Metadata-Version: 1.1
Name: planemo
Version: 0.58.2
Summary: Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
Home-page: https://github.com/galaxyproject/planemo
Author: Galaxy Project and Community
Author-email: jmchilton@gmail.com
License: AFL
Description: .. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png
           :alt: Planemo Logo
           :align: center
           :figwidth: 100%
           :target: https://github.com/galaxyproject/planemo
        
        Command-line utilities to assist in developing Galaxy_ and `Common Workflow Language`_ tools.
        
        .. image:: https://readthedocs.org/projects/planemo/badge/?version=latest
           :target: http://planemo.readthedocs.io/en/latest/?badge=latest
           :alt: Documentation Status
        
        .. image:: https://badge.fury.io/py/planemo.svg
           :target: https://pypi.python.org/pypi/planemo/
           :alt: Planemo on the Python Package Index (PyPI)
        
        .. image:: https://travis-ci.org/galaxyproject/planemo.png?branch=master
           :target: https://travis-ci.org/galaxyproject/planemo
           :alt: Build Status
        
        .. image:: https://travis-ci.org/jmchilton/planemo-extended-tests.svg?branch=master
            :target: https://travis-ci.org/jmchilton/planemo-extended-tests
            :alt: Build Status of Extended Tests
        
        .. image:: https://coveralls.io/repos/galaxyproject/planemo/badge.svg?branch=master
           :target: https://coveralls.io/r/galaxyproject/planemo?branch=master
           :alt: Coverage Status
        
        * Free software: Academic Free License version 3.0
        * Documentation: https://planemo.readthedocs.io.
        * Code: https://github.com/galaxyproject/planemo
        
        
        Quick Start
        -----------
        
        -----------------
        Obtaining
        -----------------
        
        For a traditional Python installation of Planemo, first set up a virtualenv
        for ``planemo`` (this example creates a new one in ``.venv``) and then
        install with ``pip``. Planemo requires pip 7.0 or newer.
        
        ::
        
            $ virtualenv .venv; . .venv/bin/activate
            $ pip install "pip>=7" # Upgrade pip if needed.
            $ pip install planemo
        
        For information on updating Planemo, installing the latest development release,
        or installing Planemo via `Bioconda <https://github.com/bioconda/bioconda-recipes>`__
        - checkout the `installation <http://planemo.readthedocs.io/en/latest/installation.html>`__
        documentation.
        
        Planemo is also available as a `virtual appliance
        <https://planemo.readthedocs.io/en/latest/appliance.html>`_ bundled
        with a preconfigured Galaxy server and set up for Galaxy_ and
        `Common Workflow Language`_ tool development.
        You can choose from open virtualization format (OVA_, .ova) or Docker_
        appliances.
        
        -----------------
        Basics - Galaxy
        -----------------
        
        This quick start will assume you have a directory with one or more Galaxy
        tool XML files. If no such directory is available, one can be quickly created for
        demonstrating ``planemo`` as follows ``project_init --template=demo mytools; cd mytools``.
        
        Planemo can check tool XML files for common problems and best
        practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
        (also aliased as ``l``).
        
        ::
        
            $ planemo lint
        
        Like many ``planemo`` commands - by default this will search the
        current directory and use all tool files it finds. It can be explicitly
        passed a path to tool files or a directory of tool files.
        
        ::
        
            $ planemo l randomlines.xml
        
        The ``lint`` command takes in additional options related to
        reporting levels, exit code, etc. These options are described
        in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
        or (like with all commands) can be accessed by passing ``--help`` to it.
        
        ::
        
            $ planemo l --help
            Usage: planemo lint [OPTIONS] TOOL_PATH
        
        Once tools are syntactically correct - it is time to test. The ``test``
        `command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__
        can be used to test a tool or a directory of tools.
        
        ::
        
        	$ planemo test --galaxy_root=../galaxy randomlines.xml
        
        If no ``--galaxy_root`` is defined, Planemo will download and configure
        a disposable Galaxy instance for testing.
        
        Planemo will create a HTML output report in the current directory named
        ``tool_test_output.html`` (override with ``--test_output``). See an
        `example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_
        of such a report for Tophat.
        
        Once tools have been linted and tested - the tools can be viewed in a
        Galaxy interface using the ``serve`` (``s``) `command
        <http://planemo.readthedocs.org/en/latest/commands.html#serve-command>`__.
        
        ::
        
        	$ planemo serve
        
        Like ``test``, ``serve`` requires a Galaxy root and one can be
        explicitly specified with ``--galaxy_root`` or installed dynamically
        with ``--install_galaxy``.
        
        For more information on building Galaxy tools in general please check out
        `Building Galaxy Tools Using Planemo`_.
        
        ----------------------------------
        Basics - Common Workflow Language
        ----------------------------------
        
        This quick start will assume you have a directory with one or more `Common Workflow
        Language`_ YAML files. If no such directory is available, one can be quickly created for
        demonstrating ``planemo`` as follows ``planemo project_init --template=seqtk_complete_cwl mytools; cd mytools``.
        
        Planemo can check tools YAML files for common problems and best
        practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
        (also aliased as ``l``).
        
        ::
        
            $ planemo lint
        
        Like many ``planemo`` commands - by default this will search the
        current directory and use all tool files it finds. It can be explicitly
        passed a path to tool files or a directory of tool files.
        
        ::
        
            $ planemo l seqtk_seq.cwl
        
        The ``lint`` command takes in additional options related to
        reporting levels, exit code, etc. These options are described
        in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
        or (like with all commands) can be accessed by passing ``--help`` to it.
        
        ::
        
            $ planemo l --help
            Usage: planemo lint [OPTIONS] TOOL_PATH
        
        Once tools are syntactically correct - it is time to test. The ``test``
        `command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__
        can be used to test a CWL tool, workflow, or a directories thereof.
        
        ::
        
          $ planemo test --engine cwltool seqtk_seq.cwl
        
        Planemo will create a HTML output report in the current directory named
        ``tool_test_output.html``. Check out the file ``seqtk_seq_tests.yml`` for
        an example of Planemo test for a CWL tool. A test consists of any number of
        jobs (with input descriptions) and corresponding output assertions.
        
