxyproject/planemo/commit/19b2ee9
+.. _9da8387: https://github.com/galaxyproject/planemo/commit/9da8387
+.. _08cef54: https://github.com/galaxyproject/planemo/commit/08cef54
+.. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc
+.. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc
+.. _Issue 573: https://github.com/galaxyproject/planemo/issues/573
+.. _Pull Request 579: https://github.com/galaxyproject/planemo/pull/579
+.. _ccdd2d5: https://github.com/galaxyproject/planemo/commit/ccdd2d5
+.. _e925ba1: https://github.com/galaxyproject/planemo/commit/e925ba1
+.. _ea5324f: https://github.com/galaxyproject/planemo/commit/ea5324f
+.. _ca88b0c: https://github.com/galaxyproject/planemo/commit/ca88b0c
+.. _b6d8294: https://github.com/galaxyproject/planemo/commit/b6d8294
+.. _6a6f164: https://github.com/galaxyproject/planemo/commit/6a6f164
+.. _d6da3a8: https://github.com/galaxyproject/planemo/commit/d6da3a8
+.. _1ef05d2: https://github.com/galaxyproject/planemo/commit/1ef05d2
+.. _7cca2e4: https://github.com/galaxyproject/planemo/commit/7cca2e4
+.. _34538de: https://github.com/galaxyproject/planemo/commit/34538de
+.. _6f91719: https://github.com/galaxyproject/planemo/commit/6f91719
+.. _Pull Request 566: https://github.com/galaxyproject/planemo/pull/566
+.. _Pull Request 559: https://github.com/galaxyproject/planemo/pull/559
+.. _Pull Request 561: https://github.com/galaxyproject/planemo/pull/561
+.. _Pull Request 565: https://github.com/galaxyproject/planemo/pull/565
+.. _Pull Request 555: https://github.com/galaxyproject/planemo/pull/555
+.. _a8e797b: https://github.com/galaxyproject/planemo/commit/a8e797b
+.. _6c03de8: https://github.com/galaxyproject/planemo/commit/6c03de8
+.. _ef4b9f4: https://github.com/galaxyproject/planemo/commit/ef4b9f4
+.. _f7b6c7e: https://github.com/galaxyproject/planemo/commit/f7b6c7e
+.. _07d94bd: https://github.com/galaxyproject/planemo/commit/07d94bd
+.. _ca19910: https://github.com/galaxyproject/planemo/commit/ca19910
+.. _24008ab: https://github.com/galaxyproject/planemo/commit/24008ab
+.. _ce44e87: https://github.com/galaxyproject/planemo/commit/ce44e87
+.. _Pull Request 550: https://github.com/galaxyproject/planemo/pull/550
+.. _c2204b3: https://github.com/galaxyproject/planemo/commit/c2204b3
+.. _c262b6d: https://github.com/galaxyproject/planemo/commit/c262b6d
+.. _Pull Request 539: https://github.com/galaxyproject/planemo/pull/539
+.. _Pull Request 541: https://github.com/galaxyproject/planemo/pull/541
+.. _Pull Request 540: https://github.com/galaxyproject/planemo/pull/540
+.. _Pull Request 545: https://github.com/galaxyproject/planemo/pull/545
+.. _Pull Request 546: https://github.com/galaxyproject/planemo/pull/546
+.. _3ceaa40: https://github.com/galaxyproject/planemo/commit/3ceaa40
+.. _057f4f0: https://github.com/galaxyproject/planemo/commit/057f4f0
+.. _9fdf490: https://github.com/galaxyproject/planemo/commit/9fdf490
+.. _8c088c6: https://github.com/galaxyproject/planemo/commit/8c088c6
+.. _e2398fb: https://github.com/galaxyproject/planemo/commit/e2398fb
+.. _Pull Request 526: https://github.com/galaxyproject/planemo/pull/526
+.. _Pull Request 528: https://github.com/galaxyproject/planemo/pull/528
+.. _Pull Request 525: https://github.com/galaxyproject/planemo/pull/525
+.. _a811e65: https://github.com/galaxyproject/planemo/commit/a811e65
+.. _Pull Request 521: https://github.com/galaxyproject/planemo/pull/521
+.. _a066afb: https://github.com/galaxyproject/planemo/commit/a066afb
+.. _Pull Request 512: https://github.com/galaxyproject/planemo/pull/512
+.. _08bb354: https://github.com/galaxyproject/planemo/commit/08bb354
+.. _Pull Request 513: https://github.com/galaxyproject/planemo/pull/513
+.. _Pull Request 510: https://github.com/galaxyproject/planemo/pull/510
