{
    "info": {
        "author": "Galaxy Project and Community",
        "author_email": "jmchilton@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: Academic Free License (AFL)",
            "Natural Language :: English",
            "Operating System :: POSIX",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Software Development",
            "Topic :: Software Development :: Code Generators",
            "Topic :: Software Development :: Testing"
        ],
        "description": ".. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png\n   :alt: Planemo Logo\n   :align: center\n   :figwidth: 100%\n   :target: https://github.com/galaxyproject/planemo\n\nCommand-line utilities to assist in developing Galaxy_ and `Common Workflow Language`_ tools.\n\n.. image:: https://readthedocs.org/projects/planemo/badge/?version=latest\n   :target: http://planemo.readthedocs.io/en/latest/?badge=latest\n   :alt: Documentation Status\n\n.. image:: https://badge.fury.io/py/planemo.svg\n   :target: https://pypi.python.org/pypi/planemo/\n   :alt: Planemo on the Python Package Index (PyPI)\n\n.. image:: https://travis-ci.org/galaxyproject/planemo.png?branch=master\n   :target: https://travis-ci.org/galaxyproject/planemo\n   :alt: Build Status\n\n.. image:: https://travis-ci.org/jmchilton/planemo-extended-tests.svg?branch=master\n    :target: https://travis-ci.org/jmchilton/planemo-extended-tests\n    :alt: Build Status of Extended Tests\n\n.. image:: https://coveralls.io/repos/galaxyproject/planemo/badge.svg?branch=master\n   :target: https://coveralls.io/r/galaxyproject/planemo?branch=master\n   :alt: Coverage Status\n\n* Free software: Academic Free License version 3.0\n* Documentation: https://planemo.readthedocs.io.\n* Code: https://github.com/galaxyproject/planemo\n\n\nQuick Start\n-----------\n\n-----------------\nObtaining\n-----------------\n\nFor a traditional Python installation of Planemo, first set up a virtualenv\nfor ``planemo`` (this example creates a new one in ``.venv``) and then\ninstall with ``pip``. Planemo requires pip 7.0 or newer.\n\n::\n\n    $ virtualenv .venv; . .venv/bin/activate\n    $ pip install \"pip>=7\" # Upgrade pip if needed.\n    $ pip install planemo\n\nFor information on updating Planemo, installing the latest development release,\nor installing Planemo via `Bioconda <https://github.com/bioconda/bioconda-recipes>`__\n- checkout the `installation <http://planemo.readthedocs.io/en/latest/installation.html>`__\ndocumentation.\n\nPlanemo is also available as a `virtual appliance\n<https://planemo.readthedocs.io/en/latest/appliance.html>`_ bundled\nwith a preconfigured Galaxy server and set up for Galaxy_ and\n`Common Workflow Language`_ tool development.\nYou can choose from open virtualization format (OVA_, .ova) or Docker_\nappliances.\n\n-----------------\nBasics - Galaxy\n-----------------\n\nThis quick start will assume you have a directory with one or more Galaxy\ntool XML files. If no such directory is available, one can be quickly created for\ndemonstrating ``planemo`` as follows ``project_init --template=demo mytools; cd mytools``.\n\nPlanemo can check tool XML files for common problems and best\npractices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_\n(also aliased as ``l``).\n\n::\n\n    $ planemo lint\n\nLike many ``planemo`` commands - by default this will search the\ncurrent directory and use all tool files it finds. It can be explicitly\npassed a path to tool files or a directory of tool files.\n\n::\n\n    $ planemo l randomlines.xml\n\nThe ``lint`` command takes in additional options related to\nreporting levels, exit code, etc. These options are described\nin the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_\nor (like with all commands) can be accessed by passing ``--help`` to it.\n\n::\n\n    $ planemo l --help\n    Usage: planemo lint [OPTIONS] TOOL_PATH\n\nOnce tools are syntactically correct - it is time to test. The ``test``\n`command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__\ncan be used to test a tool or a directory of tools.\n\n::\n\n\t$ planemo test --galaxy_root=../galaxy randomlines.xml\n\nIf no ``--galaxy_root`` is defined, Planemo will download and configure\na disposable Galaxy instance for testing.\n\nPlanemo will create a HTML output report in the current directory named\n``tool_test_output.html`` (override with ``--test_output``). See an\n`example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_\nof such a report for Tophat.\n\nOnce tools have been linted and tested - the tools can be viewed in a\nGalaxy interface using the ``serve`` (``s``) `command\n<http://planemo.readthedocs.org/en/latest/commands.html#serve-command>`__.\n\n::\n\n\t$ planemo serve\n\nLike ``test``, ``serve`` requires a Galaxy root and one can be\nexplicitly specified with ``--galaxy_root`` or installed dynamically\nwith ``--install_galaxy``.\n\nFor more information on building Galaxy tools in general please check out\n`Building Galaxy Tools Using Planemo`_.\n\n----------------------------------\nBasics - Common Workflow Language\n----------------------------------\n\nThis quick start will assume you have a directory with one or more `Common Workflow\nLanguage`_ YAML files. If no such directory is available, one can be quickly created for\ndemonstrating ``planemo`` as follows ``planemo project_init --template=seqtk_complete_cwl mytools; cd mytools``.\n\nPlanemo can check tools YAML files for common problems and best\npractices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_\n(also aliased as ``l``).\n\n::\n\n    $ planemo lint\n\nLike many ``planemo`` commands - by default this will search the\ncurrent directory and use all tool files it finds. It can be explicitly\npassed a path to tool files or a directory of tool files.\n\n::\n\n    $ planemo l seqtk_seq.cwl\n\nThe ``lint`` command takes in additional options related to\nreporting levels, exit code, etc. These options are described\nin the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_\nor (like with all commands) can be accessed by passing ``--help`` to it.\n\n::\n\n    $ planemo l --help\n    Usage: planemo lint [OPTIONS] TOOL_PATH\n\nOnce tools are syntactically correct - it is time to test. The ``test``\n`command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__\ncan be used to test a CWL tool, workflow, or a directories thereof.\n\n::\n\n  $ planemo test --engine cwltool seqtk_seq.cwl\n\nPlanemo will create a HTML output report in the current directory named\n``tool_test_output.html``. Check out the file ``seqtk_seq_tests.yml`` for\nan example of Planemo test for a CWL tool. A test consists of any number of\njobs (with input descriptions) and corresponding output assertions.\n\nCheckout the `Commmon Workflow User Guide`_ for more information on developing\nCWL tools in general and  `Building Common Workflow Language Tools`_ for more\ninformation on using Planemo to develop CWL tools.\n\n---------\nTool Shed\n---------\n\nPlanemo can help you publish tools to the Galaxy Tool Shed.\nCheck out `Publishing to the Tool Shed`_ for more information.\n\n------\nConda\n------\n\nPlanemo can help develop tools and Conda packages in unison.\nCheck out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda>`__ or `CWL\n<http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda-cwl>`__ version of the \"Dependencies and Conda\" tutorial\nfor more information.\n\n-----------------------\nDocker and Containers\n-----------------------\n\nPlanemo can help develop tools that run in \"Best Practice\" containers for\nscientific workflows. Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-containers>`__ or `CWL\n<http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers-cwl>`__ version of the \"Dependencies and Containers\" tutorial for more information.\n\n.. _Galaxy: http://galaxyproject.org/\n.. _GitHub: https://github.com/\n.. _Conda: http://conda.pydata.org/\n.. _Docker: https://www.docker.com/\n.. _Vagrant: https://www.vagrantup.com/\n.. _Travis CI: http://travis-ci.org/\n.. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam\n.. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc\n.. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html\n.. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html\n.. _Common Workflow Language: https://www.commonwl.org/\n.. _Commmon Workflow User Guide: http://www.commonwl.org/user_guide/\n.. _Building Common Workflow Language Tools: http://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html\n.. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format\n\n\n\n\n\nHistory\n-------\n\n.. to_doc\n\n---------------------\n0.62.1 (2019-10-14)\n---------------------\n\n* Init & update submodules when installing and creating packages. Stop\n  distributing eggs (thanks to `@nsoranzo`_). 1ab8530_\n\n---------------------\n0.62.0 (2019-10-11)\n---------------------\n\n* Use ``unicodify()`` on exceptions and subprocess outputs (thanks to\n  `@nsoranzo`_) `Pull Request 944`_\n* Do not override ``None`` with empty string (thanks to `@ic4f`_). `Pull Request\n  950`_\n* Update Docker template for training material generation (thanks to\n  `@bedroesb`_). `Pull Request 958`_\n* Add support for suite of repos with different owners (thanks to `@nsoranzo`_).\n  `Pull Request 959`_\n* Link for collection details updated in the docs (thanks to `@martin-raden`_).\n  `Pull Request 963`_\n* Move most tests to Python 3.7, drop Python 3.4 (thanks to `@nsoranzo`_).\n  `Pull Request 964`_\n* Remove confusing warning `Pull Request 966`_\n\n---------------------\n0.61.0 (2019-07-08)\n---------------------\n\n* Training - fix empty repeat + some formatting (thanks to `@bebatut`_). `Pull\n  Request 926`_\n* Training - add bibliography to tutorial template (thanks to `@shiltemann`_).\n  `Pull Request 938`_\n* Training - support new class definition for input in workflow step (thanks to\n  `@bebatut`_). `Pull Request 943`_\n* Various tool tutorial fixes ahead of GCC 2019 (thanks to `@nsoranzo`_).\n  `Pull Request 940`_\n* Return validation error if doi is empty (thanks to `@nsoranzo`_).\n  `Pull Request 937`_\n\n---------------------\n0.60.0 (2019-05-31)\n---------------------\n\n* Return validation error if doi is empty `Pull Request 937`_\n* Add junit as test reporter (thanks to `@selten`_). `Pull Request 935`_\n* Update galaxy.xsd for new python 3 compatibility attribute (thanks to `@martenson`_). `Pull Request\n  931`_\n* Documentation: add a little warning for <param ... multiple=\"true\"> (thanks to\n  `@bernt-matthias`_). `Pull Request 930`_\n\n---------------------\n0.59.0 (2019-05-09)\n---------------------\n\n* Add ability to test data manager tools (thanks to `@mvdbeek`_).\n  `Pull Request 912`_\n* Update Training for new requirement definition (thanks to `@bebatut`_).\n  `Pull Request 913`_\n* Drop amqp workaround (thanks to `@mvdbeek`_). `Pull Request 917`_\n* Use ``yaml.safe_load()`` instead of deprecated ``load()`` (thanks to `@nsoranzo`_).\n  `Pull Request 921`_\n* Allow converting ``tool_test_report.json`` to xunit (thanks to `@mvdbeek`_).\n  `Pull Request 918`_\n* Fix error if testcase.data.job does not exist (thanks to `@mvdbeek`_).\n  `Pull Request 924`_\n* Fix deprecated ``getchildren()`` (thanks to `@nsoranzo`_).\n  `Pull Request 925`_\n\n---------------------\n0.58.2 (2019-03-01)\n---------------------\n\n* Fix display of tool ids in planemo html report (thanks to `@mvdbeek`_).\n  `Pull Request 908`_\n* Single quotes for file names (thanks to `@bernt-matthias`_). `Pull Request\n  909`_\n* Fix doc linting (thanks to `@mvdbeek`_). `Pull Request 910`_\n* Update TS categories (thanks to `@nsoranzo`_). 07dc6e0_\n* Close tag in doc help, to help with copy&paste (thanks to `@blankenberg`_).\n  `Pull Request 914`_\n* Update the tool XSD file (thanks to `@bgruening`_). `Pull Request 915`_\n\n---------------------\n0.58.1 (2019-01-03)\n---------------------\n\n* Update galaxy-lib requirement to 18.9.2 to add Python 3.7 support (thanks to\n  `@nsoranzo`_). `Pull Request 906`_\n* Fix command run by `planemo test --skip_venv` (thanks to `@nsoranzo`_).\n  `Pull Request 907`_\n\n---------------------\n0.58.0 (2019-01-01)\n---------------------\n\n* Remove deprecated ``sudo: false`` from .travis.yml (thanks to `@nsoranzo`_).\n  `Pull Request 902`_\n* Do not skip Galaxy client build for ``planemo serve``. Install Galaxy when the\n  directory specified with ``--galaxy_root`` does not exist or is empty. (thanks\n  to `@nsoranzo`_). `Pull Request 895`_, `Issue 845`_\n\n---------------------\n0.57.1 (2018-11-23)\n---------------------\n\n* Fix username validation for shed linting (thanks to `@martenson`_).