        Checkout the `Commmon Workflow User Guide`_ for more information on developing
        CWL tools in general and  `Building Common Workflow Language Tools`_ for more
        information on using Planemo to develop CWL tools.
        
        ---------
        Tool Shed
        ---------
        
        Planemo can help you publish tools to the Galaxy Tool Shed.
        Check out `Publishing to the Tool Shed`_ for more information.
        
        ------
        Conda
        ------
        
        Planemo can help develop tools and Conda packages in unison.
        Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda>`__ or `CWL
        <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda-cwl>`__ version of the "Dependencies and Conda" tutorial
        for more information.
        
        -----------------------
        Docker and Containers
        -----------------------
        
        Planemo can help develop tools that run in "Best Practice" containers for
        scientific workflows. Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-containers>`__ or `CWL
        <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers-cwl>`__ version of the "Dependencies and Containers" tutorial for more information.
        
        .. _Galaxy: http://galaxyproject.org/
        .. _GitHub: https://github.com/
        .. _Conda: http://conda.pydata.org/
        .. _Docker: https://www.docker.com/
        .. _Vagrant: https://www.vagrantup.com/
        .. _Travis CI: http://travis-ci.org/
        .. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam
        .. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc
        .. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html
        .. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html
        .. _Common Workflow Language: https://www.commonwl.org/
        .. _Commmon Workflow User Guide: http://www.commonwl.org/user_guide/
        .. _Building Common Workflow Language Tools: http://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html
        .. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format
        
        
        
        
        
        History
        -------
        
        .. to_doc
        
        ---------------------
        0.58.2 (2019-03-01)
        ---------------------
        
        * Fix display of tool ids in planemo html report (thanks to `@mvdbeek`_).
          `Pull Request 908`_
        * Single quotes for file names (thanks to `@bernt-matthias`_). `Pull Request
          909`_
        * Fix doc linting (thanks to `@mvdbeek`_). `Pull Request 910`_
        * Update TS categories (thanks to `@nsoranzo`_). 07dc6e0_
        * Close tag in doc help, to help with copy&paste (thanks to `@blankenberg`_).
          `Pull Request 914`_
        * Update the tool XSD file (thanks to `@bgruening`_). `Pull Request 915`_
        
        ---------------------
        0.58.1 (2019-01-03)
        ---------------------
        
        * Update galaxy-lib requirement to 18.9.2 to add Python 3.7 support (thanks to
          `@nsoranzo`_). `Pull Request 906`_
        * Fix command run by `planemo test --skip_venv` (thanks to `@nsoranzo`_).
          `Pull Request 907`_
        
        ---------------------
        0.58.0 (2019-01-01)
        ---------------------
        
        * Remove deprecated ``sudo: false`` from .travis.yml (thanks to `@nsoranzo`_).
          `Pull Request 902`_
        * Do not skip Galaxy client build for ``planemo serve``. Install Galaxy when the
          directory specified with ``--galaxy_root`` does not exist or is empty. (thanks
          to `@nsoranzo`_). `Pull Request 895`_, `Issue 845`_
        
        ---------------------
        0.57.1 (2018-11-23)
        ---------------------
        
        * Fix username validation for shed linting (thanks to `@martenson`_).
          `Pull Request 899`_, `Issue 898`_
        
        ---------------------
        0.57.0 (2018-11-19)
        ---------------------
        
        * Allow ``workflow_convert`` to convert a native ``.ga`` workflows to format 2 (yaml).
          `Pull Request 896`_
        * New command (``workflow_edit``) to open workflow in a synchronized graphical editor.
          `Pull Request 894`_
        * Conda tutorial fixes (thanks to `@nsoranzo`_). `Pull Request 876`_
        * Enable ``--conda_use_local`` option for ``planemo test`` (thanks to
          `@nsoranzo`_). `Pull Request 876`_
        * When testing, skip workflow outputs that do not have a `label` set (thanks to
          `@bgruening`_). `Pull Request 893`_
        * Add ``__repr__`` for ``TestCase`` to improve debugging Planemo
          (thanks to `@bgruening`_). `Pull Request 892`_
        * Increase IO polling interval over time (thanks to `@martenson`_).
          `Pull Request 891`_
        * Sync galaxy xsd and fix tests (thanks to `@mvdbeek`_).
          `Pull Request 889`_
        * Linting fix for ``W605`` (thanks to `@martenson`_). `Pull Request 888`_
        * Add icon for repeat parameters in training (thanks to `@bebatut`_).
          `Pull Request 887`_
        
        ---------------------
        0.56.0 (2018-10-30)
        ---------------------
        
        * Allow selection of Python version when starting managed Galaxy
          (thanks to `@mvdbeek`_). `Pull Request 874`_
        * Change the channel priority of conda (again). (thanks to `@bgruening`_).
          `Pull Request 867`_
        * Some small english corrections (thanks to `@erasche`_). `Pull Request 868`_
        * Print the list of excluded paths when running ``ci_find_repos``
          (thanks to `@nsoranzo`_). `Pull Request 877`_
        * Improved XSD lint reporting. `Pull Request 871`_
        * Fix Planemo writing a file called ``gx_venv_None``. `Pull Request 870`_
        * Update cwltool and galaxy-lib dependencies for Python 3.7 (thanks to
          `@nsoranzo`_). `Pull Request 864`_
        * Fix to make workflow testing more robust.
          `Pull Request 882`_
        
        ---------------------
        0.55.0 (2018-09-12)
        ---------------------
        
        * Add commands to create Galaxy training materials (thanks to `@bebatut`_).
          `Pull Request 861`_
        * Fix `planemo test` when TEMP env variable contain spaces (thanks to
          `@nsoranzo`_).
          `Pull Request 851`_
        * Support testing a completely remote galaxy instance (thanks to `@erasche`_).
          `Pull Request 856`_
        * Allow naming history from command line (thanks to `@erasche`_).
          `Pull Request 860`_
        * Sync galaxy.xsd from galaxy repo (thanks to `@nsoranzo`_).
          `Pull Request 866`_
        * Fix ServeTestCase.test_shed_serve test (thanks to `@nsoranzo`). bad810a_
        