+.. _e890ab5: https://github.com/galaxyproject/planemo/commit/e890ab5
+.. _Pull Request 507: https://github.com/galaxyproject/planemo/pull/507
+.. _d53bcd6: https://github.com/galaxyproject/planemo/commit/d53bcd6
+.. _725b232: https://github.com/galaxyproject/planemo/commit/725b232
+.. _Pull Request 498: https://github.com/galaxyproject/planemo/pull/498
+.. _01584c5: https://github.com/galaxyproject/planemo/commit/01584c5
+.. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9
+.. _0298510: https://github.com/galaxyproject/planemo/commit/0298510
+.. _02a08a0: https://github.com/galaxyproject/planemo/commit/02a08a0
+.. _05cc9f4: https://github.com/galaxyproject/planemo/commit/05cc9f485ee87bc344e3f43bb1cfd025a16a6247
+.. _069e7ba: https://github.com/galaxyproject/planemo/commit/069e7ba
+.. _08de8de: https://github.com/galaxyproject/planemo/commit/08de8de
+.. _0bd4ff0: https://github.com/galaxyproject/planemo/commit/0bd4ff0
+.. _0e4f70a: https://github.com/galaxyproject/planemo/commit/0e4f70a
+.. _0f8cb10: https://github.com/galaxyproject/planemo/commit/0f8cb10
+.. _13a5ae7: https://github.com/galaxyproject/planemo/commit/13a5ae7
+.. _15804be: https://github.com/galaxyproject/planemo/commit/15804be
+.. _15d33c7: https://github.com/galaxyproject/planemo/commit/15d33c7
+.. _182fe57: https://github.com/galaxyproject/planemo/commit/182fe57
+.. _1927168: https://github.com/galaxyproject/planemo/commit/1927168
+.. _1982076: https://github.com/galaxyproject/planemo/commit/1982076
+.. _19900a6: https://github.com/galaxyproject/planemo/commit/19900a6
+.. _1a157d4: https://github.com/galaxyproject/planemo/commit/1a157d4
+.. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493
+.. _1c6cfbb: https://github.com/galaxyproject/planemo/commit/1c6cfbb
+.. _1c7ee5b: https://github.com/galaxyproject/planemo/commit/1c7ee5b
+.. _1cd0e2d: https://github.com/galaxyproject/planemo/commit/1cd0e2d
+.. _1e3668a: https://github.com/galaxyproject/planemo/commit/1e3668a
+.. _2052db0: https://github.com/galaxyproject/planemo/commit/2052db0
+.. _20a8680: https://github.com/galaxyproject/planemo/commit/20a86807cb7ea87db2dbc0197ae08a40df3ab2bc
+.. _21bb463: https://github.com/galaxyproject/planemo/commit/21bb463ad6c321bcb669603049a5e89a69766ad9
+.. _25ef0d5: https://github.com/galaxyproject/planemo/commit/25ef0d5
+.. _26e378e: https://github.com/galaxyproject/planemo/commit/26e378e
+.. _26e3cdb: https://github.com/galaxyproject/planemo/commit/26e3cdb
+.. _2a7c792: https://github.com/galaxyproject/planemo/commit/2a7c792
+.. _2ae2b49: https://github.com/galaxyproject/planemo/commit/2ae2b49
+.. _2e41e0a: https://github.com/galaxyproject/planemo/commit/2e41e0a
+.. _2f66fc3: https://github.com/galaxyproject/planemo/commit/2f66fc3
+.. _30a9c3f: https://github.com/galaxyproject/planemo/commit/30a9c3f
+.. _32c6e7f: https://github.com/galaxyproject/planemo/commit/32c6e7f78bb8f04d27615cfd8948b0b89f27b4e6
+.. _33294d2: https://github.com/galaxyproject/planemo/commit/33294d2
+.. _334f2d4: https://github.com/galaxyproject/planemo/commit/334f2d4
+.. _343902d: https://github.com/galaxyproject/planemo/commit/343902d
+.. _3499ca0: https://github.com/galaxyproject/planemo/commit/3499ca0a15affcaf8ac9efc55880da40b0626679
+.. _358a42c: https://github.com/galaxyproject/planemo/commit/358a42c
+.. _36ac6d8: https://github.com/galaxyproject/planemo/commit/36ac6d8
+.. _36f7cb1: https://github.com/galaxyproject/planemo/commit/36f7cb114f77731f90860d513a930e10ce5c1ba5
+.. _37dcc07: https://github.com/galaxyproject/planemo/commit/37dcc07
+.. _39fedd2: https://github.com/galaxyproject/planemo/commit/39fedd2
+.. _3f4ab44: https://github.com/galaxyproject/planemo/commit/3f4ab44
+.. _40a1f57: https://github.com/galaxyproject/planemo/commit/40a1f57
+.. _411a8da: https://github.com/galaxyproject/planemo/commit/411a8da21c92ba37c7ad95bfce9928d9b8fd998e