\n  `Pull Request 899`_, `Issue 898`_\n\n---------------------\n0.57.0 (2018-11-19)\n---------------------\n\n* Allow ``workflow_convert`` to convert a native ``.ga`` workflows to format 2 (yaml).\n  `Pull Request 896`_\n* New command (``workflow_edit``) to open workflow in a synchronized graphical editor.\n  `Pull Request 894`_\n* Conda tutorial fixes (thanks to `@nsoranzo`_). `Pull Request 876`_\n* Enable ``--conda_use_local`` option for ``planemo test`` (thanks to\n  `@nsoranzo`_). `Pull Request 876`_\n* When testing, skip workflow outputs that do not have a `label` set (thanks to\n  `@bgruening`_). `Pull Request 893`_\n* Add ``__repr__`` for ``TestCase`` to improve debugging Planemo\n  (thanks to `@bgruening`_). `Pull Request 892`_\n* Increase IO polling interval over time (thanks to `@martenson`_).\n  `Pull Request 891`_\n* Sync galaxy xsd and fix tests (thanks to `@mvdbeek`_).\n  `Pull Request 889`_\n* Linting fix for ``W605`` (thanks to `@martenson`_). `Pull Request 888`_\n* Add icon for repeat parameters in training (thanks to `@bebatut`_).\n  `Pull Request 887`_\n\n---------------------\n0.56.0 (2018-10-30)\n---------------------\n\n* Allow selection of Python version when starting managed Galaxy\n  (thanks to `@mvdbeek`_). `Pull Request 874`_\n* Change the channel priority of conda (again). (thanks to `@bgruening`_).\n  `Pull Request 867`_\n* Some small english corrections (thanks to `@erasche`_). `Pull Request 868`_\n* Print the list of excluded paths when running ``ci_find_repos``\n  (thanks to `@nsoranzo`_). `Pull Request 877`_\n* Improved XSD lint reporting. `Pull Request 871`_\n* Fix Planemo writing a file called ``gx_venv_None``. `Pull Request 870`_\n* Update cwltool and galaxy-lib dependencies for Python 3.7 (thanks to\n  `@nsoranzo`_). `Pull Request 864`_\n* Fix to make workflow testing more robust.\n  `Pull Request 882`_\n\n---------------------\n0.55.0 (2018-09-12)\n---------------------\n\n* Add commands to create Galaxy training materials (thanks to `@bebatut`_).\n  `Pull Request 861`_\n* Fix `planemo test` when TEMP env variable contain spaces (thanks to\n  `@nsoranzo`_).\n  `Pull Request 851`_\n* Support testing a completely remote galaxy instance (thanks to `@erasche`_).\n  `Pull Request 856`_\n* Allow naming history from command line (thanks to `@erasche`_).\n  `Pull Request 860`_\n* Sync galaxy.xsd from galaxy repo (thanks to `@nsoranzo`_).\n  `Pull Request 866`_\n* Fix ServeTestCase.test_shed_serve test (thanks to `@nsoranzo`). bad810a_\n\n---------------------\n0.54.0 (2018-06-06)\n---------------------\n\n* Better support for testings against different versions of Galaxy efficiently and robustly.\n  `Pull Request 849`_\n* New database version (thanks to `@bgruening`_).\n  `Pull Request 847`_\n* Hyperlink DOIs against preferred resolver (thanks to `@katrinleinweber`_).\n  `Pull Request 850`_\n* Tests for collection inputs to workflows. `Pull Request 843`_\n* Bring in Ephemeris sleep function - hopefully makes serve tests a bit more robust.\n  b12b117_\n* More tutorial testing, tutorial updates.\n  016b923_, 324c776_, 2002b49_\n* More isolated ``test_shed_upload.py`` tests. 72d2ca7_\n* Add filetype support for workflow test inputs (thanks to `@bgruening`_).\n  `Pull Request 842`_\n* Add ``--no_shed_install`` option, to prevent shed installs as part of workflow testing.\n  `Pull Request 841`_\n* Small docs fix (thanks to `@erasche`_). `Pull Request 848`_\n\n---------------------\n0.53.0 (2018-05-22)\n---------------------\n\n* Make Planemo testing easier for CWL tools and workflows in various ways and update\n  tutorials to reflect these simplifications. `Pull Request 837`_\n* Test and fix running workflow tests against externally managed Galaxy servers.\n  `Pull Request 833`_, `Pull Request 836`_\n* Allow using URIs for inputs of workflow test. `Pull Request 840`_\n* Slide Galaxy testing window to include 18.05 and drop 17.09. `Pull Request 838`_\n\n---------------------\n0.52.0 (2018-05-20)\n---------------------\n\n* Allow optional disabling of Galaxy single user mode. `Pull Request 835`_\n* Fix for path pasting options during workflow testing. `Pull Request 834`_\n\n---------------------\n0.51.0 (2018-05-19)\n---------------------\n\n* Fix essentially all Conda_ and BioContainers_ related functionality to allow parity between\n  CWL_ and existing Galaxy functionality - fixes and enhances many commands including ``lint``,\n  ``conda_install``, ``conda_env``, ``test``, ``run``, and ``mull``.\n  `Pull Request 828`_\n* Add two new tutorials for `Conda\n  <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda>`__\n  and `Container\n  <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers>`__\n  development with CWL tools that mirrors the existing tutorials for Galaxy tools - including new\n  CWL exercises, answers, and example project templates.\n  347c622_\n* Improve the CWL generated by the ``tool_init`` command to properly deal with\n  ``SoftwareRequirement`` s and generate more idiomatic CWL.\n  `Pull Request 820`_, a5c72e3_\n* Add new engine type (``--engine toil``) for testing and running CWL_ tools (requires\n  manually installing Toil_ with ``pip install toil`` in Planemo's environment).\n  `Pull Request 831`_\n* Add `documentation <http://planemo.readthedocs.io/en/latest/test_format.html>`__\n  for the Galaxy Workflow and CWL_ test format files (includes information on configuring\n  various test engines).\n  `Pull Request 832`_\n* Better default logging config for CWL development. `Pull Request 830`_\n* Various fixes for the ``conda_search`` command. `Pull Request 826`_\n* Fix test coverage configuration. `Pull Request 822`_\n* Reorganize .travis.yml for clarity. `Pull Request 829`_\n* More isolated, robust unit tests that use git_.\n  `Pull Request 827`_, `Pull Request 818`_\n* Fix default list of best-practice Conda channels. `Pull Request 825`_\n* Refactor tests to speed up quick tests - fewer buggy URLs fetched in \"quick\" mode.\n  `Pull Request 823`_\n* Fix upload configuration of workflow testing to default (overrideable) external Galaxies\n  to not use path pasting.\n  `Pull Request 816`_\n* Fix test number parsing for workflow tests. `Pull Request 817`_\n\n---------------------\n0.50.1 (2018-05-11)\n---------------------\n\n* Fix the process of waiting on Galaxy to boot up for the Docker Galaxy container ``--engine``.\n\n---------------------\n0.50.0 (2018-05-10)\n---------------------\n\n* Fixes and small CLI tweaks to get the Docker Galaxy container working as an ``--engine`` for the\n  run, serve, and test commands.\n\n---------------------\n0.49.2 (2018-05-09)\n---------------------\n\n* Various small fixes for new external Galaxy engine type.\n\n---------------------\n0.49.1 (2018-05-06)\n---------------------\n\n* Fix PyPI_ README rendering for 0.49.0 release changes.\n\n---------------------\n0.49.0 (2018-05-06)\n---------------------\n\n* Implement external Galaxy engine. `Pull Request 781`_\n* Restructure serve testing code for reuse. `Pull Request 795`_\n* Improve test report handling for JSON generated via galaxy-lib testing\n  script. `Pull Request 799`_\n* Improve how various branches of Galaxy are tested. `Pull Request 800`_\n* Added documentation for ``GALAXY_MEMORY_MB`` (thanks to `@bernt-matthias`_).\n  `Pull Request 801`_\n* Log tool config in verbose logging mode. `Pull Request 802`_\n* Replace ``r`` channel with ``conda-forge`` (thanks to `@bgruening`_).\n  `Pull Request 805`_\n* Sync ``galaxy.xsd`` with latest Galaxy updates (thanks to `@nsoranzo`_).\n  `Pull Request 806`_\n* Use ``requests.get()`` when validating http URLs (thanks to `@nsoranzo`_).\n  `Pull Request 809`_\n* Do not consider tools with \"deprecated\" in the path (thanks to\n  `@bgruening`_). `Pull Request 810`_\n* Automatically load tools shipped with Galaxy when testing, running, or serving\n  workflows that reference these tools. `Pull Request 790`_\n* Revise README and touch up documentation in general. `Pull Request 787`_\n* Various small changes to testing and test framework. `Pull Request 792`_\n* Various Python 3 fixes. 8cfe9e9_, 41f7df1_\n* Fixes for Galaxy 18.0X releases.\n  `Pull Request 803`_, dc443d6_\n\n---------------------\n0.48.0 (2018-02-28)\n---------------------\n\n* Run all CI tests against Python 3 (thanks to `@nsoranzo`_).\n  `Pull Request 768`_ and `Pull Request 774`_\n* Python 3 fix - subprocess with ``universal_newlines=True``\n  (thanks to `@peterjc`_).\n  `Pull Request 764`_\n* Record CWL_ conformance test results using JUnit xml\n  (thanks to `@mr-c`_).\n  `Pull Request 756`_\n* Restore run test case for simple Galaxy tools.\n  `Pull Request 769`_\n* Enhancements to Galaxy profiles and workflow testing.\n  `Pull Request 773`_\n* Fix resolving & installing shed repositories from workflows for ``test``\n  and ``run`` commands.\n  `Pull Request 776`_\n* Implement planemo command to convert format 2 workflows into .ga workflows.\n  `Pull Request 771`_\n* Add a native Galaxy workflow (.ga) testing test.\n  `Pull Request 770`_\n* Drop Brew support but add more detailed install instructions.\n  `Pull Request 761`_\n* Clean up CWL_ conformance test execution. `Pull Request 753`_\n* Assorted small CWL_ and deamon serve fixes. `Pull Request 759`_\n\n\n---------------------\n0.47.0 (2017-11-18)\n---------------------\n\n* Update to the latest Galaxy tool XSD  (thanks to `@nsoranzo`_).\n  `Pull Request 747`_\n* Re-fix problem when shed_update would fail if nothing to update\n  (thanks to `@nsoranzo`_). `Pull Request 747`_\n* Update instructions for installation via conda (thanks to `@nsoranzo`_) .\n  `Pull Request 743`_\n* Bug fix for MacOS `chmod` doesn't support `--recursive` flag.\n  (thanks to `@dfornika`_). `Pull Request 739`_\n* Bug fix to also `socket.error` when linting URLs\n  (thanks to `@nsoranzo`_). `Pull Request 738`_\n* Disable broken tests. `Pull Request 745`_\n\n---------------------\n0.46.1 (2017-09-26)\n---------------------\n\n* Rev to latest versions of bioblend_ and `galaxy-lib`_ for various fixes\n  related to CWL_.\n\n---------------------\n0.46.0 (2017-09-15)\n---------------------\n\n* Change behavior of ``--docker`` flag, for a few releases it would require\n  Galaxy use a container for every non-upload tool. This breaks various\n  conversion tools for instance and so was reverted.\n  `Pull Request 733`_\n* Add 'Accept' header when linting doc URLs (thanks to `@nsoranzo`_).\n  `Pull Request 725`_\n* Fix `--conda_auto_install` help (thanks to `@nsoranzo`_).\n  `Pull Request 727`_\n* Incremental progress toward CWL support via Galaxy.\n  `Pull Request 729`_, `Pull Request 732`_\n* Update galaxy-lib to latest version to fix various issues.\n  `Pull Request 730`_\n* Fix lint detected problems with documentation.\n  `Pull Request 731`_\n\n---------------------\n0.45.0 (2017-09-06)\n---------------------\n\n* Update to the latest `galaxy-lib`_ for Conda fixes. (thanks `@nsoranzo`_)\n  and updated CWL_ utilities.  `Pull Request 716`_, `Pull Request 723`_\n* Update Conda_ channel order to sync with Bioconda_\n  (thanks to `@nsoranzo`_). `Pull Request 715`_\n* Experimental support running CWL_ workflows through the CWL_ fork of Galaxy.\n* Mention ``planemo command --help`` in main help\n  (thanks to `@peterjc`_). `Pull Request 709`_\n* Bugfix handle ``None`` requirement versions when registering containers\n  (thanks to `@bgruening`_). `Pull Request 704`_\n* Bugfix for dependencies by pinning ruamel.yaml version\n  (thanks to `@mvdbeek`_). `Pull Request 720`_\n\n---------------------\n0.44.0 (2017-06-22)\n---------------------\n\n* Fix and improve Galaxy root option specification options.\n  `Pull Request 701`_, 8a608e0_\n* Update `planemo mull` to use a default action of `build-and-test` since\n  `build` no longer cleans up itself. ecc1bc2_\n* Add a command to pre-install Involucro_.\n  `Pull Request 702`_\n\n---------------------\n0.43.0 (2017-06-22)\n---------------------\n\n* Remove stdio from generated tools - just use exit_code for everything.\n  91b6fa0_\n* Implement some ad-hoc documentation tests. `Pull Request 699`_\n* A large number of small enhancements and fixes for the documentation and\n  example projects.\n\n---------------------\n0.42.1 (2017-06-16)\n---------------------\n\n* Fix Readme typos (thanks to `@manabuishii`_) 904d77a_\n* Fix `container_register` to create pull requests against the newly finalized home of the\n  multi-package-containers registry repository.\n  9636682_\n* Fix `use_global_config` and `use_env_var` for options with unspecified defaults.