        ---------------------
        0.54.0 (2018-06-06)
        ---------------------
        
        * Better support for testings against different versions of Galaxy efficiently and robustly.
          `Pull Request 849`_
        * New database version (thanks to `@bgruening`_).
          `Pull Request 847`_
        * Hyperlink DOIs against preferred resolver (thanks to `@katrinleinweber`_).
          `Pull Request 850`_
        * Tests for collection inputs to workflows. `Pull Request 843`_
        * Bring in Ephemeris sleep function - hopefully makes serve tests a bit more robust.
          b12b117_
        * More tutorial testing, tutorial updates.
          016b923_, 324c776_, 2002b49_
        * More isolated ``test_shed_upload.py`` tests. 72d2ca7_
        * Add filetype support for workflow test inputs (thanks to `@bgruening`_).
          `Pull Request 842`_
        * Add ``--no_shed_install`` option, to prevent shed installs as part of workflow testing.
          `Pull Request 841`_
        * Small docs fix (thanks to `@erasche`_). `Pull Request 848`_
        
        ---------------------
        0.53.0 (2018-05-22)
        ---------------------
        
        * Make Planemo testing easier for CWL tools and workflows in various ways and update
          tutorials to reflect these simplifications. `Pull Request 837`_
        * Test and fix running workflow tests against externally managed Galaxy servers.
          `Pull Request 833`_, `Pull Request 836`_
        * Allow using URIs for inputs of workflow test. `Pull Request 840`_
        * Slide Galaxy testing window to include 18.05 and drop 17.09. `Pull Request 838`_
        
        ---------------------
        0.52.0 (2018-05-20)
        ---------------------
        
        * Allow optional disabling of Galaxy single user mode. `Pull Request 835`_
        * Fix for path pasting options during workflow testing. `Pull Request 834`_
        
        ---------------------
        0.51.0 (2018-05-19)
        ---------------------
        
        * Fix essentially all Conda_ and BioContainers_ related functionality to allow parity between
          CWL_ and existing Galaxy functionality - fixes and enhances many commands including ``lint``,
          ``conda_install``, ``conda_env``, ``test``, ``run``, and ``mull``.
          `Pull Request 828`_
        * Add two new tutorials for `Conda
          <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda>`__
          and `Container
          <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers>`__
          development with CWL tools that mirrors the existing tutorials for Galaxy tools - including new
          CWL exercises, answers, and example project templates.
          347c622_
        * Improve the CWL generated by the ``tool_init`` command to properly deal with
          ``SoftwareRequirement`` s and generate more idiomatic CWL.
          `Pull Request 820`_, a5c72e3_
        * Add new engine type (``--engine toil``) for testing and running CWL_ tools (requires
          manually installing Toil_ with ``pip install toil`` in Planemo's environment).
          `Pull Request 831`_
        * Add `documentation <http://planemo.readthedocs.io/en/latest/test_format.html>`__
          for the Galaxy Workflow and CWL_ test format files (includes information on configuring
          various test engines).
          `Pull Request 832`_
        * Better default logging config for CWL development. `Pull Request 830`_
        * Various fixes for the ``conda_search`` command. `Pull Request 826`_
        * Fix test coverage configuration. `Pull Request 822`_
        * Reorganize .travis.yml for clarity. `Pull Request 829`_
        * More isolated, robust unit tests that use git_.
          `Pull Request 827`_, `Pull Request 818`_
        * Fix default list of best-practice Conda channels. `Pull Request 825`_
        * Refactor tests to speed up quick tests - fewer buggy URLs fetched in "quick" mode.
          `Pull Request 823`_
        * Fix upload configuration of workflow testing to default (overrideable) external Galaxies
          to not use path pasting.
          `Pull Request 816`_
        * Fix test number parsing for workflow tests. `Pull Request 817`_
        
        ---------------------
        0.50.1 (2018-05-11)
        ---------------------
        
        * Fix the process of waiting on Galaxy to boot up for the Docker Galaxy container ``--engine``.
        
        ---------------------
        0.50.0 (2018-05-10)
        ---------------------
        
        * Fixes and small CLI tweaks to get the Docker Galaxy container working as an ``--engine`` for the
          run, serve, and test commands.
        
        ---------------------
        0.49.2 (2018-05-09)
        ---------------------
        
        * Various small fixes for new external Galaxy engine type.
        
        ---------------------
        0.49.1 (2018-05-06)
        ---------------------
        
        * Fix PyPI_ README rendering for 0.49.0 release changes.
        
        ---------------------
        0.49.0 (2018-05-06)
        ---------------------
        
        * Implement external Galaxy engine. `Pull Request 781`_
        * Restructure serve testing code for reuse. `Pull Request 795`_
        * Improve test report handling for JSON generated via galaxy-lib testing
          script. `Pull Request 799`_
        * Improve how various branches of Galaxy are tested. `Pull Request 800`_
        * Added documentation for ``GALAXY_MEMORY_MB`` (thanks to `@bernt-matthias`_).
          `Pull Request 801`_
        * Log tool config in verbose logging mode. `Pull Request 802`_
        * Replace ``r`` channel with ``conda-forge`` (thanks to `@bgruening`_).
          `Pull Request 805`_
        * Sync ``galaxy.xsd`` with latest Galaxy updates (thanks to `@nsoranzo`_).
          `Pull Request 806`_
        * Use ``requests.get()`` when validating http URLs (thanks to `@nsoranzo`_).
          `Pull Request 809`_
        * Do not consider tools with "deprecated" in the path (thanks to
          `@bgruening`_). `Pull Request 810`_
        * Automatically load tools shipped with Galaxy when testing, running, or serving
          workflows that reference these tools. `Pull Request 790`_
        * Revise README and touch up documentation in general. `Pull Request 787`_
        * Various small changes to testing and test framework. `Pull Request 792`_
        * Various Python 3 fixes. 8cfe9e9_, 41f7df1_
        * Fixes for Galaxy 18.0X releases.
          `Pull Request 803`_, dc443d6_
        