+.. _44de95c: https://github.com/galaxyproject/planemo/commit/44de95c0d7087a5822941959f9a062f6382e329b
+.. _45135ff: https://github.com/galaxyproject/planemo/commit/45135ff
+.. _4823c5e: https://github.com/galaxyproject/planemo/commit/4823c5e
+.. _49c5c1e: https://github.com/galaxyproject/planemo/commit/49c5c1e
+.. _4c71299: https://github.com/galaxyproject/planemo/commit/4c71299
+.. _4cd571c: https://github.com/galaxyproject/planemo/commit/4cd571c
+.. _4d29bf1: https://github.com/galaxyproject/planemo/commit/4d29bf1
+.. _4d6f7d9: https://github.com/galaxyproject/planemo/commit/4d6f7d9
+.. _4e1377c: https://github.com/galaxyproject/planemo/commit/4e1377c
+.. _4f61025: https://github.com/galaxyproject/planemo/commit/4f61025
+.. _508dce7: https://github.com/galaxyproject/planemo/commit/508dce7
+.. _53a6766: https://github.com/galaxyproject/planemo/commit/53a6766cdebdddc976189f6dc6a264bb4105c4bf
+.. _53edd99: https://github.com/galaxyproject/planemo/commit/53edd99
+.. _552059f: https://github.com/galaxyproject/planemo/commit/552059f
+.. _572e754: https://github.com/galaxyproject/planemo/commit/572e754
+.. _5b97f2e: https://github.com/galaxyproject/planemo/commit/5b97f2e
+.. _5d08b67: https://github.com/galaxyproject/planemo/commit/5d08b67
+.. _5d7db92: https://github.com/galaxyproject/planemo/commit/5d7db92
+.. _5e0b6d1: https://github.com/galaxyproject/planemo/commit/5e0b6d1
+.. _63cd431: https://github.com/galaxyproject/planemo/commit/63cd431
+.. _63e456c: https://github.com/galaxyproject/planemo/commit/63e456c
+.. _6409449: https://github.com/galaxyproject/planemo/commit/6409449
+.. _6514ff5: https://github.com/galaxyproject/planemo/commit/6514ff5
+.. _65b999d: https://github.com/galaxyproject/planemo/commit/65b999d21bacc133a80ecf5f61e0728afec66ccc
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+.. _6bcf699: https://github.com/galaxyproject/planemo/commit/6bcf699
+.. _6d0f502: https://github.com/galaxyproject/planemo/commit/6d0f502
+.. _6d81a94: https://github.com/galaxyproject/planemo/commit/6d81a94
+.. _6e1e726: https://github.com/galaxyproject/planemo/commit/6e1e726
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+.. _764ce01: https://github.com/galaxyproject/planemo/commit/764ce01
+.. _775bf49: https://github.com/galaxyproject/planemo/commit/775bf49
+.. _776773c: https://github.com/galaxyproject/planemo/commit/776773c
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+.. _7c69bf6: https://github.com/galaxyproject/planemo/commit/7c69bf6
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+.. _8117e03: https://github.com/galaxyproject/planemo/commit/8117e03
+.. _8207026: https://github.com/galaxyproject/planemo/commit/8207026
+.. _826d371: https://github.com/galaxyproject/planemo/commit/826d371
+.. _82e8b1f: https://github.com/galaxyproject/planemo/commit/82e8b1f17eae526aeb341cb4fffb8d09d73bb419
+.. _834bfb2: https://github.com/galaxyproject/planemo/commit/834bfb2929d367892a3abe9c0b88d5a0277d7905
+.. _83e227a: https://github.com/galaxyproject/planemo/commit/83e227a
+.. _85b9614: https://github.com/galaxyproject/planemo/commit/85b961465f46351507f80ddc3758349535060502
+.. _89674cb: https://github.com/galaxyproject/planemo/commit/89674cb
+.. _8b31850: https://github.com/galaxyproject/planemo/commit/8b31850
+.. _8e96864: https://github.com/galaxyproject/planemo/commit/8e96864
+.. _8eda729: https://github.com/galaxyproject/planemo/commit/8eda729
+.. _912df02: https://github.com/galaxyproject/planemo/commit/912df02
+.. _916f610: https://github.com/galaxyproject/planemo/commit/916f610
+.. _93b7bda: https://github.com/galaxyproject/planemo/commit/93b7bda
+.. _94097c7: https://github.com/galaxyproject/planemo/commit/94097c7
+.. _9427b47: https://github.com/galaxyproject/planemo/commit/9427b47