\n  475104c_\n\n\n---------------------\n0.42.0 (2017-06-15)\n---------------------\n\n* Conda/Container documentation and option naming improvements. `Pull Request\n  684`_\n* Sync `galaxy.xsd` with latest upstream Galaxy updates (thanks to `@nsoranzo`_).\n  `Pull Request 687`_\n* Fix `ci_find_repos` command to not filter repos whose only modifications where\n  in subdirs (thanks to `@nsoranzo`_).\n  `Pull Request 688`_\n* Update `container_register` for mulled version 2 and repository name changes.\n  `Pull Request 689`_\n* Better pull request messages for the `container_register` command.\n  `Pull Request 690`_\n\n---------------------\n0.41.0 (2017-06-05)\n---------------------\n\n* Fix ``shed_update`` not fail if there is nothing to update\n  (thanks to `@nsoranzo`_). `Issue 494`_, `Pull Request 680`_\n* Conda documentation and option naming improvements.\n  `Pull Request 683`_\n* Implement ``container_register`` for tool repositories.\n  `Pull Request 675`_\n* Fix ``hub`` binary installation for Mac OS X.\n  `Pull Request 682`_\n\n---------------------\n0.40.1 (2017-05-03)\n---------------------\n\n* Fix data manager configuration to not conflict with original Galaxy at\n  ``galaxy_root`` (thanks to `@nsoranzo`_). `Pull Request 662`_\n* Fix ``filter_paths()`` to not partial match paths when filtering shed repositories\n  (thanks to `@nsoranzo`_). `Pull Request 665`_\n* Fix description when creating ``.shed.yml`` files (thanks to `@RJMW`_).\n  `Pull Request 664`_\n\n---------------------\n0.40.0 (2017-03-16)\n---------------------\n\n* Implement instructions and project template for GA4GH Tool Execution\n  Challenge Phase 1. 84c4a73_\n* Eliminate Conda hack forcing ``/tmp`` as temp directory. b4ae44d_\n* Run dependency script tests in isolated directories. 32f41c9_\n* Fix OS X bug in ``planemo run`` by reworking it to wait using urllib instead of sockets.\n  3129216_\n\n---------------------\n0.39.0 (2017-03-15)\n---------------------\n\n* Implement documentation and examples for Conda-based dependency development (under\n  \"Advanced\" topics).\n  `Pull Request 642`_, `Pull Request 643`_\n* Implement documentation and examples for container-based dependency development (under\n  \"Advanced\" topics).\n  0a1abfe_\n* Implement a ``planemo conda_search`` command for searching best practice channels\n  from the command line.\n  `Pull Request 642`_\n* Allow Planemo to work with locally built Conda packages using the ``--conda_use_local``\n  command.\n  `Pull Request 643`_, `Issue 620`_\n* Implement an ``open`` (or just ``o``) command to quickly open the last test results\n  (or any file if supplied). `Pull Request 641`_\n* Linting improvements and fixes due to `galaxy-lib`_ update.\n  * WARN on test output names not found or not matching.\n  * INFO correct information about stdio if profile version is found.\n  * WARN if profile version is incorrect.\n  * INFO profile version\n  * Fix ``assert_command`` not detected as a valid test (fixes  `Issue 260`_).\n* Have ``lint --conda_requirements`` check that at least one actual requirement is found.\n  6638caa_\n* Allow ``conda_install`` to work with packages as well as just tools.\n  8faf661_\n* Add ``--global`` option to conda_install to install requirements into global Conda setup\n  instead of using an environment.\n  8faf661_\n* Implement ``planemo lint --biocontainer`` that checks that a tool has an available BioContainer\n  registered.\n  0a1abfe_\n* Add more options and more documentation to the ``planemo mull`` command.\n  0a1abfe_\n* Hack around a bug in Conda 4.2 that makes it so ``planemo mull`` doesn't work out of the box on\n  Mac OS X.\n  0a1abfe_\n* Allow URIs to be used instead of paths for a couple operations. ce0dc4e_\n* Implement non-strict CWL parsing option. 4c0f100_\n* Fixes for changes to cwltool_ and general CWL-relate functionality.\n  3c95b7b_, 06bcf19_, 525de8f_, 9867e56_, 9ab4a0d_\n* Eliminate deprecated XML-based abstraction from ``planemo.tools``. 04238d3_\n* Fix ``MANIFEST.in`` entry that was migrated to galaxy-lib. ced5ce2_\n* Various fixes for the command ``conda_env``. `Pull Request 640`_\n* Improved command help - both formatting and content. `Pull Request 639`_\n* Implement a ``--no_dependency_resolution`` option disabling conda dependency\n  resolver.\n  `Pull Request 635`_, `Issue 633`_\n* Tests for new linting logic. `Pull Request 638`_\n* Fix bug where tool IDs needs to be lowercase for the shed (thanks to\n  `@bgruening`_).\n  `Pull Request 649`_\n* Update seqtk version targetted by intro docs. e343b67_\n* Various other Conda usability improvements. `Pull Request 634`_\n\n---------------------\n0.38.1 (2017-02-06)\n---------------------\n\n* Fix bug with ``shed_lint --urls`` introduced in 0.38.0.\n  84ebc1f_\n\n---------------------\n0.38.0 (2017-02-06)\n---------------------\n\n* Trim down the default amount of logging during testing.\n  `Pull Request 629`_, `Issue 515`_\n* Improved log messages during shed operations. 08c067c_\n* Update tool XSD against latest Galaxy.\n  fca4183_, 03c9658_\n* Fix bug where ``shed_lint --tools`` for a suite lints the same tools multiple\n  times.\n  `Issue 564`_, `Pull Request 628`_\n\n---------------------\n0.37.0 (2017-01-25)\n---------------------\n\n* Update to the latest `galaxy-lib`_ release. This means new installs start with\n  Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes many\n  Conda_ related bugs.\n* Change defaults so that Conda automatically initializes and performs tool installs\n  by default from within the spawned Galaxy server. The trio of flags\n  ``--conda_dependency_resolution``, ``--conda_auto_install``, and ``--conda_auto_init``\n  are effectively enabled by default now. 4595953_\n* Use the Galaxy cached dependency manager by default (thanks to `@abretaud`_).\n  `Pull Request 612`_\n* Test Conda dependency resolution for more versions of Galaxy including the forthcoming\n  release of 17.01.\n* Update to the latest Galaxy tool XSD for various tool linting fixes. 32acd68_\n* Fix pip ignores for ``bioconda_scripts`` (thanks to `@nturaga`_)\n  `Pull Request 614`_\n\n---------------------\n0.36.1 (2016-12-12)\n---------------------\n\n* Fix move error when using ``project_init``.\n  `Issue 388`_, `Pull Request 610`_\n* Improved integration testing for ``test`` command. `Pull Request 609`_\n* Update CWL links to v1.0 (thanks to `@mr-c`_).\n  `Pull Request 608`_\n\n---------------------\n0.36.0 (2016-12-11)\n---------------------\n\n* Bring in latest tool XSD file from Galaxy (thanks to `@peterjc`_).\n  `Pull Request 605`_\n* PEP8 fixes for various linting problems\n  (thanks to `@peterjc`_).\n  `Pull Request 606`_\n* Update tool syntax URL to new URL (thanks to `@mvdbeek`_).\n  `Pull Request 602`_\n\n---------------------\n0.35.0 (2016-11-14)\n---------------------\n\n* Native support for building bioconductor tools and recipes\n  (thanks to `@nturaga`_). `Pull Request 570`_\n* Fixes for running Galaxy via docker-galaxy-stable (thanks to\n  `@bgruening`_). 50d3c4a_\n* Import order linting fixes (thanks to `@bgruening`_).\n\n---------------------\n0.34.1 (2016-10-12)\n---------------------\n\n* Mimic web browser to validate user help URLs fixing `Issue 578`_\n  (thanks to `@peterjc`_). `Pull Request 591`_\n* Fix for Bioconda recipes depending on ``conda-forge`` (thanks to `@nsoranzo`_).\n  `Pull Request 590`_\n\n\n---------------------\n0.34.0 (2016-10-05)\n---------------------\n\n* Implement ``mull`` command to build containers for tools based on Conda_\n  recipes matching requirement definitions. 08cef54_\n* Implement ``--mulled_containers`` flag on ``test``, ``serve``, and ``run``\n  commands to run tools in \"mulled\" containers. Galaxy will first search\n  locally cache containers (such as ones built with ``mull``), then search\n  the mulled namespace of `quay.io`_, and finally build one on-demand if\n  needed using `galaxy-lib`_ and Involucro_ developed by `@thriqon`_.\n* Implement ``--conda_requirements`` flag on ``lint`` command to ensure requirements\n  can be resolved in best practice channels. 9da8387_\n* Allow ``conda_install`` command over multiple tool paths. 2e4e5fc_\n* Update pip_ as part of setting virtual environment in ``Makefile`` target.\n  19b2ee9_\n* Add script to auto-update Bioconda_ recipe for Planemo and open a pull request.\n  f0da66f_\n\n---------------------\n0.33.2 (2016-09-28)\n---------------------\n\n* Fix HISTORY.rst link problem that prevented correct display of content on PyPI_.\n\n---------------------\n0.33.1 (2016-09-28)\n---------------------\n\n* Fix ``lint --urls`` false positives by being more restrictive with what is considered a URL\n  (fixed by `@erasche`_ after detailed report from `@peterjc`_).\n  `Issue 573`_, `Pull Request 579`_\n\n---------------------\n0.33.0 (2016-09-23)\n---------------------\n\n* Enable XSD validation of tools by default (restore old behavior with\n  ``planemo lint --no_xsd``). 1ef05d2_\n* Implement a ``conda_lint`` command to lint Conda_ recipes based\n  on `anaconda-verify`_. 6a6f164_\n* Implement ``clone`` and ``pull_request`` commands to ease PRs\n  (with documentation fixes from `@martenson`_).\n  e925ba1_, ea5324f_\n* Update `galaxy.xsd`_ to allow version_command's to have an interpreter\n  attribute. 7cca2e4_\n* Apply improvement from `@nsoranzo`_ for Planemo's use of\n  `git diff <https://git-scm.com/docs/git-diff>`__.\n  6f91719_\n* Pull in downstream refactoring of ``tool_init`` code from `@nturaga`_'s\n  Bioconductor_ work. ccdd2d5_\n* Update to latest `Tool Factory`_ code from `tools-iuc`_. ca88b0c_\n* Small code cleanups. b6d8294_, d6da3a8_\n* Fixup docs in ``planemo.xml.validation``.\n* Allow skipping newly required lxml_ dependency in `setup.py`_. 34538de_\n\n---------------------\n0.32.0 (2016-09-16)\n---------------------\n\n* Enhance ``planemo lint --xsd`` to use a fairly complete and newly official XSD\n  definition. `Pull Request 566`_\n* Migrate and update documentation related to tool XML macros and handling\n  multiple outputs from the Galaxy wiki (with help from `@bgruening`_, `@mvdbeek`_,\n  and `@nsoranzo`_). `Pull Request 559`_\n* Documentation fixes (thanks to `@ramezrawas`_). `Pull Request 561`_\n* Do not fail URL linting in case of too many requests (thanks to `@nsoranzo`_).\n  `Pull Request 565`_\n\n---------------------\n0.31.0 (2016-09-06)\n---------------------\n\n* Implement new commands to ``ci_find_repos`` and ``ci_find_tools`` to ease\n  CI scripting.\n  `Pull Request 555`_\n\n---------------------\n0.30.2 (2016-09-01)\n---------------------\n\n* Fix another problem with Conda_ prefix handling when using\n  ``--conda_dependency_resolution``. f7b6c7e_\n\n---------------------\n0.30.1 (2016-09-01)\n---------------------\n\n* Fix a problem with Conda_ prefix handling when using\n  ``--conda_dependency_resolution``. f7b6c7e_\n* Fix for quote problem in ``update_planemo_recipe.bash``. 6c03de8_\n* Fix to restore linting of ``tests/`` directory and fix import order throughout\n  module. ef4b9f4_\n\n---------------------\n0.30.0 (2016-09-01)\n---------------------\n\n* Update to the latest `galaxy-lib`_ release and change Conda_ semantics to match\n  recent updates to Galaxy. For the most robust Conda_ usage - use planemo 0.30+\n  with Galaxy 16.07 or master.\n  07d94bd_\n* Implement the ``--conda_auto_init`` flag for ``conda_install``. ca19910_\n* Allow the environment variable ``PLANEMO_CONDA_PREFIX`` to set a default\n  for ``--conda_prefix``.\n  24008ab_\n* Fixup documentation regarding installs and Conda_. ce44e87_\n* Fix and lint Python module import order throughout project.\n  `Pull Request 550`_\n* Use ``cp`` rather than symlink to ``$DOWNLOAD_CACHE`` in the\n  ``dependency_script`` command (thanks to `@peterjc`_).  c2204b3_\n* Fixes for the Homebrew recipe updater. c262b6d_\n\n---------------------\n0.29.1 (2016-08-19)\n---------------------\n\n* Improved handling of Python 2.7 specific dependencies.\n\n---------------------\n0.29.0 (2016-08-19)\n---------------------\n\n* Look for sha256sum checksums during shed_lint (thanks to `@peterjc`_).\n  `Pull Request 539`_\n* An assortment fixes and enhancements to the ``dependency_script`` command\n  (thanks to `@peterjc`_). `Pull Request 541`_, `Pull Request 545`_\n* Fix shed_build to respect exclude: in .shed.yml (thanks to `@nsoranzo`_).\n  `Pull Request 540`_\n* Fix linting of tool URLs (thanks to `@nsoranzo`_). `Pull Request 546`_\n\n---------------------\n0.28.0 (2016-08-17)\n---------------------\n\n* Fixes for bioblend_ v0.8.0 (thanks to `@nsoranzo`_). 9fdf490_\n* Enable shed repo type update (thanks to `@nsoranzo`_). 3ceaa40_\n* Create suite repositories with repository_suite_definition type by default\n  (thanks to `@nsoranzo`_).