        ---------------------
        0.48.0 (2018-02-28)
        ---------------------
        
        * Run all CI tests against Python 3 (thanks to `@nsoranzo`_).
          `Pull Request 768`_ and `Pull Request 774`_
        * Python 3 fix - subprocess with ``universal_newlines=True``
          (thanks to `@peterjc`_).
          `Pull Request 764`_
        * Record CWL_ conformance test results using JUnit xml
          (thanks to `@mr-c`_).
          `Pull Request 756`_
        * Restore run test case for simple Galaxy tools.
          `Pull Request 769`_
        * Enhancements to Galaxy profiles and workflow testing.
          `Pull Request 773`_
        * Fix resolving & installing shed repositories from workflows for ``test``
          and ``run`` commands.
          `Pull Request 776`_
        * Implement planemo command to convert format 2 workflows into .ga workflows.
          `Pull Request 771`_
        * Add a native Galaxy workflow (.ga) testing test.
          `Pull Request 770`_
        * Drop Brew support but add more detailed install instructions.
          `Pull Request 761`_
        * Clean up CWL_ conformance test execution. `Pull Request 753`_
        * Assorted small CWL_ and deamon serve fixes. `Pull Request 759`_
        
        
        ---------------------
        0.47.0 (2017-11-18)
        ---------------------
        
        * Update to the latest Galaxy tool XSD  (thanks to `@nsoranzo`_).
          `Pull Request 747`_
        * Re-fix problem when shed_update would fail if nothing to update
          (thanks to `@nsoranzo`_). `Pull Request 747`_
        * Update instructions for installation via conda (thanks to `@nsoranzo`_) .
          `Pull Request 743`_
        * Bug fix for MacOS `chmod` doesn't support `--recursive` flag.
          (thanks to `@dfornika`_). `Pull Request 739`_
        * Bug fix to also `socket.error` when linting URLs
          (thanks to `@nsoranzo`_). `Pull Request 738`_
        * Disable broken tests. `Pull Request 745`_
        
        ---------------------
        0.46.1 (2017-09-26)
        ---------------------
        
        * Rev to latest versions of bioblend_ and `galaxy-lib`_ for various fixes
          related to CWL_.
        
        ---------------------
        0.46.0 (2017-09-15)
        ---------------------
        
        * Change behavior of ``--docker`` flag, for a few releases it would require
          Galaxy use a container for every non-upload tool. This breaks various
          conversion tools for instance and so was reverted.
          `Pull Request 733`_
        * Add 'Accept' header when linting doc URLs (thanks to `@nsoranzo`_).
          `Pull Request 725`_
        * Fix `--conda_auto_install` help (thanks to `@nsoranzo`_).
          `Pull Request 727`_
        * Incremental progress toward CWL support via Galaxy.
          `Pull Request 729`_, `Pull Request 732`_
        * Update galaxy-lib to latest version to fix various issues.
          `Pull Request 730`_
        * Fix lint detected problems with documentation.
          `Pull Request 731`_
        
        ---------------------
        0.45.0 (2017-09-06)
        ---------------------
        
        * Update to the latest `galaxy-lib`_ for Conda fixes. (thanks `@nsoranzo`_)
          and updated CWL_ utilities.  `Pull Request 716`_, `Pull Request 723`_
        * Update Conda_ channel order to sync with Bioconda_
          (thanks to `@nsoranzo`_). `Pull Request 715`_
        * Experimental support running CWL_ workflows through the CWL_ fork of Galaxy.
        * Mention ``planemo command --help`` in main help
          (thanks to `@peterjc`_). `Pull Request 709`_
        * Bugfix handle ``None`` requirement versions when registering containers
          (thanks to `@bgruening`_). `Pull Request 704`_
        * Bugfix for dependencies by pinning ruamel.yaml version
          (thanks to `@mvdbeek`_). `Pull Request 720`_
        
        ---------------------
        0.44.0 (2017-06-22)
        ---------------------
        
        * Fix and improve Galaxy root option specification options.
          `Pull Request 701`_, 8a608e0_
        * Update `planemo mull` to use a default action of `build-and-test` since
          `build` no longer cleans up itself. ecc1bc2_
        * Add a command to pre-install Involucro_.
          `Pull Request 702`_
        
        ---------------------
        0.43.0 (2017-06-22)
        ---------------------
        
        * Remove stdio from generated tools - just use exit_code for everything.
          91b6fa0_
        * Implement some ad-hoc documentation tests. `Pull Request 699`_
        * A large number of small enhancements and fixes for the documentation and
          example projects.
        
        ---------------------
        0.42.1 (2017-06-16)
        ---------------------
        
        * Fix Readme typos (thanks to `@manabuishii`_) 904d77a_
        * Fix `container_register` to create pull requests against the newly finalized home of the
          multi-package-containers registry repository. 
          9636682_
        * Fix `use_global_config` and `use_env_var` for options with unspecified defaults.
          475104c_
        
        
        ---------------------
        0.42.0 (2017-06-15)
        ---------------------
        
        * Conda/Container documentation and option naming improvements. `Pull Request
          684`_
        * Sync `galaxy.xsd` with latest upstream Galaxy updates (thanks to `@nsoranzo`_).
          `Pull Request 687`_
        * Fix `ci_find_repos` command to not filter repos whose only modifications where
          in subdirs (thanks to `@nsoranzo`_).
          `Pull Request 688`_
        * Update `container_register` for mulled version 2 and repository name changes.
          `Pull Request 689`_
        * Better pull request messages for the `container_register` command.
          `Pull Request 690`_
        
        ---------------------
        0.41.0 (2017-06-05)
        ---------------------
        
        * Fix ``shed_update`` not fail if there is nothing to update
          (thanks to `@nsoranzo`_). `Issue 494`_, `Pull Request 680`_
        * Conda documentation and option naming improvements.
          `Pull Request 683`_
        * Implement ``container_register`` for tool repositories.
          `Pull Request 675`_
        * Fix ``hub`` binary installation for Mac OS X.
          `Pull Request 682`_
        
        ---------------------
        0.40.1 (2017-05-03)
        ---------------------
        
        * Fix data manager configuration to not conflict with original Galaxy at
          ``galaxy_root`` (thanks to `@nsoranzo`_). `Pull Request 662`_
        * Fix ``filter_paths()`` to not partial match paths when filtering shed repositories
          (thanks to `@nsoranzo`_). `Pull Request 665`_
        * Fix description when creating ``.shed.yml`` files (thanks to `@RJMW`_).
          `Pull Request 664`_
        