+.. _94645ed: https://github.com/galaxyproject/planemo/commit/94645ed
+.. _949a36d: https://github.com/galaxyproject/planemo/commit/949a36d
+.. _95d5cba: https://github.com/galaxyproject/planemo/commit/95d5cba
+.. _965511d: https://github.com/galaxyproject/planemo/commit/965511d
+.. _988de1d: https://github.com/galaxyproject/planemo/commit/988de1d
+.. _98fdc8c: https://github.com/galaxyproject/planemo/commit/98fdc8c
+.. _99ee51a: https://github.com/galaxyproject/planemo/commit/99ee51a
+.. _9bf1eab: https://github.com/galaxyproject/planemo/commit/9bf1eab
+.. _9e746b4: https://github.com/galaxyproject/planemo/commit/9e746b455e3b15219878cddcdeda722979639401
+.. _9f3957d: https://github.com/galaxyproject/planemo/commit/9f3957d
+.. _9ff0d2d: https://github.com/galaxyproject/planemo/commit/9ff0d2d
+.. _CWL: http://www.commonwl.org/
+.. _Issue 108: https://github.com/galaxyproject/planemo/issues/108
+.. _Issue 114: https://github.com/galaxyproject/planemo/issues/114
+.. _Issue 118: https://github.com/galaxyproject/planemo/issues/118
+.. _Issue 124: https://github.com/galaxyproject/planemo/issues/#124
+.. _Issue 138: https://github.com/galaxyproject/planemo/issues/#138
+.. _Issue 139: https://github.com/galaxyproject/planemo/issues/139
+.. _Issue 150: https://github.com/galaxyproject/planemo/issues/150
+.. _Issue 156: https://github.com/galaxyproject/planemo/issues/156
+.. _Issue 158: https://github.com/galaxyproject/planemo/issues/158
+.. _Issue 159: https://github.com/galaxyproject/planemo/issues/159
+.. _Issue 15: https://github.com/galaxyproject/planemo/issues/15
+.. _Issue 161: https://github.com/galaxyproject/planemo/issues/161
+.. _Issue 167: https://github.com/galaxyproject/planemo/issues/167
+.. _Issue 168: https://github.com/galaxyproject/planemo/issues/168
+.. _Issue 169: https://github.com/galaxyproject/planemo/issues/169
+.. _Issue 170: https://github.com/galaxyproject/planemo/issues/170
+.. _Issue 176: https://github.com/galaxyproject/planemo/issues/176
+.. _Issue 179: https://github.com/galaxyproject/planemo/issues/179
+.. _Issue 180: https://github.com/galaxyproject/planemo/issues/180
+.. _Issue 181: https://github.com/galaxyproject/planemo/issues/181
+.. _Issue 184: https://github.com/galaxyproject/planemo/issues/184
+.. _Issue 186: https://github.com/galaxyproject/planemo/issues/186
+.. _Issue 188: https://github.com/galaxyproject/planemo/issues/188
+.. _Issue 189: https://github.com/galaxyproject/planemo/issues/189
+.. _Issue 192: https://github.com/galaxyproject/planemo/issues/192
+.. _Issue 205: https://github.com/galaxyproject/planemo/issues/205
+.. _Issue 206: https://github.com/galaxyproject/planemo/issues/206
+.. _Issue 209: https://github.com/galaxyproject/planemo/issues/209
+.. _Issue 211: https://github.com/galaxyproject/planemo/issues/211
+.. _Issue 217: https://github.com/galaxyproject/planemo/issues/217
+.. _Issue 223: https://github.com/galaxyproject/planemo/issues/223
+.. _Issue 231: https://github.com/galaxyproject/planemo/issues/231
+.. _Issue 233: https://github.com/galaxyproject/planemo/issues/233
+.. _Issue 240: https://github.com/galaxyproject/planemo/issues/240
+.. _Issue 243: https://github.com/galaxyproject/planemo/issues/243
+.. _Issue 245: https://github.com/galaxyproject/planemo/issues/245
+.. _Issue 246: https://github.com/galaxyproject/planemo/issues/246
+.. _Issue 272: https://github.com/galaxyproject/planemo/issues/272
+.. _Issue 303: https://github.com/galaxyproject/planemo/issues/303
+.. _Issue 313: https://github.com/galaxyproject/planemo/issues/313
+.. _Issue 329: https://github.com/galaxyproject/planemo/issues/329
+.. _Issue 333: https://github.com/galaxyproject/planemo/issues/333
+.. _Issue 361: https://github.com/galaxyproject/planemo/issues/361