\n  057f4f0_\n* Include ``shed_lint`` in script run by ``travis_init`` (thanks to `@peterjc`_).\n  `Pull Request 528`_\n* Minor polish to the ``travis_init`` command (thanks to `@peterjc`_).\n  `Pull Request 512`_\n* Update pip_ and setuptools on TravisCI; fix travis_init (thanks to `@peterjc`_).\n  `Pull Request 521`_\n* Shorten command one line descriptions for main help (thanks to `@peterjc`_).\n  `Pull Request 510`_\n* Use ``planemo test --no_cache_galaxy`` under TravisCI (thanks to `@peterjc`_).\n  `Pull Request 513`_\n* Improve and fix docs ahead of GCC 2016 (thanks to `@martenson`_).\n  `Pull Request 498`_, 725b232_\n* Add description of ``expect_num_outputs`` to planemo FAQ. a066afb_\n* Revise planemo tools docs to be more explicit about collection identifiers.\n  a811e65_\n* Add more docs on existing dynamic tool output features. `Pull Request 526`_\n* Fix serve command doc (thanks to `@nsoranzo`_). 8c088c6_\n* Fix `make lint-readme` (RST link errors) (thanks to `@peterjc`_).\n  `Pull Request 525`_\n* Add union bedgraph example to project templates (for GCC demo example).\n  d53bcd6_\n* Add Flow Cytometry Analysis, Data Export, and Constructive Solid Geometry as\n  shed categories (thanks to `@bgruening`_, `@gregvonkuster`_, and `@nsoranzo`_).\n  e890ab5_, 08bb354_, e2398fb_\n* Remove duplicated attribute in docs/writing/bwa-mem_v5.xml (thanks to\n  Paul Stewart `@pstew`_).\n  `Pull Request 507`_\n\n---------------------\n0.27.0 (2016-06-22)\n---------------------\n\n* Use ephemeris to handle syncing shed tools for workflow actions.\n  1c6cfbb_\n* More planemo testing enhancements for testing artifacts that aren't\n  Galaxy tools. `Pull Request 491`_\n* Implement ``docker_galaxy`` engine type. eb039c0_, `Issue 15`_\n* Enhance profiles to be Dockerized Galaxy-aware. `Pull Request 488`_\n* Add linter for DOI type citation - thanks to `@mvdbeek`_.\n  `Pull Request 484`_\n\n---------------------\n0.26.0 (2016-05-20)\n---------------------\n\n* Implement ``Engine`` and ``Runnable`` abstractions - Planemo now has\n  beta support for testing Galaxy workflows and CWL_ tools with Galaxy and\n  any CWL_ artifact with cwltool_.\n  `Pull Request 454`_, 7be1bf5_\n* Fix missing command_line in test output json. e38c436_\n* More explicit Galaxy ``job_conf.xml`` handling, fixes bugs caused by\n  ``galaxy_root`` having existing and incompatible ``job_conf.xml`` files\n  and makes it possible to specify defaults with fixed server name. c4dfd55_\n* Introduce profile commands (``profile_create``, ``profile_delete``, and\n  ``profile_list``) and profile improvements (automatic postgres database\n  creation support). `Pull Request 480`_, a87899b_\n* Rework Galaxy test reporting to use structured data instead of XUnit\n  data. 4d29bf1_\n* Refactor Galaxy configuration toward support for running Galaxy in\n  docker-galaxy-stable. `Pull Request 479`_\n\n---------------------\n0.25.1 (2016-05-11)\n---------------------\n\n* Tweak dependencies to try to fix cwltool_ related issues - such\n  as `Issue 475`_.\n\n---------------------\n0.25.0 (2016-05-11)\n---------------------\n\n* Implement Galaxy \"profiles\" - the ability to configure\n  perisistent, named environments for ``serve`` and ``test``.\n  5d08b67_\n* Greatly improved ``serve`` command - make ``test-data``\n  available as an FTP folder, (on 16.07) automatically log\n  in an admin user, and many more options (such as those\n  required for \"profiles\" and a ``--daemon`` mode).\n* Two fixes to ensure more consistent, dependable ``test`` output.\n  `Pull Request 472`_, f3c6917_\n* Add code and documentation for linting (``lint``) and\n  building (``tool_init``) CWL_ tools. a4e6958_, b0b867e_,\n  4cd571c_\n* If needed for Conda_ workaround, shorten ``config_directory``\n  path (thanks to `@mvdbeek`_). efc5f30_\n* Fix ``--no_cache_galaxy`` option (thanks to Gildas Le\n  Corguill\u00e9). d8f2038_\n* Target draft 3 of CWL_ instead of draft 2. 775bf49_\n* Fix ``cwltool`` dependency version - upstream changes broke\n  compatibility. `65b999d`_\n* Add documentation section and slides about recent Galaxy\n  tool framework changes (with fix from `@remimarenco`_). 069e7ba_\n* Add IUC standards to Planemo docs. 2ae2b49_\n* Improve collection-related contents in documentation\n  (thanks in part to `@martenson`_).\n  fea51fc_, 13a5ae7_\n* Add documentation on ``GALAXY_SLOTS`` and running planemo\n  on a cluster. 45135ff_, e0acf91_\n* Revise command-line handling framework for consistency and\n  extension - allow extra options to be configured as\n  defaults ``~/.planemo.yml`` including ``--job_config_file``\n  and Conda_ configuration options. e769118_, 26e378e_\n* Fix ``tool_init`` commans options typos (thanks to\n  Nitesh Turaga). 826d371_\n* Refactor galaxy-related modules into submodules of a new\n  ``planemo.galaxy`` package. 8e96864_\n* Fix error message typo (thanks to `@blankenberg`_). b1c8f1d_\n* Update documentation for recent command additions. 3f4ab44_\n* Rename option ``--galaxy_sqlite_database`` option to\n  ``--galaxy_database_seed`` and fix it so it actually works.\n  f7554d1_\n* Add ``--extra_tools`` option to ``serve`` command. 02a08a0_\n* Update project testing to include linting documentation\n  (``docs/``), Python import order, and docstrings.\n  a13a120_, 6e1e726_, 95d5cba_\n\n\n---------------------\n0.24.2 (2016-04-25)\n---------------------\n\n* Revert \"check ``.shed.yml`` owner against credentials during shed\n  creation\", test was incorrect and preventing uploads.\n  `Pull Request 425`_, `Issue 246`_\n\n---------------------\n0.24.1 (2016-04-08)\n---------------------\n\n* Fix test summary report. `Pull Request 429`_\n* Improve error reporting when running ``shed_test``. ce8e1be_\n* Improved code comments and tests for shed related functionality.\n  89674cb_\n* Rev `galaxy-lib`_ dependency to 16.4.1 to fix wget usage in\n  newer versions of wget. d76b489_\n\n---------------------\n0.24.0 (2016-03-29)\n---------------------\n\n* Drop support for Python 2.6. 93b7bda_\n* A variety of fixes for ``shed_update``.\n  `Pull Request 428`_, `Issue 416`_\n* Fix reporting of metadata updates for invalid shed updates.\n  `Pull Request 426`_, `Issue 420`_\n* Check ``.shed.yml`` owner against credentials during shed creation.\n  `Pull Request 425`_, `Issue 246`_\n* Fix logic error if there is a problem with ``shed_create``. 358a42c_\n* Tool documentation improvements. 0298510_, a58a3b8_\n\n---------------------\n0.23.0 (2016-02-15)\n---------------------\n\n* Fix duplicated attributes with Conda_ resolver (thanks\n  to Bj\u00f6rn Gr\u00fcning). `Pull Request 403`_\n* Upgrade to latest version of `galaxy-lib`_ for more linting.\n* Attempt to better handle conditional dependency on cwltool.\n\n---------------------\n0.22.2 (2016-01-14)\n---------------------\n\n* Fixed bug targetting forthcoming release of Galaxy 16.01.\n\n---------------------\n0.22.1 (2016-01-14)\n---------------------\n\n* Fixed problem with PyPI_ build artifacts due to submodule's not\n  being initialized during previous release.\n\n---------------------\n0.22.0 (2016-01-13)\n---------------------\n\n* Add ``--skip_venv`` to support running Galaxy 16.01 inside of\n  conda environments. 9f3957d_\n* Implement conda support. f99f6c1_, ad3b2f0_, 5e0b6d1_\n* Update LICENSE for Planemo to match Galaxy. 15d33c7_\n* Depend on new `galaxy-lib`_ on PyPI_ instead of previous hacks....\n  `Pull Request 394`_\n* Fix egg caching against master/15.10. 6d0f502_\n* Fix bug causing shed publishing of ``.svn`` directories.\n  `Issue 391`_\n* Bug fixes for Conda_ support thanks to `@bgruening`_. 63e456c_\n* Fix document issues thanks to `@einon`_.\n  `Pull Request 390`_\n* Improve client for shed publishing to support newer shed backend\n  being developed by `@erasche`_. `Pull Request 394`_\n* Tool Shed ``repo_id`` change, `@erasche`_. `Pull Request 398`_\n* Various other small changes to testing, project structure, and\n  Python 3 support.\n\n---------------------\n0.21.1 (2015-11-29)\n---------------------\n\n* Fix serious regression to ``test`` command. 94097c7_\n* Small fixes to release process. 4e1377c_, 94645ed_\n\n---------------------\n0.21.0 (2015-11-29)\n---------------------\n\n* If ``virtualenv`` not on ``PATH``, have Planemo create one for Galaxy.\n  5b97f2e_\n* Add documentation section on testing tools installed in an existing\n  Galaxy instance. 1927168_\n* When creating a virtualenv for Galaxy, prefer Python 2.7.\n  e0577e7_\n* Documentation fixes and improvements thanks to `@martenson`_.\n  0f8cb10_, 01584c5_, b757791_\n* Specify a minimum ``six`` version requirement. 1c7ee5b_\n* Add script to test a planemo as a wheel. 6514ff5_, `Issue 184`_\n* Fix empty macro loading. `Issue 362`_\n* Fix an issue when you run ``shed_diff --shed_target local`` thanks\n  to Gwendoline Andres and Gildas Le Corguill\u00e9 at ABiMS Roscoff.\n  `Pull Request 375`_\n* Fix ``shed_diff`` printing to stdout if ``-o`` isn't specified.\n  f3394e7_\n* Small ``shed_diff`` improvements to XML diffing and XUnit reporting.\n  af7448c_, 83e227a_\n* More logging of ``shed_diff`` results if ``--verbose`` flagged.\n  9427b47_\n* Add ``test_report`` command for rebuilding reports from structured JSON.\n  99ee51a_\n* Fix option bug with Click 6.0 thanks to `@bgruening`_. 2a7c792_\n* Improved error messages for test commands. fdce74c_\n* Various fixes for Python 3. 2f66fc3_, 7572e99_, 8eda729_, 764ce01_\n* Use newer travis container infrastructure for testing. 6d81a94_\n* Test case fixes. 98fdc8c_, 0e4f70a_\n\n---------------------\n0.20.0 (2015-11-11)\n---------------------\n\n* More complete I/O capturing for XUnit. 6409449_\n* Check for select parameter without options when linting tools.\n  `Issue 373`_\n* Add ``--cwl_engine`` argument to ``cwl_run`` command. dd94ddc_\n* Fixes for select parameter linting. 8b31850_\n* Fix to demultiplexing repositories after tool uploads. `Issue 361`_\n* Fix to update planemo for Galaxy wheels. 25ef0d5_\n* Various fixes for Python 2.6 and Python 3.\n  c1713d2_, 916f610_, c444855_\n\n---------------------\n0.19.0 (2015-11-03)\n---------------------\n\n* Initial implementation of ``cwl_run`` command that runs a\n  CWL tool and job file through Galaxy. 49c5c1e_\n* Add ``--cwl`` flag to ``serve`` to experimentally serve CWL tools\n  in Galaxy.\n  `Pull Request 339`_\n* Implement highly experimental ``cwl_script`` command to convert\n  a CWL job to a bash script. 508dce7_\n* Add name to all XUnit reports (thanks to `@erasche`_).\n  `Pull Request 343`_\n* Capture stdout and stderr for ``shed_diff`` and ``shed_update``\n  XUnit reports. `Pull Request 344`_\n* More tool linting (conditionals) thanks to `@erasche`_.\n  `Pull Request 350`_\n* UTF-8 fixes when handling XUnit reports. `Pull Request 345`_\n* Add `Epigenetics` as Tool Shed category. `Pull Request 351`_\n* Merge changes to common modules shared between Galaxy, Planemo, and Pulsar (thanks to `@natefoo`_).\n  `Pull Request 356`_\n* Add ``--cite_url`` to ``tool_init``. fdb1b51_\n* ``tool_init`` bug fix. f854138_\n* Fix `setup.py`_ for cwltool and bioblend_ changes. 1a157d4_\n* Add option to specify template sqlite database locally. c23569f_\n* Add example IPython notebooks to docs. c8640b6_\n\n---------------------\n0.18.1 (2015-10-22)\n---------------------\n\n* Fix issue with test reporting not being populated. 19900a6_\n\n---------------------\n0.18.0 (2015-10-20)\n---------------------\n\n* Improvements to ``docker_shell`` usability (thanks to `@kellrott`_).\n  `Pull Request 334`_\n* Add docker pull attempt when missing Dockerfile (thanks to `@kellrott`_).\n  `Pull Request 333`_\n* Fix bug inferring which files are tool files (thanks to `@erasche`_).\n  `Pull Request 335`_, `Issue 313`_\n* Initial work toward automating brew recipe update. 4d6f7d9_, `Issue 329`_\n\n---------------------\n0.17.0 (2015-10-19)\n---------------------\n\n* Implement basic XUnit report option for ``shed_update`` (thanks to `@martenson`_).\n  `Pull Request 322`_\n* Fix issues with producing test outputs. 572e754_\n* Xunit reporting improvements - refactoring, times, diff output (thanks to `@erasche`_).\n  `Pull Request 330`_\n* Implement project governance policy and update developer code of conduct to\n  match that of the Galaxy project. `Pull Request 316`_\n* Update filters for account for new ``.txt`` and ``.md`` test outputs\n  (thanks to `@erasche`_). `Pull Request 327`_\n* Add verbose logging to galaxy test output handling problems. 5d7db92_\n* Flake8 fixes (thanks to `@martenson`_). 