        ---------------------
        0.40.0 (2017-03-16)
        ---------------------
        
        * Implement instructions and project template for GA4GH Tool Execution
          Challenge Phase 1. 84c4a73_
        * Eliminate Conda hack forcing ``/tmp`` as temp directory. b4ae44d_
        * Run dependency script tests in isolated directories. 32f41c9_
        * Fix OS X bug in ``planemo run`` by reworking it to wait using urllib instead of sockets.
          3129216_
        
        ---------------------
        0.39.0 (2017-03-15)
        ---------------------
        
        * Implement documentation and examples for Conda-based dependency development (under
          "Advanced" topics).
          `Pull Request 642`_, `Pull Request 643`_
        * Implement documentation and examples for container-based dependency development (under
          "Advanced" topics).
          0a1abfe_
        * Implement a ``planemo conda_search`` command for searching best practice channels
          from the command line.
          `Pull Request 642`_
        * Allow Planemo to work with locally built Conda packages using the ``--conda_use_local``
          command.
          `Pull Request 643`_, `Issue 620`_
        * Implement an ``open`` (or just ``o``) command to quickly open the last test results
          (or any file if supplied). `Pull Request 641`_
        * Linting improvements and fixes due to `galaxy-lib`_ update.
          * WARN on test output names not found or not matching.
          * INFO correct information about stdio if profile version is found.
          * WARN if profile version is incorrect.
          * INFO profile version
          * Fix ``assert_command`` not detected as a valid test (fixes  `Issue 260`_).
        * Have ``lint --conda_requirements`` check that at least one actual requirement is found.
          6638caa_
        * Allow ``conda_install`` to work with packages as well as just tools.
          8faf661_
        * Add ``--global`` option to conda_install to install requirements into global Conda setup
          instead of using an environment.
          8faf661_
        * Implement ``planemo lint --biocontainer`` that checks that a tool has an available BioContainer
          registered.
          0a1abfe_
        * Add more options and more documentation to the ``planemo mull`` command.
          0a1abfe_
        * Hack around a bug in Conda 4.2 that makes it so ``planemo mull`` doesn't work out of the box on
          Mac OS X.
          0a1abfe_
        * Allow URIs to be used instead of paths for a couple operations. ce0dc4e_
        * Implement non-strict CWL parsing option. 4c0f100_
        * Fixes for changes to cwltool_ and general CWL-relate functionality.
          3c95b7b_, 06bcf19_, 525de8f_, 9867e56_, 9ab4a0d_
        * Eliminate deprecated XML-based abstraction from ``planemo.tools``. 04238d3_
        * Fix ``MANIFEST.in`` entry that was migrated to galaxy-lib. ced5ce2_
        * Various fixes for the command ``conda_env``. `Pull Request 640`_
        * Improved command help - both formatting and content. `Pull Request 639`_
        * Implement a ``--no_dependency_resolution`` option disabling conda dependency
          resolver.
          `Pull Request 635`_, `Issue 633`_
        * Tests for new linting logic. `Pull Request 638`_
        * Fix bug where tool IDs needs to be lowercase for the shed (thanks to
          `@bgruening`_).
          `Pull Request 649`_
        * Update seqtk version targetted by intro docs. e343b67_
        * Various other Conda usability improvements. `Pull Request 634`_
        
        ---------------------
        0.38.1 (2017-02-06)
        ---------------------
        
        * Fix bug with ``shed_lint --urls`` introduced in 0.38.0.
          84ebc1f_
        
        ---------------------
        0.38.0 (2017-02-06)
        ---------------------
        
        * Trim down the default amount of logging during testing.
          `Pull Request 629`_, `Issue 515`_
        * Improved log messages during shed operations. 08c067c_
        * Update tool XSD against latest Galaxy.
          fca4183_, 03c9658_
        * Fix bug where ``shed_lint --tools`` for a suite lints the same tools multiple
          times.
          `Issue 564`_, `Pull Request 628`_
        
        ---------------------
        0.37.0 (2017-01-25)
        ---------------------
        
        * Update to the latest `galaxy-lib`_ release. This means new installs start with
          Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes many
          Conda_ related bugs.
        * Change defaults so that Conda automatically initializes and performs tool installs
          by default from within the spawned Galaxy server. The trio of flags
          ``--conda_dependency_resolution``, ``--conda_auto_install``, and ``--conda_auto_init``
          are effectively enabled by default now. 4595953_
        * Use the Galaxy cached dependency manager by default (thanks to `@abretaud`_).
          `Pull Request 612`_
        * Test Conda dependency resolution for more versions of Galaxy including the forthcoming
          release of 17.01.
        * Update to the latest Galaxy tool XSD for various tool linting fixes. 32acd68_
        * Fix pip ignores for ``bioconda_scripts`` (thanks to `@nturaga`_)
          `Pull Request 614`_
        
        ---------------------
        0.36.1 (2016-12-12)
        ---------------------
        
        * Fix move error when using ``project_init``.
          `Issue 388`_, `Pull Request 610`_
        * Improved integration testing for ``test`` command. `Pull Request 609`_
        * Update CWL links to v1.0 (thanks to `@mr-c`_).
          `Pull Request 608`_
        
        ---------------------
        0.36.0 (2016-12-11)
        ---------------------
        
        * Bring in latest tool XSD file from Galaxy (thanks to `@peterjc`_).
          `Pull Request 605`_
        * PEP8 fixes for various linting problems 
          (thanks to `@peterjc`_).
          `Pull Request 606`_
        * Update tool syntax URL to new URL (thanks to `@mvdbeek`_).
          `Pull Request 602`_
        
        ---------------------
        0.35.0 (2016-11-14)
        ---------------------
        
        * Native support for building bioconductor tools and recipes
          (thanks to `@nturaga`_). `Pull Request 570`_
        * Fixes for running Galaxy via docker-galaxy-stable (thanks to
          `@bgruening`_). 50d3c4a_
        * Import order linting fixes (thanks to `@bgruening`_).
        