+.. _Issue 362: https://github.com/galaxyproject/planemo/issues/362
+.. _Issue 373: https://github.com/galaxyproject/planemo/issues/373
+.. _Issue 391: https://github.com/galaxyproject/planemo/issues/391
+.. _Issue 416: https://github.com/galaxyproject/planemo/issues/416
+.. _Issue 420: https://github.com/galaxyproject/planemo/issues/420
+.. _Issue 475: https://github.com/galaxyproject/planemo/issues/475
+.. _Issue 61: https://github.com/galaxyproject/planemo/issues/61
+.. _Issue 70: https://github.com/galaxyproject/planemo/issues/70
+.. _Issue 78: https://github.com/galaxyproject/planemo/issues/78
+.. _Issue 80: https://github.com/galaxyproject/planemo/issues/80
+.. _Issue 83: https://github.com/galaxyproject/planemo/issues/83
+.. _Issue 88: https://github.com/galaxyproject/planemo/issues/88
+.. _Issue 89: https://github.com/galaxyproject/planemo/issues/#89
+.. _Issue 91: https://github.com/galaxyproject/planemo/issues/#91
+.. _Pull Request 101: https://github.com/galaxyproject/planemo/pull/101
+.. _Pull Request 102: https://github.com/galaxyproject/planemo/pull/102
+.. _Pull Request 104: https://github.com/galaxyproject/planemo/pull/104
+.. _Pull Request 111: https://github.com/galaxyproject/planemo/pull/111
+.. _Pull Request 113: https://github.com/galaxyproject/planemo/pull/113
+.. _Pull Request 129: https://github.com/galaxyproject/planemo/pull/129
+.. _Pull Request 130: https://github.com/galaxyproject/planemo/pull/130
+.. _Pull Request 143: https://github.com/galaxyproject/planemo/pull/143
+.. _Pull Request 151: https://github.com/galaxyproject/planemo/pull/151
+.. _Pull Request 155: https://github.com/galaxyproject/planemo/pull/155
+.. _Pull Request 164: https://github.com/galaxyproject/planemo/pull/164
+.. _Pull Request 171: https://github.com/galaxyproject/planemo/pull/171
+.. _Pull Request 173: https://github.com/galaxyproject/planemo/pull/173
+.. _Pull Request 175: https://github.com/galaxyproject/planemo/pull/175
+.. _Pull Request 185: https://github.com/galaxyproject/planemo/pull/185
+.. _Pull Request 186: https://github.com/galaxyproject/planemo/pull/186
+.. _Pull Request 187: https://github.com/galaxyproject/planemo/pull/187
+.. _Pull Request 190: https://github.com/galaxyproject/planemo/pull/190
+.. _Pull Request 196: https://github.com/galaxyproject/planemo/pull/196
+.. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1
+.. _Pull Request 200: https://github.com/galaxyproject/planemo/pull/200
+.. _Pull Request 203: https://github.com/galaxyproject/planemo/pull/203
+.. _Pull Request 206: https://github.com/galaxyproject/planemo/pull/206
+.. _Pull Request 207: https://github.com/galaxyproject/planemo/pull/207
+.. _Pull Request 208: https://github.com/galaxyproject/planemo/pull/208
+.. _Pull Request 210: https://github.com/galaxyproject/planemo/pull/210
+.. _Pull Request 213: https://github.com/galaxyproject/planemo/pull/213
+.. _Pull Request 215: https://github.com/galaxyproject/planemo/pull/215
+.. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216
+.. _Pull Request 22: https://github.com/galaxyproject/planemo/pull/22
+.. _Pull Request 230: https://github.com/galaxyproject/planemo/pull/230
+.. _Pull Request 235: https://github.com/galaxyproject/planemo/pull/235
+.. _Pull Request 23: https://github.com/galaxyproject/planemo/pull/23
+.. _Pull Request 251: https://github.com/galaxyproject/planemo/pull/251
+.. _Pull Request 253: https://github.com/galaxyproject/planemo/pull/253
+.. _Pull Request 254: https://github.com/galaxyproject/planemo/pull/254
+.. _Pull Request 255: https://github.com/galaxyproject/planemo/pull/255
+.. _Pull Request 256: https://github.com/galaxyproject/planemo/pull/256
+.. _Pull Request 277: https://github.com/galaxyproject/planemo/pull/277
+.. _Pull Request 278: https://github.com/galaxyproject/planemo/pull/278