949a36d_\n* Remove uses of deprecated ``mktemp`` Python standard library function\n  (thanks to `@erasche`_). `Pull Request 330`_\n\n---------------------\n0.16.0 (2015-10-07)\n---------------------\n\n* Adding new command ``dependency_script`` to convert Tool Shed dependencies\n  into shell scripts - thanks to `@peterjc`_.\n  `Pull Request 310`_, f798c7e_, `Issue 303`_\n* Implement profiles in sheds section of the ``~/.planemo.yml``.\n  `Pull Request 314`_\n\n---------------------\n0.15.0 (2015-10-01)\n---------------------\n\n* Template framework for reporting including new markdown and plain\n  text reporting options for testing - thanks to `@erasche`_.\n  `Pull Request 304`_\n* XUnit style reporting for ``shed_diff`` command - thanks to\n  `@erasche`_. `Pull Request 305`_\n* Add new ``shed_build`` command for building repository tarballs -\n  thanks to `@kellrott`_. `Pull Request 297`_\n* Fix exit code handling for ``lint`` commands - thanks to `@mvdbeek`_.\n  `Pull Request 292`_\n* Improved documentation for ``serve`` command - thanks to `@lparsons`_.\n  `Pull Request 312`_\n* Tiny backward compatible Python 3 tweaks for `Tool Factory`_ - thanks\n  to `@peterjc`_. dad2d9d_\n* Fixed detection of virtual environment in ``Makefile`` - thanks to\n  `@lparsons`_. `Pull Request 311`_\n* Updates to Galaxy XSD - thanks to `@mr-c`_. `Pull Request 309`_\n* Allow reading shed key option from an environment variable.\n  `Pull Request 307`_\n* Allow specifying host to serve Galaxy using ``-host`` - thanks in\n  part to `@chambm`_. `Pull Request 301`_\n* Allow specifying defaults for ``-host`` and ``--port`` in\n  ``~/.planemo.yml``. `Pull Request 301`_\n* Improve ``~/.planemo.yml`` sample comments - thanks to `@martenson`_.\n  `Pull Request 287`_\n* Update tool shed categories - thanks to `@bgruening`_. `Pull Request 285`_\n* Improved output readibility for ``diff`` command - thanks to `@martenson`_. `Pull Request 284`_\n\n---------------------\n0.14.0 (2015-08-06)\n---------------------\n\n* Allow ``-t`` as shorthand for ``--shed_target`` (thanks to Peter Cock).\n  `Pull Request 278`_\n* Fix ``tool_init`` command to use ``from_work_dir`` only if file in command\n  (thanks to bug report and initial fix outline by Gildas Le Corguill\u00e9).\n  `Pull Request 277`_\n* Various documentation fixes (thanks in part to Peter Cock and Daniel\n  Blankenberg). `Pull Request 256`_, `Pull Request 253`_, `Pull Request 254`_,\n  `Pull Request 255`_, `Pull Request 251`_, `Issue 272`_\n\n---------------------\n0.13.2 (2015-07-06)\n---------------------\n\n* Fix project_init for missing files. cb5b906_\n* Various documentation improvements.\n\n---------------------\n0.13.1 (2015-07-01)\n---------------------\n\n* Fix for ``shed_init`` producing non-standard type hints. `Issue 243`_,\n  f0610d7_\n* Fix tool linting for parameters that define an ``argument`` but not a\n  ``name``. `Issue 245`_, aad1eed_\n* Many doc updates including a tutorial for developing tools in a test-driven\n  fashion and instructions for using the planemo appliance through Kitematic\n  (with Kitematic screenshots from E. Rasche).\n\n---------------------\n0.13.0 (2015-06-28)\n---------------------\n\n* If planemo cannot find a Galaxy root, it will now automatically fetch\n  one (specifing ``--galaxy_install`` will still force a fetch).\n  `Pull Request 235`_\n* `Docuementation <http://planemo.readthedocs.org/en/latest/appliance.html>`__\n  has been updated to reflect new and vastly improved Docker and Vagrant\n  virtual appliances are now available, as well as a new VirtualBox OVA\n  variant.\n* Update linting for new tool XML features (including ``detect_errors``\n  and output collections). `Issue 233`_, 334f2d4_\n* Fix ``shed_test`` help text. `Issue 223`_\n* Fix code typo (thanks to Nicola Soranzo). `Pull Request 230`_\n* Improvements to algorithm used to guess if an XML file is a tool XML file.\n  `Issue 231`_\n* Fix configuration file handling bug. `Issue 240`_\n\n---------------------\n0.12.2 (2015-05-23)\n---------------------\n\n* Fix ``shed_test`` and ``shed_serve`` for test and local tool sheds.\n  f3cafaa_\n\n---------------------\n0.12.1 (2015-05-21)\n---------------------\n\n* Fix to ensure the tab completion script is in the Python source tarball\n  (required for setting up tab-completion for Homebrew). 6b4e7a6_\n\n---------------------\n0.12.0 (2015-05-21)\n---------------------\n\n* Implement a ``--failed`` flag for the ``test`` command to rerun\n  previously faied tests. `Pull Request 210`_\n* Implement ``shed_update`` to upload contents and update repository\n  metadata. `Pull Request 216`_\n* Implement ``shed_test`` and ``shed_serve`` commands to test and view\n  published artifacts in the Tool Shed. `Pull Request 213`_, `Issue 176`_\n* Add shell tab-completion script. 37dcc07_\n* Many more commands allow specifing multiple tool and/or repository targets.\n  `Issue 150`_\n* Add -m as alias for --message in planemo shed_upload (thanks to\n  Peter Cock). `Pull Request 200`_\n* Add ``--ensure_metadata`` option to ``shed_lint`` to ensure ``.shed.yml``\n  files contain many repository. `Pull Request 215`_\n* More developer documentation, additional ``make`` targets including ones\n  for setting up git pre-commit hooks. cc8abb6_, `Issue 209`_\n* Small README improvement (thanks to Martin \u010cech) b53006d_\n* Fixes for shed operation error handling (thanks to Martin \u010cech).\n  `Pull Request 203`_,  `Pull Request 206`_\n* Fix for \"smart\" ``shed_diff`` not in the repository root directory\n  (thanks to Peter Cock). `Pull Request 207`_, `Issue 205`_\n* Recursive ``shed_diff`` with directories not yet in Tool Shed.\n  `Pull Request 208`_\n* Improve error handling and reporting for problematic ``--shed_target``\n  values. `Issue 217`_\n* Fix typos in lint messages. `Issue 211`_\n\n\n---------------------\n0.11.1 (2015-05-12)\n---------------------\n\n* Fix default behavior for ``planemo lint`` to use current directory if\n  explicit paths are not supplied. 1e3668a_\n\n---------------------\n0.11.0 (2015-05-12)\n---------------------\n\n* More compact syntax for defining multiple custom inclusions in ``.shed.yml``\n  files - thanks to Peter Cock. `Issue 180`_, `Pull Request 185`_,\n  `Pull Request 196`_\n* Prevent ambigous destinations when defining custom inclusions in\n  ``.shed.yml``- thanks to Peter Cock. `Pull Request 186`_\n* ``lint`` now warns if tool ids contain whitespace. `Pull Request 190`_\n* Handle empty tar-balls gracefully on older Python versions - thanks\n  to Peter Cock. `Pull Request 187`_\n* Tweak quoting in ``cp`` command - thanks to Peter Cock. 6bcf699_\n* Fix regression causing testing to no longer produce \"pretty\" test\n  results under certain circumstances. `Issue 188`_\n* Fix for recursive ``shed_diff`` folder naming. `Issue 192`_\n* Fix output definitions to ``tool_init`` command. `Issue 189`_\n\n---------------------\n0.10.0 (2015-05-06)\n---------------------\n\n* Extend ``shed_lint`` to check for valid actions in tool_dependencies.xml\n  files. 8117e03_\n* Extend ``shed_lint`` to check for required files based on repository type.\n  `Issue 156`_\n* Ignore common editor backup files during ``shed_upload``. `Issue 179`_\n* Fix missing file when installing from source via PyPI_. `Issue 181`_\n* Fix ``lint`` to verify ``data`` inputs specify a ``format`` attribute.\n  8117e03_\n* Docstring fix thanks to `@peterjc`_. fe7ad46_\n\n\n---------------------\n0.9.0 (2015-05-03)\n---------------------\n\n* Add new logo to the README thanks to `@petrkadlec`_ from `puradesign.cz\n  <http://puradesign.cz/en>`__ and `@carlfeberhard`_ from the Galaxy Project.\n  `Issue 108`_\n* Implement smarter ``shed_diff`` command - it now produces a meaningful\n  exit codes and doesn't report differences if these correspond to attributes\n  that will be automatically populated by the Tool Shed. `Issue 167`_\n* Use new smarter ``shed_diff`` code to implement a new ``--check_diff``\n  option for ``shed_upload`` - to check for meaningful differences before\n  updating repositories. `Issue 168`_\n* Record git commit hash during ``shed_upload`` if the ``.shed.yml`` is\n  located in a git repository. `Issue 170`_\n* Allow ``shed_`` operations to operate on git URLs directly. `Issue 169`_\n* Fail if missing file inclusion statements encountered during ``.shed.yml``\n  repository resolution - bug reported by `@peterjc`_. `Issue 158`_\n* Improved exception handling for tool shed operations including new\n  ``--fail_fast`` command-line option. * `Issue 114`_, `Pull Request 173`_\n* Implement more validation when using the ``shed_init`` command. 1cd0e2d_\n* Add ``-r/--recursive`` option to ``shed_download`` and ``shed_diff``\n  commands and allow these commands to work with ``.shed.yml`` files defining\n  multipe repositories. 40a1f57_\n* Add ``--port`` option to the ``serve`` and ``tool_factory`` commands.\n  15804be_\n* Fix problem introduced with `setup.py`_ during the 0.9.0 development cycle\n  - thanks to `@peterjc`_. `Pull Request 171`_\n* Fix clone bug introduced during 0.9.0 development cycle - thanks to\n  `@bgruening`_. `Pull Request 175`_\n\n---------------------\n0.8.4 (2015-04-30)\n---------------------\n\n* Fix for Travis CI testing picking up invalid tests (reported by `@takadonet`_). `Issue 161`_\n* Fix tar ordering for consistency (always sort by name) - thanks to `@peterjc`_.  `Pull Request 164`_, `Issue 159`_\n* Fix exception handling related to tool shed operations - thanks to `@peterjc`_. `Pull Request 155`_, b86fe1f_\n\n---------------------\n0.8.3 (2015-04-29)\n---------------------\n\n* Fix bug where ``shed_lint`` was not respecting the ``-r/--recursive`` flag.\n  9ff0d2d_\n* Fix bug where planemo was producing tar files incompatible with the Tool\n  Shed for package and suite repositories. a2ee135_\n\n---------------------\n0.8.2 (2015-04-29)\n---------------------\n\n* Fix bug with ``config_init`` command thanks to `@bgruening`_. `Pull Request 151`_\n* Fix unnessecary ``lint`` warning about ``parallelism`` tag reported by\n  `@peterjc`_. 9bf1eab_\n\n---------------------\n0.8.1 (2015-04-28)\n---------------------\n\n* Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.\n\n---------------------\n0.8.0 (2015-04-27)\n---------------------\n\n* Implement the new ``shed_lint`` command that verifies various aspects of tool\n  shed repositories - including XSD_ validation of ``repository_dependencies.xml``\n  and ``tool_dependencies.xml`` files, best practices for README files, and the\n  contents of ``.shed.yml`` files. This requires the lxml_ library to be available\n  to Planemo or the application xmllint_ to be on its ``PATH``. `Pull Request 130`_\n  `Issue 89`_ `Issue 91`_ 912df02_ d26929e_ 36ac6d8_\n* Option to enable experimental XSD_ based validation of tools when ``lint``\n  is executed with the new ``--xsd`` flag. This validation occurs against the\n  unofficial `Galaxy Tool XSD project <https://github.com/JeanFred/Galaxy-XSD>`__\n  maintained by `@JeanFred`_. This requires the lxml_ library to be\n  available to Planemo or the application xmllint_ to be on its ``PATH``.\n  `Pull Request 130`_ 912df02_\n* Allow skipping specific linters when using the ``lint`` command using the new\n  ``--skip`` option. 26e3cdb_\n* Implement sophisticated options in ``.shed.yml`` to map a directory to many,\n  custom Tool Shed repositories during shed operaitons such ``shed_upload``\n  including automatically mapping tools to their own directories and automatically\n  building suites repositories. `Pull Request 143`_\n* Make ``shed_upload`` more intelligent when building tar files so that package\n  and suite repositories may have README files in source control and they will\n  just be filtered out during upload. 53edd99_\n* Implement a new ``shed_init`` command that will help bootstrap ``.shed.yml``\n  files in the specified directory. cc1a447_\n* Extend ``shed_init`` to automatically build a ``repository_rependencies.xml``\n  file corresponding to a Galaxy workflow (``.ga`` file). `Issue 118`_ 988de1d_\n* In addition to a single file or directory, allow ``lint`` to be passed multiple\n  files. 343902d_ `Issue 139`_\n* Add ``-r/--recursive`` option to ``shed_create`` and ``lint`` commands. 63cd431_\n  01f2af9_\n* Improved output formatting and option to write diffs to a file for the\n  ``shed_diff`` command. 965511d_\n* Fix lint problem when using new Galaxy testing features such as expecting\n  job failures and verifing job output. `Issue 138`_\n* Fix typo in ``test`` help thanks to first time contributor `@pvanheus`_.