        ---------------------
        0.34.1 (2016-10-12)
        ---------------------
        
        * Mimic web browser to validate user help URLs fixing `Issue 578`_
          (thanks to `@peterjc`_). `Pull Request 591`_
        * Fix for Bioconda recipes depending on ``conda-forge`` (thanks to `@nsoranzo`_).
          `Pull Request 590`_
        
        
        ---------------------
        0.34.0 (2016-10-05)
        ---------------------
        
        * Implement ``mull`` command to build containers for tools based on Conda_
          recipes matching requirement definitions. 08cef54_
        * Implement ``--mulled_containers`` flag on ``test``, ``serve``, and ``run``
          commands to run tools in "mulled" containers. Galaxy will first search
          locally cache containers (such as ones built with ``mull``), then search
          the mulled namespace of `quay.io`_, and finally build one on-demand if
          needed using `galaxy-lib`_ and Involucro_ developed by `@thriqon`_.
        * Implement ``--conda_requirements`` flag on ``lint`` command to ensure requirements
          can be resolved in best practice channels. 9da8387_
        * Allow ``conda_install`` command over multiple tool paths. 2e4e5fc_
        * Update pip_ as part of setting virtual environment in ``Makefile`` target.
          19b2ee9_
        * Add script to auto-update Bioconda_ recipe for Planemo and open a pull request.
          f0da66f_
        
        ---------------------
        0.33.2 (2016-09-28)
        ---------------------
        
        * Fix HISTORY.rst link problem that prevented correct display of content on PyPI_.
        
        ---------------------
        0.33.1 (2016-09-28)
        ---------------------
        
        * Fix ``lint --urls`` false positives by being more restrictive with what is considered a URL
          (fixed by `@erasche`_ after detailed report from `@peterjc`_).
          `Issue 573`_, `Pull Request 579`_
        
        ---------------------
        0.33.0 (2016-09-23)
        ---------------------
        
        * Enable XSD validation of tools by default (restore old behavior with
          ``planemo lint --no_xsd``). 1ef05d2_
        * Implement a ``conda_lint`` command to lint Conda_ recipes based
          on `anaconda-verify`_. 6a6f164_
        * Implement ``clone`` and ``pull_request`` commands to ease PRs
          (with documentation fixes from `@martenson`_).
          e925ba1_, ea5324f_
        * Update `galaxy.xsd`_ to allow version_command's to have an interpreter
          attribute. 7cca2e4_
        * Apply improvement from `@nsoranzo`_ for Planemo's use of git_ 
          `diff <https://git-scm.com/docs/git-diff>`__.
          6f91719_
        * Pull in downstream refactoring of ``tool_init`` code from `@nturaga`_'s 
          Bioconductor_ work. ccdd2d5_
        * Update to latest `Tool Factory`_ code from `tools-iuc`_. ca88b0c_
        * Small code cleanups. b6d8294_, d6da3a8_
        * Fixup docs in ``planemo.xml.validation``.
        * Allow skipping newly required lxml_ dependency in `setup.py`_. 34538de_
            
        
        ---------------------
        0.32.0 (2016-09-16)
        ---------------------
        
        * Enhance ``planemo lint --xsd`` to use a fairly complete and newly official XSD
          definition. `Pull Request 566`_
        * Migrate and update documentation related to tool XML macros and handling 
          multiple outputs from the Galaxy wiki (with help from `@bgruening`_, `@mvdbeek`_,
          and `@nsoranzo`_). `Pull Request 559`_
        * Documentation fixes (thanks to `@ramezrawas`_). `Pull Request 561`_
        * Do not fail URL linting in case of too many requests (thanks to `@nsoranzo`_).
          `Pull Request 565`_
        
        ---------------------
        0.31.0 (2016-09-06)
        ---------------------
        
        * Implement new commands to ``ci_find_repos`` and ``ci_find_tools`` to ease
          CI scripting.
          `Pull Request 555`_
            
        
        ---------------------
        0.30.2 (2016-09-01)
        ---------------------
        
        * Fix another problem with Conda_ prefix handling when using
          ``--conda_dependency_resolution``. f7b6c7e_
        
        ---------------------
        0.30.1 (2016-09-01)
        ---------------------
        
        * Fix a problem with Conda_ prefix handling when using
          ``--conda_dependency_resolution``. f7b6c7e_
        * Fix for quote problem in ``update_planemo_recipe.bash``. 6c03de8_
        * Fix to restore linting of ``tests/`` directory and fix import order 
          throughout module. ef4b9f4_
        
        ---------------------
        0.30.0 (2016-09-01)
        ---------------------
        
        * Update to the latest `galaxy-lib`_ release and change Conda_ semantics to match
          recent updates to Galaxy. For the most robust Conda_ usage - use planemo 0.30+
          with Galaxy 16.07 or master.
          07d94bd_
        * Implement the ``--conda_auto_init`` flag for ``conda_install``. ca19910_
        * Allow the environment variable ``PLANEMO_CONDA_PREFIX`` to set a default
          for ``--conda_prefix``.
          24008ab_
        * Fixup documentation regarding installs and Conda_. ce44e87_
        * Fix and lint Python module import order throughout project.
          `Pull Request 550`_
        * Use ``cp`` rather than symlink to ``$DOWNLOAD_CACHE`` in the
          ``dependency_script`` command (thanks to `@peterjc`_).  c2204b3_
        * Fixes for the Homebrew recipe updater. c262b6d_
        
        ---------------------
        0.29.1 (2016-08-19)
        ---------------------
        
        * Improved handling of Python 2.7 specific dependencies.
        
        ---------------------
        0.29.0 (2016-08-19)
        ---------------------
        
        * Look for sha256sum checksums during shed_lint (thanks to `@peterjc`_).
          `Pull Request 539`_
        * An assortment fixes and enhancements to the ``dependency_script`` command
          (thanks to `@peterjc`_). `Pull Request 541`_, `Pull Request 545`_
        * Fix shed_build to respect exclude: in .shed.yml (thanks to `@nsoranzo`_).
          `Pull Request 540`_
        * Fix linting of tool URLs (thanks to `@nsoranzo`_). `Pull Request 546`_ 
        