+.. _Pull Request 284: https://github.com/galaxyproject/planemo/pull/284
+.. _Pull Request 285: https://github.com/galaxyproject/planemo/pull/285
+.. _Pull Request 287: https://github.com/galaxyproject/planemo/pull/287
+.. _Pull Request 292: https://github.com/galaxyproject/planemo/pull/292
+.. _Pull Request 297: https://github.com/galaxyproject/planemo/pull/297
+.. _Pull Request 29: https://github.com/galaxyproject/planemo/pull/29
+.. _Pull Request 301: https://github.com/galaxyproject/planemo/pull/301
+.. _Pull Request 304: https://github.com/galaxyproject/planemo/pull/304
+.. _Pull Request 305: https://github.com/galaxyproject/planemo/pull/305
+.. _Pull Request 307: https://github.com/galaxyproject/planemo/pull/307
+.. _Pull Request 309: https://github.com/galaxyproject/planemo/pull/309
+.. _Pull Request 310: https://github.com/galaxyproject/planemo/pull/310
+.. _Pull Request 311: https://github.com/galaxyproject/planemo/pull/311
+.. _Pull Request 312: https://github.com/galaxyproject/planemo/pull/312
+.. _Pull Request 314: https://github.com/galaxyproject/planemo/pull/314
+.. _Pull Request 316: https://github.com/galaxyproject/planemo/pull/316
+.. _Pull Request 322: https://github.com/galaxyproject/planemo/pull/322
+.. _Pull Request 327: https://github.com/galaxyproject/planemo/pull/327
+.. _Pull Request 330: https://github.com/galaxyproject/planemo/pull/330
+.. _Pull Request 333: https://github.com/galaxyproject/planemo/pull/333
+.. _Pull Request 334: https://github.com/galaxyproject/planemo/pull/334
+.. _Pull Request 335: https://github.com/galaxyproject/planemo/pull/335
+.. _Pull Request 339: https://github.com/galaxyproject/planemo/pull/339
+.. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33
+.. _Pull Request 343: https://github.com/galaxyproject/planemo/pull/343
+.. _Pull Request 344: https://github.com/galaxyproject/planemo/pull/344
+.. _Pull Request 345: https://github.com/galaxyproject/planemo/pull/345
+.. _Pull Request 350: https://github.com/galaxyproject/planemo/pull/350
+.. _Pull Request 351: https://github.com/galaxyproject/planemo/pull/351
+.. _Pull Request 356: https://github.com/galaxyproject/planemo/pull/356
+.. _Pull Request 375: https://github.com/galaxyproject/planemo/pull/375
+.. _Pull Request 390: https://github.com/galaxyproject/planemo/pull/390
+.. _Pull Request 394: https://github.com/galaxyproject/planemo/pull/394
+.. _Pull Request 398: https://github.com/galaxyproject/planemo/pull/398
+.. _Pull Request 403: https://github.com/galaxyproject/planemo/pull/403
+.. _Pull Request 40: https://github.com/galaxyproject/planemo/pull/40
+.. _Pull Request 425: https://github.com/galaxyproject/planemo/pull/425
+.. _Pull Request 426: https://github.com/galaxyproject/planemo/pull/426
+.. _Pull Request 428: https://github.com/galaxyproject/planemo/pull/428
+.. _Pull Request 429: https://github.com/galaxyproject/planemo/pull/429
+.. _Pull Request 454: https://github.com/galaxyproject/planemo/pull/454
+.. _Pull Request 472: https://github.com/galaxyproject/planemo/pull/472
+.. _Pull Request 479: https://github.com/galaxyproject/planemo/pull/479
+.. _Pull Request 480: https://github.com/galaxyproject/planemo/pull/480
+.. _Pull Request 484: https://github.com/galaxyproject/planemo/pull/484
+.. _Pull Request 488: https://github.com/galaxyproject/planemo/pull/488
+.. _Pull Request 491: https://github.com/galaxyproject/planemo/pull/491
+.. _Pull Request 51: https://github.com/galaxyproject/planemo/pull/51
+.. _Pull Request 56: https://github.com/galaxyproject/planemo/pull/56
+.. _Pull Request 63: https://github.com/galaxyproject/planemo/pull/63
+.. _Pull Request 68: https://github.com/galaxyproject/planemo/pull/68
+.. _Pull Request 6: https://github.com/galaxyproject/planemo/pull/6