\n  `Pull Request 129`_ 1982076_\n* Fix NPE on empty ``help`` element when linting tools. `Issue 124`_\n* Fix ``lint`` warnings when ``configfiles`` are defined in a tool. 1a85493_\n* Fix for empty ``.shed.yml`` files. b7d9e96_\n* Fix the ``test`` command for newer versions of nose_. 33294d2_\n* Update help content and documentation to be clear ``normalize`` should not\n  be used to update the contents of tool files at this time. 08de8de_\n* Warn on unknown ``command`` attributes when linting tools (anything but\n  ``interpreter``). 4f61025_\n* Various design, documentation (including new documentation on Tool Shed\n  `publishing <http://planemo.readthedocs.org/en/latest/publishing.html>`__),\n  and testing related improvements (test coverage has risen from 65% to over\n  80% during this release cycle).\n\n---------------------\n0.7.0 (2015-04-13)\n---------------------\n\n* Implement `shed_create` command to create Tool Shed repositories from\n  ``.shed.yml`` files (thanks to E. Rasche). `Pull Request 101`_\n* Allow automatic creation of missing repositories  during ``shed_upload``\n  with the new ``--force_repository_creation`` flag (thanks to E. Rasche).\n  `Pull Request 102`_\n* Allow specifying files to exclude in ``.shed.yml`` when creating tar files\n  for ``shed_upload`` (thanks to Bj\u00f6rn Gr\u00fcning). `Pull Request 99`_\n* Resolve symbolic links when building Tool Shed tar files with\n  ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 104`_\n* Add a `Contributor Code of Conduct\n  <https://planemo.readthedocs.org/en/latest/conduct.html>`__.\n  `Pull Request 113`_\n* Omit ``tool_test_output.json`` from Tool Shed tar file created with\n  ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 111`_\n* Update required version of bioblend_ to ``0.5.3``. Fixed `Issue 88`_.\n* Initial work on implementing tests cases for Tool Shed functionality.\n  182fe57_\n* Fix incorrect link in HTML test report (thanks to Martin \u010cech). 4c71299_\n* Download Galaxy from the new, official Github repository. 7c69bf6_\n* Update travis_test to install stable planemo from PyPI_. 39fedd2_\n* Enable caching on ``--install_galaxy`` by default (disable with\n  ``--no_cache_galaxy``). d755fe7_\n\n---------------------\n0.6.0 (2015-03-16)\n---------------------\n\n* Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc...\n* Fix ``tool_init`` to quote file names (thanks to Peter Cock).  `Pull Request 98`_.\n* Allow ignoring file patterns in ``.shed.yml`` (thanks to Bj\u00f6rn Gr\u00fcning). `Pull Request 99`_\n* Add ``--macros`` flag to ``tool_init`` command to generate a macro file as part of tool generation. ec6e30f_\n* Add linting of tag order for tool XML files. 4823c5e_\n* Add linting of ``stdio`` tags in tool XML files. 8207026_\n* More tests, much higher test coverage. 0bd4ff0_\n\n---------------------\n0.5.0 (2015-02-22)\n---------------------\n\n* Implement ``--version`` option. `Issue 78`_\n* Implement ``--no_cleanup`` option for ``test`` and ``serve`` commands to\n  persist temp files. 2e41e0a_\n* Fix bug that left temp files undeleted. `Issue 80`_\n* More improvements to release process. fba3874_\n\n---------------------\n0.4.2 (2015-02-21)\n---------------------\n\n* Fix `setup.py`_ for installing non-Python data from PyPI_ (required newer\n  for ``tool_factory`` command and reStructuredText linting). Thanks to\n  Damion Dooley for the bug report. `Issue 83`_\n\n---------------------\n0.4.1 (2015-02-16)\n---------------------\n\n* Fix README.rst so it renders properly on PyPI_.\n\n---------------------\n0.4.0 (2015-02-16)\n---------------------\n\n* Implement ``tool_init`` command for bootstrapping creation of new\n  tools (with `tutorial <http://planemo.readthedocs.org/en/latest/writing.html>`_.) 78f8274_\n* Implement ``normalize`` command for reorganizing tool XML and macro\n  debugging. e8c1d45_\n* Implement ``tool_factory`` command to spin up Galaxy pre-configured the\n  `Tool Factory`_. 9e746b4_\n* Added basic linting of ``command`` blocks. b8d90ab_\n* Improved linting of ``help`` blocks, including verifying valid\n  `reStructuredText`. 411a8da_\n* Fix bug related to ``serve`` command not killing Galaxy properly when complete. 53a6766_\n* Have ``serve`` command display tools at the top level instead of in shallow sections. badc25f_\n* Add additional dependencies to ``setup.py`` more functionality works out\n  of the box. 85b9614_\n* Fix terrible error message related to bioblend_ being unavailable.\n  `Issue 70`_\n* Various smaller documentation and project structure improvements.\n\n---------------------\n0.3.1 (2015-02-15)\n---------------------\n\n* Fixes to get PyPI_ workflow working properly.\n\n---------------------\n0.3.0 (2015-02-13)\n---------------------\n\n* Add option (``-r``) to the ``shed_upload`` command to recursively upload\n  subdirectories (thanks to E. Rasche). `Pull Request 68`_\n* Fix diff formatting in test reports (thanks to E. Rasche).\n  `Pull Request 63`_\n* Grab updated test database to speed up testing (thanks to approach from\n  E. Rasche and Dannon Baker). `Issue 61`_, dff4f33_\n* Fix test data command-line argument name (was ``test-data`` now it is\n  ``test_data``). 834bfb2_\n* Use ``tool_data_table_conf.xml.sample`` file if\n  ``tool_data_table_conf.xml.test`` is unavailable. Should allow some\n  new tools to be tested without modifying Galaxy's global\n  ``tool_data_table_conf.xml`` file. ac4f828_\n\n---------------------\n0.2.0 (2015-01-13)\n---------------------\n\n* Improvements to way Planemo loads its own copy of Galaxy modules to prevent\n  various conflicts when launching Galaxy from Planemo. `Pull Request 56`_\n* Allow setting various test output options in ``~/.planemo.yml`` and disabling\n  JSON output. 21bb463_\n* More experimental Brew and Tool Shed options that should not be considered\n  part of Planemo's stable API. See bit.ly/gxbrew1 for more details.\n* Fix ``project_init`` for BSD tar (thanks to Nitesh Turaga for the bug\n  report.) a4110a8_\n* Documentation fixes for tool linting command (thanks to Nicola Soranzo).\n  `Pull Request 51`_\n\n---------------------\n0.1.0 (2014-12-16)\n---------------------\n\n* Moved repository URL to https://github.com/galaxyproject/planemo.\n* Support for publishing to the Tool Shed. `Pull Request 6`_\n* Support for producing diffs (``shed_diff``) between local repositories and\n  the Tool Shed (based on scripts by Peter Cock). `Pull Request 33`_\n* Use tool's local test data when available - add option for configuring\n  ``test-data`` target. `Pull Request 1`_\n* Support for testing tool features dependent on cached data. 44de95c_\n* Support for generating XUnit tool test reports. 82e8b1f_\n* Prettier HTML reports for tool tests. 05cc9f4_\n* Implement ``share_test`` command for embedding test result links in pull\n  requests. `Pull Request 40`_\n* Fix for properly resolving links during Tool Shed publishing (thanks to Dave\n  Bouvier). `Pull Request 29`_\n* Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061_\n* Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan\n  Blankenberg). a2c13e4_\n* Automate more of Travis CI testing so the scripts added to tool repository\n  can be smaller. 20a8680_\n* Documentation fixes for Travis CI (thanks to Peter Cock). `Pull Request 22`_,\n  `Pull Request 23`_\n* Various documentation fixes (thanks to Martin \u010cech). 36f7cb1_, b9232e5_\n* Various smaller fixes for Docker support, tool linting, and documentation.\n\n---------------------\n0.0.1 (2014-10-04)\n---------------------\n\n* Initial work on the project - commands for testing, linting, serving Galaxy\n  tools - and more experimental features involving Docker and Homebrew. 7d07782_\n\n.. github_links\n.. _1ab8530: https://github.com/galaxyproject/planemo/commit/1ab8530\n.. _Pull Request 966: https://github.com/galaxyproject/planemo/pull/966\n.. _Pull Request 964: https://github.com/galaxyproject/planemo/pull/964\n.. _Pull Request 963: https://github.com/galaxyproject/planemo/pull/963\n.. _Pull Request 959: https://github.com/galaxyproject/planemo/pull/959\n.. _Pull Request 958: https://github.com/galaxyproject/planemo/pull/958\n.. _Pull Request 950: https://github.com/galaxyproject/planemo/pull/950\n.. _Pull Request 944: https://github.com/galaxyproject/planemo/pull/944\n.. _Pull Request 926: https://github.com/galaxyproject/planemo/pull/926\n.. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937\n.. _Pull Request 938: https://github.com/galaxyproject/planemo/pull/938\n.. _Pull Request 943: https://github.com/galaxyproject/planemo/pull/943\n.. _Pull Request 940: https://github.com/galaxyproject/planemo/pull/940\n.. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937\n.. _Pull Request 935: https://github.com/galaxyproject/planemo/pull/935\n.. _Pull Request 931: https://github.com/galaxyproject/planemo/pull/931\n.. _Pull Request 930: https://github.com/galaxyproject/planemo/pull/930\n.. _Pull Request 913: https://github.com/galaxyproject/planemo/pull/913\n.. _Pull Request 917: https://github.com/galaxyproject/planemo/pull/917\n.. _Pull Request 921: https://github.com/galaxyproject/planemo/pull/921\n.. _Pull Request 918: https://github.com/galaxyproject/planemo/pull/918\n.. _Pull Request 924: https://github.com/galaxyproject/planemo/pull/924\n.. _Pull Request 925: https://github.com/galaxyproject/planemo/pull/925\n.. _Pull Request 912: https://github.com/galaxyproject/planemo/pull/912\n.. _Pull Request 915: https://github.com/galaxyproject/planemo/pull/915\n.. _Pull Request 914: https://github.com/galaxyproject/planemo/pull/914\n.. _07dc6e0: https://github.com/galaxyproject/planemo/commit/07dc6e0\n.. _Pull Request 910: https://github.com/galaxyproject/planemo/pull/910\n.. _Pull Request 909: https://github.com/galaxyproject/planemo/pull/909\n.. _Pull Request 908: https://github.com/galaxyproject/planemo/pull/908\n.. _Pull Request 907: https://github.com/galaxyproject/planemo/pull/907\n.. _Pull Request 906: https://github.com/galaxyproject/planemo/pull/906\n.. _Pull Request 902: https://github.com/galaxyproject/planemo/pull/902\n.. _Pull Request 895: https://github.com/galaxyproject/planemo/pull/895\n.. _Issue 845: https://github.com/galaxyproject/planemo/issues/845\n.. _Issue 898: https://github.com/galaxyproject/planemo/issues/898\n.. _Pull Request 899: https://github.com/galaxyproject/planemo/pull/899\n.. _Pull Request 896: https://github.com/galaxyproject/planemo/pull/896\n.. _Pull Request 894: https://github.com/galaxyproject/planemo/pull/894\n.. _Pull Request 876: https://github.com/galaxyproject/planemo/pull/876\n.. _Pull Request 893: https://github.com/galaxyproject/planemo/pull/893\n.. _Pull Request 892: https://github.com/galaxyproject/planemo/pull/892\n.. _Pull Request 891: https://github.com/galaxyproject/planemo/pull/891\n.. _Pull Request 889: https://github.com/galaxyproject/planemo/pull/889\n.. _Pull Request 888: https://github.com/galaxyproject/planemo/pull/888\n.. _Pull Request 887: https://github.com/galaxyproject/planemo/pull/887\n.. _Pull Request 882: https://github.com/galaxyproject/planemo/pull/882\n.. _Pull Request 877: https://github.com/galaxyproject/planemo/pull/877\n.. _Pull Request 874: https://github.com/galaxyproject/planemo/pull/874\n.. _Pull Request 871: https://github.com/galaxyproject/planemo/pull/871\n.. _Pull Request 870: https://github.com/galaxyproject/planemo/pull/870\n.. _Pull Request 864: https://github.com/galaxyproject/planemo/pull/864\n.. _Pull Request 867: https://github.com/galaxyproject/planemo/pull/867\n.. _Pull Request 868: https://github.com/galaxyproject/planemo/pull/868\n.. _bad810a: https://github.com/galaxyproject/planemo/commit/bad810a\n.. _Pull Request 851: https://github.com/galaxyproject/planemo/pull/851\n.. _Pull Request 856: https://github.com/galaxyproject/planemo/pull/856\n.. _Pull Request 860: https://github.com/galaxyproject/planemo/pull/860\n.. _Pull Request 866: https://github.com/galaxyproject/planemo/pull/866\n.. _Pull Request 861: https://github.com/galaxyproject/planemo/pull/861\n.. _324c776: https://github.com/galaxyproject/planemo/commit/324c776\n.. _72d2ca7: https://github.com/galaxyproject/planemo/commit/72d2ca7\n.. _b12b117: https://github.com/galaxyproject/planemo/commit/b12b117\n.. _016b923: https://github.com/galaxyproject/planemo/commit/016b923\n.. _2002b49: https://github.com/galaxyproject/planemo/commit/2002b49\n.. _Pull Request 843: https://github.com/galaxyproject/planemo/pull/843\n.. _Pull Request 842: https://github.com/galaxyproject/planemo/pull/842\n.. _Pull Request 841: https://github.com/galaxyproject/planemo/pull/841\n.. _Pull Request 847: https://github.com/galaxyproject/planemo/pull/847\n.. _Pull Request 848: https://github.com/galaxyproject/planemo/pull/848\n.. _Pull