        ---------------------
        0.28.0 (2016-08-17)
        ---------------------
        
        * Fixes for bioblend_ v0.8.0 (thanks to `@nsoranzo`_). 9fdf490_ 
        * Enable shed repo type update (thanks to `@nsoranzo`_). 3ceaa40_
        * Create suite repositories with repository_suite_definition type by default
          (thanks to `@nsoranzo`_).
          057f4f0_
        * Include ``shed_lint`` in script run by ``travis_init`` (thanks to `@peterjc`_).
          `Pull Request 528`_
        * Minor polish to the ``travis_init`` command (thanks to `@peterjc`_).
          `Pull Request 512`_
        * Update pip_ and setuptools on TravisCI; fix travis_init (thanks to `@peterjc`_).
          `Pull Request 521`_
        * Shorten command one line descriptions for main help (thanks to `@peterjc`_).
          `Pull Request 510`_
        * Use ``planemo test --no_cache_galaxy`` under TravisCI (thanks to `@peterjc`_).
          `Pull Request 513`_
        * Improve and fix docs ahead of GCC 2016 (thanks to `@martenson`_).
          `Pull Request 498`_, 725b232_
        * Add description of ``expect_num_outputs`` to planemo FAQ. a066afb_
        * Revise planemo tools docs to be more explicit about collection identifiers.
          a811e65_
        * Add more docs on existing dynamic tool output features. `Pull Request 526`_
        * Fix serve command doc (thanks to `@nsoranzo`_). 8c088c6_
        * Fix `make lint-readme` (RST link errors) (thanks to `@peterjc`_).
          `Pull Request 525`_
        * Add union bedgraph example to project templates (for GCC demo example). 
          d53bcd6_
        * Add Flow Cytometry Analysis, Data Export, and Constructive Solid Geometry as
          shed categories (thanks to `@bgruening`_, `@gregvonkuster`_, and `@nsoranzo`_).
          e890ab5_, 08bb354_, e2398fb_
        * Remove duplicated attribute in docs/writing/bwa-mem_v5.xml (thanks to
          Paul Stewart `@pstew`_).
          `Pull Request 507`_
        
        ---------------------
        0.27.0 (2016-06-22)
        ---------------------
        
        * Use ephemeris to handle syncing shed tools for workflow actions.
          1c6cfbb_
        * More planemo testing enhancements for testing artifacts that aren't
          Galaxy tools. `Pull Request 491`_
        * Implement ``docker_galaxy`` engine type. eb039c0_, `Issue 15`_
        * Enhance profiles to be Dockerized Galaxy-aware. `Pull Request 488`_
        * Add linter for DOI type citation - thanks to `@mvdbeek`_.
          `Pull Request 484`_
        
        ---------------------
        0.26.0 (2016-05-20)
        ---------------------
        
        * Implement ``Engine`` and ``Runnable`` abstractions - Planemo now has
          beta support for testing Galaxy workflows and CWL_ tools with Galaxy and
          any CWL_ artifact with cwltool_.
          `Pull Request 454`_, 7be1bf5_
        * Fix missing command_line in test output json. e38c436_
        * More explicit Galaxy ``job_conf.xml`` handling, fixes bugs caused by
          ``galaxy_root`` having existing and incompatible ``job_conf.xml`` files
          and makes it possible to specify defaults with fixed server name. c4dfd55_
        * Introduce profile commands (``profile_create``, ``profile_delete``, and
          ``profile_list``) and profile improvements (automatic postgres database
          creation support). `Pull Request 480`_, a87899b_
        * Rework Galaxy test reporting to use structured data instead of XUnit
          data. 4d29bf1_
        * Refactor Galaxy configuration toward support for running Galaxy in
          docker-galaxy-stable. `Pull Request 479`_    
        
        ---------------------
        0.25.1 (2016-05-11)
        ---------------------
        
        * Tweak dependencies to try to fix cwltool_ related issues - such
          as `Issue 475`_.
        
        ---------------------
        0.25.0 (2016-05-11)
        ---------------------
        
        * Implement Galaxy "profiles" - the ability to configure 
          perisistent, named environments for ``serve`` and ``test``.
          5d08b67_
        * Greatly improved ``serve`` command - make ``test-data``
          available as an FTP folder, (on 16.07) automatically log
          in an admin user, and many more options (such as those 
          required for "profiles" and a ``--daemon`` mode).
        * Two fixes to ensure more consistent, dependable ``test`` output.
          `Pull Request 472`_, f3c6917_
        * Add code and documentation for linting (``lint``) and
          building (``tool_init``) CWL_ tools. a4e6958_, b0b867e_,
          4cd571c_
        * If needed for Conda_ workaround, shorten ``config_directory`` 
          path (thanks to `@mvdbeek`_). efc5f30_
        * Fix ``--no_cache_galaxy`` option (thanks to Gildas Le 
          Corguillé). d8f2038_
        * Target draft 3 of CWL_ instead of draft 2. 775bf49_
        * Fix ``cwltool`` dependency version - upstream changes broke
          compatibility. `65b999d`_
        * Add documentation section and slides about recent Galaxy
          tool framework changes (with fix from `@remimarenco`_). 069e7ba_
        * Add IUC standards to Planemo docs. 2ae2b49_
        * Improve collection-related contents in documentation
          (thanks in part to `@martenson`_).
          fea51fc_, 13a5ae7_
        * Add documentation on ``GALAXY_SLOTS`` and running planemo
          on a cluster. 45135ff_, e0acf91_
        * Revise command-line handling framework for consistency and
          extension - allow extra options to be configured as 
          defaults ``~/.planemo.yml`` including ``--job_config_file``
          and Conda_ configuration options. e769118_, 26e378e_
        * Fix ``tool_init`` commans options typos (thanks to
          Nitesh Turaga). 826d371_
        * Refactor galaxy-related modules into submodules of a new
          ``planemo.galaxy`` package. 8e96864_
        * Fix error message typo (thanks to `@blankenberg`_). b1c8f1d_
        * Update documentation for recent command additions. 3f4ab44_
        * Rename option ``--galaxy_sqlite_database`` option to
          ``--galaxy_database_seed`` and fix it so it actually works. 
          f7554d1_
        * Add ``--extra_tools`` option to ``serve`` command. 02a08a0_
        * Update project testing to include linting documentation
          (``docs/``), Python import order, and docstrings.
          a13a120_, 6e1e726_, 95d5cba_
        
        
        ---------------------
        0.24.2 (2016-04-25)
        ---------------------
        
        * Revert "check ``.shed.yml`` owner against credentials during shed
          creation", test was incorrect and preventing uploads.
          `Pull Request 425`_, `Issue 246`_
        