+.. _Pull Request 98: https://github.com/galaxyproject/planemo/pull/98
+.. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99
+.. _XSD: http://www.w3schools.com/schema/
+.. _a13a120: https://github.com/galaxyproject/planemo/commit/a13a120
+.. _a2c13e4: https://github.com/galaxyproject/planemo/commit/a2c13e46259e3be35de1ecaae858ba818bb94734
+.. _a2ee135: https://github.com/galaxyproject/planemo/commit/a2ee135
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+.. _a4e6958: https://github.com/galaxyproject/planemo/commit/a4e6958
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+.. _a87899b: https://github.com/galaxyproject/planemo/commit/a87899b
+.. _aad1eed: https://github.com/galaxyproject/planemo/commit/aad1eed
+.. _ac4f828: https://github.com/galaxyproject/planemo/commit/ac4f82898f7006799142503a33c3978428660ce7
+.. _ad3b2f0: https://github.com/galaxyproject/planemo/commit/ad3b2f0
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+.. _af7448c: https://github.com/galaxyproject/planemo/commit/af7448c
+.. _b0b867e: https://github.com/galaxyproject/planemo/commit/b0b867e
+.. _b1c8f1d: https://github.com/galaxyproject/planemo/commit/b1c8f1d
+.. _b53006d: https://github.com/galaxyproject/planemo/commit/b53006d
+.. _b757791: https://github.com/galaxyproject/planemo/commit/b757791
+.. _b7d9e96: https://github.com/galaxyproject/planemo/commit/b7d9e96
+.. _b86fe1f: https://github.com/galaxyproject/planemo/commit/b86fe1f
+.. _b8d90ab: https://github.com/galaxyproject/planemo/commit/b8d90abab8bf53ae2e7cca4317223c01af9ab68c
+.. _b9232e5: https://github.com/galaxyproject/planemo/commit/b9232e55e713abbd1d9ce8b0b34cbec6c701dc17
+.. _badc25f: https://github.com/galaxyproject/planemo/commit/badc25fca495b61457ffb2e027f3fe9cf17c798f
+.. _bioblend: https://github.com/galaxyproject/bioblend/
+.. _c1713d2: https://github.com/galaxyproject/planemo/commit/c1713d2
+.. _c23569f: https://github.com/galaxyproject/planemo/commit/c23569f
+.. _c444855: https://github.com/galaxyproject/planemo/commit/c444855
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+.. _cc1a447: https://github.com/galaxyproject/planemo/commit/cc1a447
+.. _cc8abb6: https://github.com/galaxyproject/planemo/commit/cc8abb6
+.. _ce8e1be: https://github.com/galaxyproject/planemo/commit/ce8e1be
+.. _cwltool: https://github.com/common-workflow-language/cwltool/.. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e
+.. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e
+.. _d755fe7: https://github.com/galaxyproject/planemo/commit/d755fe7
+.. _d76b489: https://github.com/galaxyproject/planemo/commit/d76b489
+.. _d8f2038: https://github.com/galaxyproject/planemo/commit/d8f2038
+.. _dad2d9d: https://github.com/galaxyproject/planemo/commit/dad2d9d
+.. _dd94ddc: https://github.com/galaxyproject/planemo/commit/dd94ddc
+.. _dff4f33: https://github.com/galaxyproject/planemo/commit/dff4f33c750a8dbe651c38e149a26dd42e706a82
+.. _e0577e7: https://github.com/galaxyproject/planemo/commit/e0577e7
+.. _e0acf91: https://github.com/galaxyproject/planemo/commit/e0acf91
+.. _e38c436: https://github.com/galaxyproject/planemo/commit/e38c436
+.. _e769118: https://github.com/galaxyproject/planemo/commit/e769118
+.. _e8c1d45: https://github.com/galaxyproject/planemo/commit/e8c1d45f0c9a11bcf69ec2967836c3b8f432dd97
+.. _eb039c0: https://github.com/galaxyproject/planemo/commit/eb039c0
+.. _ec6e30f: https://github.com/galaxyproject/planemo/commit/ec6e30f
+.. _efc5f30: https://github.com/galaxyproject/planemo/commit/efc5f30
+.. _f0610d7: https://github.com/galaxyproject/planemo/commit/f0610d7
+.. _f3394e7: https://github.com/galaxyproject/planemo/commit/f3394e7
+.. _f3c6917: https://github.com/galaxyproject/planemo/commit/f3c6917
+.. _f3cafaa: https://github.com/galaxyproject/planemo/commit/f3cafaa