Request 849: https://github.com/galaxyproject/planemo/pull/849\n.. _Pull Request 850: https://github.com/galaxyproject/planemo/pull/850\n.. _Pull Request 836: https://github.com/galaxyproject/planemo/pull/836\n.. _Pull Request 833: https://github.com/galaxyproject/planemo/pull/833\n.. _Pull Request 837: https://github.com/galaxyproject/planemo/pull/837\n.. _Pull Request 840: https://github.com/galaxyproject/planemo/pull/840\n.. _Pull Request 838: https://github.com/galaxyproject/planemo/pull/838\n.. _Pull Request 834: https://github.com/galaxyproject/planemo/pull/834\n.. _Pull Request 835: https://github.com/galaxyproject/planemo/pull/835\n.. _347c622: https://github.com/galaxyproject/planemo/commit/347c622\n.. _Pull Request 832: https://github.com/galaxyproject/planemo/pull/832\n.. _Pull Request 831: https://github.com/galaxyproject/planemo/pull/831\n.. _Pull Request 830: https://github.com/galaxyproject/planemo/pull/830\n.. _Pull Request 829: https://github.com/galaxyproject/planemo/pull/829\n.. _Pull Request 828: https://github.com/galaxyproject/planemo/pull/828\n.. _Pull Request 826: https://github.com/galaxyproject/planemo/pull/826\n.. _Pull Request 827: https://github.com/galaxyproject/planemo/pull/827\n.. _Pull Request 825: https://github.com/galaxyproject/planemo/pull/825\n.. _Pull Request 820: https://github.com/galaxyproject/planemo/pull/820\n.. _Pull Request 823: https://github.com/galaxyproject/planemo/pull/823\n.. _Pull Request 822: https://github.com/galaxyproject/planemo/pull/822\n.. _a5c72e3: https://github.com/galaxyproject/planemo/commit/a5c72e3\n.. _Pull Request 818: https://github.com/galaxyproject/planemo/pull/818\n.. _Pull Request 816: https://github.com/galaxyproject/planemo/pull/816\n.. _Pull Request 817: https://github.com/galaxyproject/planemo/pull/817\n.. _Pull Request 795: https://github.com/galaxyproject/planemo/pull/795\n.. _Pull Request 799: https://github.com/galaxyproject/planemo/pull/799\n.. _Pull Request 800: https://github.com/galaxyproject/planemo/pull/800\n.. _Pull Request 781: https://github.com/galaxyproject/planemo/pull/781\n.. _Pull Request 801: https://github.com/galaxyproject/planemo/pull/801\n.. _Pull Request 802: https://github.com/galaxyproject/planemo/pull/802\n.. _Pull Request 803: https://github.com/galaxyproject/planemo/pull/803\n.. _Pull Request 805: https://github.com/galaxyproject/planemo/pull/805\n.. _Pull Request 806: https://github.com/galaxyproject/planemo/pull/806\n.. _Pull Request 809: https://github.com/galaxyproject/planemo/pull/809\n.. _Pull Request 810: https://github.com/galaxyproject/planemo/pull/810\n.. _Pull Request 787: https://github.com/galaxyproject/planemo/pull/787\n.. _Pull Request 792: https://github.com/galaxyproject/planemo/pull/792\n.. _dc443d6: https://github.com/galaxyproject/planemo/commit/dc443d6\n.. _8cfe9e9: https://github.com/galaxyproject/planemo/commit/8cfe9e9\n.. _41f7df1: https://github.com/galaxyproject/planemo/commit/41f7df1\n.. _Pull Request 790: https://github.com/galaxyproject/planemo/pull/790\n.. _Pull Request 776: https://github.com/galaxyproject/planemo/pull/776\n.. _Pull Request 774: https://github.com/galaxyproject/planemo/pull/774\n.. _Pull Request 773: https://github.com/galaxyproject/planemo/pull/773\n.. _Pull Request 771: https://github.com/galaxyproject/planemo/pull/771\n.. _Pull Request 770: https://github.com/galaxyproject/planemo/pull/770\n.. _Pull Request 769: https://github.com/galaxyproject/planemo/pull/769\n.. _Pull Request 768: https://github.com/galaxyproject/planemo/pull/768\n.. _Pull Request 764: https://github.com/galaxyproject/planemo/pull/764\n.. _Pull Request 761: https://github.com/galaxyproject/planemo/pull/761\n.. _Pull Request 759: https://github.com/galaxyproject/planemo/pull/759\n.. _Pull Request 756: https://github.com/galaxyproject/planemo/pull/756\n.. _Pull Request 753: https://github.com/galaxyproject/planemo/pull/753\n.. _Pull Request 747: https://github.com/galaxyproject/planemo/pull/747\n.. _Pull Request 745: https://github.com/galaxyproject/planemo/pull/745\n.. _Pull Request 743: https://github.com/galaxyproject/planemo/pull/743\n.. _Pull Request 739: https://github.com/galaxyproject/planemo/pull/739\n.. _Pull Request 738: https://github.com/galaxyproject/planemo/pull/738\n.. _Pull Request 725: https://github.com/galaxyproject/planemo/pull/725\n.. _Pull Request 727: https://github.com/galaxyproject/planemo/pull/727\n.. _Pull Request 729: https://github.com/galaxyproject/planemo/pull/729\n.. _Pull Request 730: https://github.com/galaxyproject/planemo/pull/730\n.. _Pull Request 731: https://github.com/galaxyproject/planemo/pull/731\n.. _Pull Request 733: https://github.com/galaxyproject/planemo/pull/733\n.. _Pull Request 732: https://github.com/galaxyproject/planemo/pull/732\n.. _Pull Request 704: https://github.com/galaxyproject/planemo/pull/704\n.. _Pull Request 709: https://github.com/galaxyproject/planemo/pull/709\n.. _Pull Request 715: https://github.com/galaxyproject/planemo/pull/715\n.. _Pull Request 716: https://github.com/galaxyproject/planemo/pull/716\n.. _Pull Request 720: https://github.com/galaxyproject/planemo/pull/720\n.. _Pull Request 723: https://github.com/galaxyproject/planemo/pull/723\n.. _8a608e0: https://github.com/galaxyproject/planemo/commit/8a608e0\n.. _ecc1bc2: https://github.com/galaxyproject/planemo/commit/ecc1bc2\n.. _Pull Request 702: https://github.com/galaxyproject/planemo/pull/702\n.. _Pull Request 701: https://github.com/galaxyproject/planemo/pull/701\n.. _Pull Request 699: https://github.com/galaxyproject/planemo/pull/699\n.. _91b6fa0: https://github.com/galaxyproject/planemo/commit/91b6fa0\n.. _904d77a: https://github.com/galaxyproject/planemo/commit/904d77a\n.. _9636682: https://github.com/galaxyproject/planemo/commit/9636682\n.. _475104c: https://github.com/galaxyproject/planemo/commit/475104c\n.. _Pull Request 684: https://github.com/galaxyproject/planemo/pull/684\n.. _Pull Request 687: https://github.com/galaxyproject/planemo/pull/687\n.. _Pull Request 688: https://github.com/galaxyproject/planemo/pull/688\n.. _Pull Request 689: https://github.com/galaxyproject/planemo/pull/689\n.. _Pull Request 690: https://github.com/galaxyproject/planemo/pull/690\n.. _Issue 494: https://github.com/galaxyproject/planemo/issues/494\n.. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665\n.. _Pull Request 675: https://github.com/galaxyproject/planemo/pull/675\n.. _Pull Request 680: https://github.com/galaxyproject/planemo/pull/680\n.. _Pull Request 682: https://github.com/galaxyproject/planemo/pull/682\n.. _Pull Request 683: https://github.com/galaxyproject/planemo/pull/683\n.. _Pull Request 662: https://github.com/galaxyproject/planemo/pull/662\n.. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665\n.. _Pull Request 664: https://github.com/galaxyproject/planemo/pull/664\n.. _84c4a73: https://github.com/galaxyproject/planemo/commit/84c4a73\n.. _32f41c9: https://github.com/galaxyproject/planemo/commit/32f41c9\n.. _3129216: https://github.com/galaxyproject/planemo/commit/3129216\n.. _b4ae44d: https://github.com/galaxyproject/planemo/commit/b4ae44d\n.. _3c95b7b: https://github.com/galaxyproject/planemo/commit/3c95b7b\n.. _06bcf19: https://github.com/galaxyproject/planemo/commit/06bcf19\n.. _525de8f: https://github.com/galaxyproject/planemo/commit/525de8f\n.. _9867e56: https://github.com/galaxyproject/planemo/commit/9867e56\n.. _ce0dc4e: https://github.com/galaxyproject/planemo/commit/ce0dc4e\n.. _4c0f100: https://github.com/galaxyproject/planemo/commit/4c0f100\n.. _04238d3: https://github.com/galaxyproject/planemo/commit/04238d3\n.. _ced5ce2: https://github.com/galaxyproject/planemo/commit/ced5ce2\n.. _9ab4a0d: https://github.com/galaxyproject/planemo/commit/9ab4a0d\n.. _Pull Request 640: https://github.com/galaxyproject/planemo/pull/640\n.. _0a1abfe: https://github.com/galaxyproject/planemo/commit/0a1abfe\n.. _Pull Request 649: https://github.com/galaxyproject/planemo/pull/649\n.. _Issue 620: https://github.com/galaxyproject/planemo/issues/620\n.. _Pull Request 643: https://github.com/galaxyproject/planemo/pull/643\n.. _Pull Request 642: https://github.com/galaxyproject/planemo/pull/642\n.. _Pull Request 641: https://github.com/galaxyproject/planemo/pull/641\n.. _Pull Request 639: https://github.com/galaxyproject/planemo/pull/639\n.. _Pull Request 635: https://github.com/galaxyproject/planemo/pull/635\n.. _Issue 633: https://github.com/galaxyproject/planemo/issues/633\n.. _Issue 260: https://github.com/galaxyproject/planemo/issues/260\n.. _Pull Request 638: https://github.com/galaxyproject/planemo/pull/638\n.. _6638caa: https://github.com/galaxyproject/planemo/commit/6638caa\n.. _8faf661: https://github.com/galaxyproject/planemo/commit/8faf661\n.. _e343b67: https://github.com/galaxyproject/planemo/commit/e343b67\n.. _Pull Request 634: https://github.com/galaxyproject/planemo/pull/634\n.. _84ebc1f: https://github.com/galaxyproject/planemo/commit/84ebc1f\n.. _03c9658: https://github.com/galaxyproject/planemo/commit/03c9658\n.. _08c067c: https://github.com/galaxyproject/planemo/commit/08c067c\n.. _fca4183: https://github.com/galaxyproject/planemo/commit/fca4183\n.. _Issue 564: https://github.com/galaxyproject/planemo/issues/564\n.. _Pull Request 628: https://github.com/galaxyproject/planemo/pull/628\n.. _Issue 515: https://github.com/galaxyproject/planemo/issues/515\n.. _Pull Request 629: https://github.com/galaxyproject/planemo/pull/629\n.. _Pull Request 614: https://github.com/galaxyproject/planemo/pull/614\n.. _32acd68: https://github.com/galaxyproject/planemo/commit/32acd68\n.. _4595953: https://github.com/galaxyproject/planemo/commit/4595953\n.. _Pull Request 612: https://github.com/galaxyproject/planemo/pull/612\n.. _Issue 388: https://github.com/galaxyproject/planemo/issues/388\n.. _Pull Request 610: https://github.com/galaxyproject/planemo/pull/610\n.. _Pull Request 609: https://github.com/galaxyproject/planemo/pull/609\n.. _Pull Request 608: https://github.com/galaxyproject/planemo/pull/608\n.. _Pull Request 605: https://github.com/galaxyproject/planemo/pull/605\n.. _Pull Request 606: https://github.com/galaxyproject/planemo/pull/606\n.. _Pull Request 602: https://github.com/galaxyproject/planemo/pull/602\n.. _Pull Request 570: https://github.com/galaxyproject/planemo/pull/570\n.. _9228416: https://github.com/galaxyproject/planemo/commit/9228416\n.. _50d3c4a: https://github.com/galaxyproject/planemo/commit/50d3c4a\n.. _Issue 578: https://github.com/galaxyproject/planemo/issues/578\n.. _Pull Request 591: https://github.com/galaxyproject/planemo/pull/591\n.. _Pull Request 590: https://github.com/galaxyproject/planemo/pull/590\n.. _f0da66f: https://github.com/galaxyproject/planemo/commit/f0da66f\n.. _19b2ee9: https://github.com/galaxyproject/planemo/commit/19b2ee9\n.. _9da8387: https://github.com/galaxyproject/planemo/commit/9da8387\n.. _08cef54: https://github.com/galaxyproject/planemo/commit/08cef54\n.. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc\n.. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc\n.. _Issue 573: https://github.com/galaxyproject/planemo/issues/573\n.. _Pull Request 579: https://github.com/galaxyproject/planemo/pull/579\n.. _ccdd2d5: https://github.com/galaxyproject/planemo/commit/ccdd2d5\n.. _e925ba1: https://github.com/galaxyproject/planemo/commit/e925ba1\n.. _ea5324f: https://github.com/galaxyproject/planemo/commit/ea5324f\n.. _ca88b0c: https://github.com/galaxyproject/planemo/commit/ca88b0c\n.. _b6d8294: https://github.com/galaxyproject/planemo/commit/b6d8294\n.. _6a6f164: https://github.com/galaxyproject/planemo/commit/6a6f164\n.. _d6da3a8: https://github.com/galaxyproject/planemo/commit/d6da3a8\n.. _1ef05d2: https://github.com/galaxyproject/planemo/commit/1ef05d2\n.. _7cca2e4: https://github.com/galaxyproject/planemo/commit/7cca2e4\n.. _34538de: https://github.com/galaxyproject/planemo/commit/34538de\n.. _6f91719: https://github.com/galaxyproject/planemo/commit/6f91719\n.. _Pull Request 566: https://github.com/galaxyproject/planemo/pull/566\n.. _Pull Request 559: https://github.com/galaxyproject/planemo/pull/559\n.. _Pull Request 561: https://github.com/galaxyproject/planemo/pull/561\n.. _Pull Request 565: https://github.com/galaxyproject/planemo/pull/565\n.. _Pull Request 555: https://github.com/galaxyproject/planemo/pull/555\n.. _a8e797b: https://github.com/galaxyproject/planemo/commit/a8e797b\n.. _6c03de8: https://github.com/galaxyproject/planemo/commit/6c03de8\n.. _ef4b9f4: https://github.com/galaxyproject/planemo/commit/ef4b9f4\n.. _f7b6c7e: https://github.com/galaxyproject/planemo/commit/f7b6c7e\n.. _07d94bd: https://github.com/galaxyproject/planemo/commit/07d94bd\n.. _ca19910: https://github.com/galaxyproject/planemo/commit/ca19910\n.. _24008ab: https://github.com/galaxyproject/planemo/commit/24008ab\n.. _ce44e87: https://github.com/galaxyproject/planemo/commit/ce44e87\n.. _Pull Request 550: https://github.com/galaxyproject/planemo/pull/550\n.. _c2204b3: https://github.com/galaxyproject/planemo/commit/c2204b3\n.. _c262b6d: https://github.com/galaxyproject/planemo/commit/c262b6d\n.. _Pull Request 539: https://github.com/galaxyproject/planemo/pull/539\n.. _Pull Request 541: https://github.com/galaxyproject/planemo/pull/541\n.. _Pull Request 540: https://github.com/galaxyproject/planemo/pull/540\n.. _Pull Request 545: https://github.com/galaxyproject/planemo/pull/545\n.. _Pull Request 546: https://github.com/galaxyproject/planemo/pull/546\n.. _3ceaa40: https://github.com/galaxyproject/planemo/commit/3ceaa40\n.. _057f4f0: https://github.com/galaxyproject/planemo/commit/057f4f0\n.. _9fdf490: https://github.com/galaxyproject/planemo/commit/9fdf490\n.. _8c088c6: https://github.com/galaxyproject/planemo/commit/8c088c6\n.. _e2398fb: https://github.com/galaxyproject/planemo/commit/e2398fb\n.. _Pull Request 526: https://github.com/galaxyproject/planemo/pull/526\n.. _Pull Request 528: https://github.com/galaxyproject/planemo/pull/528\n.. _Pull Request 525: https://github.com/galaxyproject/planemo/pull/525\n.. _a811e65: https://github.com/galaxyproject/planemo/commit/a811e65\n.. _Pull Request 521: https://github.com/galaxyproject/planemo/pull/521\n.. _a066afb: https://github.com/galaxyproject/planemo/commit/a066afb\n.. _Pull Request 512: https://github.com/galaxyproject/planemo/pull/512\n.. _08bb354: https://github.com/galaxyproject/planemo/commit/08bb354\n.. _Pull Request 513: https://github.com/galaxyproject/planemo/pull/513\n.. _Pull Request 510: https://github.com/galaxyproject/planemo/pull/510\n.. _e890ab5: https://github.com/galaxyproject/planemo/commit/e890ab5\n.. _Pull Request 507: https://github.com/galaxyproject/planemo/pull/507\n.. _d53bcd6: https://github.com/galaxyproject/planemo/commit/d53bcd6\n.. _725b232: https://github.com/galaxyproject/planemo/commit/725b232\n.. _Pull Request 498: https://github.com/galaxyproject/planemo/pull/498\n.. _01584c5: https://github.com/galaxyproject/planemo/commit/01584c5\n.. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9\n.. _0298510: https://github.com/galaxyproject/planemo/commit/0298510\n.. _02a08a0: https://github.com/galaxyproject/planemo/commit/02a08a0\n.. _05cc9f4: https://github.com/galaxyproject/planemo/commit/05cc9f485ee87bc344e3f43bb1cfd025a16a6247\n.. _069e7ba: https://github.com/galaxyproject/planemo/commit/069e7ba\n.. _08de8de: https://github.com/galaxyproject/planemo/commit/08de8de\n.. _0bd4ff0: https://github.com/galaxyproject/planemo/commit/0bd4ff0\n.. _0e4f70a: https://github.com/galaxyproject/planemo/commit/0e4f70a\n.. _0f8cb10: https://github.com/galaxyproject/planemo/commit/0f8cb10\n.. _13a5ae7: https://github.com/galaxyproject/planemo/commit/13a5ae7\n.. _15804be: https://github.com/galaxyproject/planemo/commit/15804be\n.. _15d33c7: https://github.com/galaxyproject/planemo/commit/15d33c7\n.. _182fe57: https://github.com/galaxyproject/planemo/commit/182fe57\n.. _1927168: https://github.com/galaxyproject/planemo/commit/1927168\n.. _1982076: https://github.com/galaxyproject/planemo/commit/1982076\n.. _19900a6: https://github.com/galaxyproject/planemo/commit/19900a6\n.. _1a157d4: https://github.com/galaxyproject/planemo/commit/1a157d4\n.. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493\n.. _1c6cfbb: https://github.com/galaxyproject/planemo/commit/1c6cfbb\n.. _1c7ee5b: https://github.com/galaxyproject/planemo/commit/1c7ee5b\n.. _1cd0e2d: https://github.com/galaxyproject/planemo/commit/1cd0e2d\n.. _1e3668a: https://github.com/galaxyproject/planemo/commit/1e3668a\n.. _2052db0: 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_94645ed: https://github.com/galaxyproject/planemo/commit/94645ed\n.. _949a36d: https://github.com/galaxyproject/planemo/commit/949a36d\n.. _95d5cba: https://github.com/galaxyproject/planemo/commit/95d5cba\n.. _965511d: https://github.com/galaxyproject/planemo/commit/965511d\n.. _988de1d: https://github.com/galaxyproject/planemo/commit/988de1d\n.. _98fdc8c: https://github.com/galaxyproject/planemo/commit/98fdc8c\n.. _99ee51a: https://github.com/galaxyproject/planemo/commit/99ee51a\n.. _9bf1eab: https://github.com/galaxyproject/planemo/commit/9bf1eab\n.. _9e746b4: https://github.com/galaxyproject/planemo/commit/9e746b455e3b15219878cddcdeda722979639401\n.. _9f3957d: https://github.com/galaxyproject/planemo/commit/9f3957d\n.. _9ff0d2d: https://github.com/galaxyproject/planemo/commit/9ff0d2d\n.. _CWL: http://www.commonwl.org/\n.. _Issue 108: https://github.com/galaxyproject/planemo/issues/108\n.. _Issue 114: https://github.com/galaxyproject/planemo/issues/114\n.. _Issue 118: https://github.com/galaxyproject/planemo/issues/118\n.. _Issue 124: https://github.com/galaxyproject/planemo/issues/#124\n.. _Issue 138: https://github.com/galaxyproject/planemo/issues/#138\n.. _Issue 139: https://github.com/galaxyproject/planemo/issues/139\n.. _Issue 150: https://github.com/galaxyproject/planemo/issues/150\n.. _Issue 156: https://github.com/galaxyproject/planemo/issues/156\n.. _Issue 158: https://github.com/galaxyproject/planemo/issues/158\n.. _Issue 159: https://github.com/galaxyproject/planemo/issues/159\n.. _Issue 15: https://github.com/galaxyproject/planemo/issues/15\n.. _Issue 161: https://github.com/galaxyproject/planemo/issues/161\n.. _Issue 167: https://github.com/galaxyproject/planemo/issues/167\n.. _Issue 168: https://github.com/galaxyproject/planemo/issues/168\n.. _Issue 169: https://github.com/galaxyproject/planemo/issues/169\n.. _Issue 170: https://github.com/galaxyproject/planemo/issues/170\n.. _Issue 176: https://github.com/galaxyproject/planemo/issues/176\n.. _Issue 179: https://github.com/galaxyproject/planemo/issues/179\n.. _Issue 180: https://github.com/galaxyproject/planemo/issues/180\n.. _Issue 181: https://github.com/galaxyproject/planemo/issues/181\n.. _Issue 184: https://github.com/galaxyproject/planemo/issues/184\n.. _Issue 186: https://github.com/galaxyproject/planemo/issues/186\n.. _Issue 188: https://github.com/galaxyproject/planemo/issues/188\n.. _Issue 189: https://github.com/galaxyproject/planemo/issues/189\n.. _Issue 192: https://github.com/galaxyproject/planemo/issues/192\n.. _Issue 205: https://github.com/galaxyproject/planemo/issues/205\n.. _Issue 206: https://github.com/galaxyproject/planemo/issues/206\n.. _Issue 209: https://github.com/galaxyproject/planemo/issues/209\n.. _Issue 211: https://github.com/galaxyproject/planemo/issues/211\n.. _Issue 217: https://github.com/galaxyproject/planemo/issues/217\n.. _Issue 223: https://github.com/galaxyproject/planemo/issues/223\n.. _Issue 231: https://github.com/galaxyproject/planemo/issues/231\n.. _Issue 233: https://github.com/galaxyproject/planemo/issues/233\n.. _Issue 240: https://github.com/galaxyproject/planemo/issues/240\n.. _Issue 243: https://github.com/galaxyproject/planemo/issues/243\n.. _Issue 245: https://github.com/galaxyproject/planemo/issues/245\n.. _Issue 246: https://github.com/galaxyproject/planemo/issues/246\n.. _Issue 272: https://github.com/galaxyproject/planemo/issues/272\n.. _Issue 303: https://github.com/galaxyproject/planemo/issues/303\n.. _Issue 313: https://github.com/galaxyproject/planemo/issues/313\n.. _Issue 329: https://github.com/galaxyproject/planemo/issues/329\n.. _Issue 333: https://github.com/galaxyproject/planemo/issues/333\n.. _Issue 361: https://github.com/galaxyproject/planemo/issues/361\n.. _Issue 362: https://github.com/galaxyproject/planemo/issues/362\n.. _Issue 373: https://github.com/galaxyproject/planemo/issues/373\n.. _Issue 391: https://github.com/galaxyproject/planemo/issues/391\n.. _Issue 416: https://github.com/galaxyproject/planemo/issues/416\n.. _Issue 420: https://github.com/galaxyproject/planemo/issues/420\n.. _Issue 475: https://github.com/galaxyproject/planemo/issues/475\n.. _Issue 61: https://github.com/galaxyproject/planemo/issues/61\n.. _Issue 70: https://github.com/galaxyproject/planemo/issues/70\n.. _Issue 78: https://github.com/galaxyproject/planemo/issues/78\n.. _Issue 80: https://github.com/galaxyproject/planemo/issues/80\n.. _Issue 83: https://github.com/galaxyproject/planemo/issues/83\n.. _Issue 88: https://github.com/galaxyproject/planemo/issues/88\n.. _Issue 89: https://github.com/galaxyproject/planemo/issues/#89\n.. _Issue 91: https://github.com/galaxyproject/planemo/issues/#91\n.. _Pull Request 101: https://github.com/galaxyproject/planemo/pull/101\n.. _Pull Request 102: https://github.com/galaxyproject/planemo/pull/102\n.. _Pull Request 104: https://github.com/galaxyproject/planemo/pull/104\n.. _Pull Request 111: https://github.com/galaxyproject/planemo/pull/111\n.. _Pull Request 113: https://github.com/galaxyproject/planemo/pull/113\n.. _Pull Request 129: https://github.com/galaxyproject/planemo/pull/129\n.. _Pull Request 130: https://github.com/galaxyproject/planemo/pull/130\n.. _Pull Request 143: https://github.com/galaxyproject/planemo/pull/143\n.. _Pull Request 151: https://github.com/galaxyproject/planemo/pull/151\n.. _Pull Request 155: https://github.com/galaxyproject/planemo/pull/155\n.. _Pull Request 164: https://github.com/galaxyproject/planemo/pull/164\n.. _Pull Request 171: https://github.com/galaxyproject/planemo/pull/171\n.. _Pull Request 173: https://github.com/galaxyproject/planemo/pull/173\n.. _Pull Request 175: https://github.com/galaxyproject/planemo/pull/175\n.. _Pull Request 185: https://github.com/galaxyproject/planemo/pull/185\n.. _Pull Request 186: https://github.com/galaxyproject/planemo/pull/186\n.. _Pull Request 187: https://github.com/galaxyproject/planemo/pull/187\n.. _Pull Request 190: https://github.com/galaxyproject/planemo/pull/190\n.. _Pull Request 196: https://github.com/galaxyproject/planemo/pull/196\n.. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1\n.. _Pull Request 200: https://github.com/galaxyproject/planemo/pull/200\n.. _Pull Request 203: https://github.com/galaxyproject/planemo/pull/203\n.. _Pull Request 206: https://github.com/galaxyproject/planemo/pull/206\n.. _Pull Request 207: https://github.com/galaxyproject/planemo/pull/207\n.. _Pull Request 208: https://github.com/galaxyproject/planemo/pull/208\n.. _Pull Request 210: https://github.com/galaxyproject/planemo/pull/210\n.. _Pull Request 213: https://github.com/galaxyproject/planemo/pull/213\n.. _Pull Request 215: https://github.com/galaxyproject/planemo/pull/215\n.. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216\n.. _Pull Request 22: https://github.com/galaxyproject/planemo/pull/22\n.. _Pull Request 230: https://github.com/galaxyproject/planemo/pull/230\n.. _Pull Request 235: https://github.com/galaxyproject/planemo/pull/235\n.. _Pull Request 23: https://github.com/galaxyproject/planemo/pull/23\n.. _Pull Request 251: https://github.com/galaxyproject/planemo/pull/251\n.. _Pull Request 253: https://github.com/galaxyproject/planemo/pull/253\n.. _Pull Request 254: https://github.com/galaxyproject/planemo/pull/254\n.. _Pull Request 255: https://github.com/galaxyproject/planemo/pull/255\n.. _Pull Request 256: https://github.com/galaxyproject/planemo/pull/256\n.. _Pull Request 277: https://github.com/galaxyproject/planemo/pull/277\n.. _Pull Request 278: https://github.com/galaxyproject/planemo/pull/278\n.. _Pull Request 284: https://github.com/galaxyproject/planemo/pull/284\n.. _Pull Request 285: 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_Pull Request 316: https://github.com/galaxyproject/planemo/pull/316\n.. _Pull Request 322: https://github.com/galaxyproject/planemo/pull/322\n.. _Pull Request 327: https://github.com/galaxyproject/planemo/pull/327\n.. _Pull Request 330: https://github.com/galaxyproject/planemo/pull/330\n.. _Pull Request 333: https://github.com/galaxyproject/planemo/pull/333\n.. _Pull Request 334: https://github.com/galaxyproject/planemo/pull/334\n.. _Pull Request 335: https://github.com/galaxyproject/planemo/pull/335\n.. _Pull Request 339: https://github.com/galaxyproject/planemo/pull/339\n.. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33\n.. _Pull Request 343: https://github.com/galaxyproject/planemo/pull/343\n.. _Pull Request 344: https://github.com/galaxyproject/planemo/pull/344\n.. _Pull Request 345: https://github.com/galaxyproject/planemo/pull/345\n.. _Pull Request 350: https://github.com/galaxyproject/planemo/pull/350\n.. _Pull Request 351: 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