+.. _f7554d1: https://github.com/galaxyproject/planemo/commit/f7554d1
+.. _f798c7e: https://github.com/galaxyproject/planemo/commit/f798c7e
+.. _f854138: https://github.com/galaxyproject/planemo/commit/f854138
+.. _f99f6c1: https://github.com/galaxyproject/planemo/commit/f99f6c1
+.. _fba3874: https://github.com/galaxyproject/planemo/commit/fba3874
+.. _fdb1b51: https://github.com/galaxyproject/planemo/commit/fdb1b51
+.. _fdce74c: https://github.com/galaxyproject/planemo/commit/fdce74c
+.. _fe7ad46: https://github.com/galaxyproject/planemo/commit/fe7ad46
+.. _fea51fc: https://github.com/galaxyproject/planemo/commit/fea51fc
+.. _lxml: http://lxml.de/
+.. _nose: https://nose.readthedocs.org/en/latest/
+.. _xmllint: http://xmlsoft.org/xmllint.html
+.. _Conda: http://conda.pydata.org/
+.. _Tool Factory: http://bioinformatics.oxfordjournals.org/content/early/2012/09/27/bioinformatics.bts573.full.pdf
+.. _git: https://git-scm.com/
+.. _anaconda-verify: https://github.com/ContinuumIO/anaconda-verify
+.. _galaxy.xsd: https://github.com/galaxyproject/planemo/blob/master/planemo/xml/xsd/tool/galaxy.xsd
+.. _setup.py: https://github.com/galaxyproject/planemo/blob/master/setup.py
+.. _Bioconductor: https://www.bioconductor.org/
+.. _tools-iuc: https://github.com/galaxyproject/tools-iuc
+.. _PyPI: https://pypi.python.org/pypi
+.. _Involucro: https://github.com/involucro/involucro
+.. _Bioconda: https://bioconda.github.io/
+.. _pip: https://pip.pypa.io/en/stable/
+.. _BioContainers: http://biocontainers.pro/
+.. _Toil: https://github.com/BD2KGenomics/toil
+.. _quay.io: https://quay.io/
+.. _galaxy-lib: https://github.com/galaxyproject/galaxy-lib
+.. _gxwf: https://github.com/simonbray/gxwf
+.. _Cheetah: https://cheetahtemplate.org/users_guide/intro.html
+.. _Allure: http://allure.qatools.ru/
+.. _@abretaud: https://github.com/abretaud
+.. _@hexylena: https://github.com/hexylena
+.. _@peterjc: https://github.com/peterjc
+.. _@mr-c: https://github.com/mr-c
+.. _@martenson: https://github.com/martenson
+.. _@nsoranzo: https://github.com/nsoranzo
+.. _@nturaga: https://github.com/nturaga
+.. _@bgruening: https://github.com/bgruening
+.. _@carlfeberhard: https://github.com/carlfeberhard
+.. _@lparsons: https://github.com/lparsons
+.. _@kellrott: https://github.com/kellrott
+.. _@mvdbeek: https://github.com/mvdbeek
+.. _@natefoo: https://github.com/natefoo
+.. _@pstew: https://github.com/pstew
+.. _@ramezrawas: https://github.com/ramezrawas
+.. _@chambm: https://github.com/chambm
+.. _@takadonet: https://github.com/takadonet
+.. _@petrkadlec: https://github.com/petrkadlec
+.. _@pvanheus: https://github.com/pvanheus
+.. _@einon: https://github.com/einon
+.. _@blankenberg: https://github.com/blankenberg
+.. _@JeanFred: https://github.com/JeanFred
+.. _@gregvonkuster: https://github.com/gregvonkuster
+.. _@remimarenco: https://github.com/remimarenco
+.. _@thriqon: https://github.com/thriqon
+.. _@RJMW: https://github.com/RJMW
+.. _@manabuishii: https://github.com/manabuishii
+.. _@dfornika: https://github.com/dfornika
+.. _@bernt-matthias: https://github.com/bernt-matthias
+.. _@katrinleinweber: https://github.com/katrinleinweber
+.. _@bebatut: https://github.com/bebatut
+.. _@selten: https://github.com/selten
+.. _@shiltemann: https://github.com/shiltemann
+.. _@bedroesb: https://github.com/bedroesb
+.. _@ic4f: https://github.com/ic4f
+.. _@martin-raden: https://github.com/martin-raden
+.. _@andreassko: https://github.com/andreassko
+.. _@mblue9: https://github.com/mblue9
+.. _@TMiguelT: https://github.com/TMiguelT
+.. _@bedroesb: https://github.com/bedroesb
+.. _@simonbray: https://github.com/simonbray

Mercurial > repos > shellac > sam_consensus_v3

comparison env/lib/python3.9/site-packages/planemo-0.74.3.dist-info/METADATA @ 0:4f3585e2f14b draft default tip