        ---------------------
        0.24.1 (2016-04-08)
        ---------------------
        
        * Fix test summary report. `Pull Request 429`_
        * Improve error reporting when running ``shed_test``. ce8e1be_
        * Improved code comments and tests for shed related functionality.
          89674cb_
        * Rev `galaxy-lib`_ dependency to 16.4.1 to fix wget usage in
          newer versions of wget. d76b489_
        
        ---------------------
        0.24.0 (2016-03-29)
        ---------------------
            
        * Drop support for Python 2.6. 93b7bda_
        * A variety of fixes for ``shed_update``.
          `Pull Request 428`_, `Issue 416`_
        * Fix reporting of metadata updates for invalid shed updates.
          `Pull Request 426`_, `Issue 420`_
        * Check ``.shed.yml`` owner against credentials during shed creation.
          `Pull Request 425`_, `Issue 246`_
        * Fix logic error if there is a problem with ``shed_create``. 358a42c_
        * Tool documentation improvements. 0298510_, a58a3b8_
        
        ---------------------
        0.23.0 (2016-02-15)
        ---------------------
        
        * Fix duplicated attributes with Conda_ resolver (thanks
          to Björn Grüning). `Pull Request 403`_
        * Upgrade to latest version of `galaxy-lib`_ for more linting.
        * Attempt to better handle conditional dependency on cwltool.
        
        ---------------------
        0.22.2 (2016-01-14)
        ---------------------
        
        * Fixed bug targetting forthcoming release of Galaxy 16.01.
        
        ---------------------
        0.22.1 (2016-01-14)
        ---------------------
        
        * Fixed problem with PyPI_ build artifacts due to submodule's not
          being initialized during previous release.
        
        ---------------------
        0.22.0 (2016-01-13)
        ---------------------
        
        * Add ``--skip_venv`` to support running Galaxy 16.01 inside of
          conda environments. 9f3957d_
        * Implement conda support. f99f6c1_, ad3b2f0_, 5e0b6d1_
        * Update LICENSE for Planemo to match Galaxy. 15d33c7_
        * Depend on new `galaxy-lib`_ on PyPI_ instead of previous hacks....
          `Pull Request 394`_
        * Fix egg caching against master/15.10. 6d0f502_
        * Fix bug causing shed publishing of ``.svn`` directories.
          `Issue 391`_
        * Bug fixes for Conda_ support thanks to `@bgruening`_. 63e456c_
        * Fix document issues thanks to `@einon`_.
          `Pull Request 390`_
        * Improve client for shed publishing to support newer shed backend
          being developed by `@erasche`_. `Pull Request 394`_
        * Tool Shed ``repo_id`` change, `@erasche`_. `Pull Request 398`_
        * Various other small changes to testing, project structure, and
          Python 3 support.
        
        ---------------------
        0.21.1 (2015-11-29)
        ---------------------
        
        * Fix serious regression to ``test`` command. 94097c7_
        * Small fixes to release process. 4e1377c_, 94645ed_
        
        ---------------------
        0.21.0 (2015-11-29)
        ---------------------
        
        * If ``virtualenv`` not on ``PATH``, have Planemo create one for Galaxy.
          5b97f2e_
        * Add documentation section on testing tools installed in an existing
          Galaxy instance. 1927168_
        * When creating a virtualenv for Galaxy, prefer Python 2.7.
          e0577e7_
        * Documentation fixes and improvements thanks to `@martenson`_.
          0f8cb10_, 01584c5_, b757791_
        * Specify a minimum ``six`` version requirement. 1c7ee5b_
        * Add script to test a planemo as a wheel. 6514ff5_, `Issue 184`_
        * Fix empty macro loading. `Issue 362`_
        * Fix an issue when you run ``shed_diff --shed_target local`` thanks
          to Gwendoline Andres and Gildas Le Corguillé at ABiMS Roscoff.
          `Pull Request 375`_
        * Fix ``shed_diff`` printing to stdout if ``-o`` isn't specified.
          f3394e7_
        * Small ``shed_diff`` improvements to XML diffing and XUnit reporting.
          af7448c_, 83e227a_
        * More logging of ``shed_diff`` results if ``--verbose`` flagged.
          9427b47_
        * Add ``test_report`` command for rebuilding reports from structured JSON.
          99ee51a_
        * Fix option bug with Click 6.0 thanks to `@bgruening`_. 2a7c792_
        * Improved error messages for test commands. fdce74c_
        * Various fixes for Python 3. 2f66fc3_, 7572e99_, 8eda729_, 764ce01_
        * Use newer travis container infrastructure for testing. 6d81a94_
        * Test case fixes. 98fdc8c_, 0e4f70a_
            
        
        
        ---------------------
        0.20.0 (2015-11-11)
        ---------------------
        
        * More complete I/O capturing for XUnit. 6409449_
        * Check for select parameter without options when linting tools.
          `Issue 373`_
        * Add ``--cwl_engine`` argument to ``cwl_run`` command. dd94ddc_
        * Fixes for select parameter linting. 8b31850_
        * Fix to demultiplexing repositories after tool uploads. `Issue 361`_
        * Fix to update planemo for Galaxy wheels. 25ef0d5_
        * Various fixes for Python 2.6 and Python 3.
          c1713d2_, 916f610_, c444855_
            
        
        ---------------------
        0.19.0 (2015-11-03)
        ---------------------
        
        * Initial implementation of ``cwl_run`` command that runs a
          CWL tool and job file through Galaxy. 49c5c1e_
        * Add ``--cwl`` flag to ``serve`` to experimentally serve CWL tools
          in Galaxy.
          `Pull Request 339`_
        * Implement highly experimental ``cwl_script`` command to convert
          a CWL job to a bash script. 508dce7_
        * Add name to all XUnit reports (thanks to `@erasche`_).
          `Pull Request 343`_
        * Capture stdout and stderr for ``shed_diff`` and ``shed_update`` 
          XUnit reports. `Pull Request 344`_
        * More tool linting (conditionals) thanks to `@erasche`_.
          `Pull Request 350`_
        * UTF-8 fixes when handling XUnit reports. `Pull Request 345`_
        * Add `Epigenetics` as Tool Shed category. `Pull Request 351`_
        * Merge changes to common modules shared between Galaxy, Planemo, and Pulsar (thanks to `@natefoo`_).
          `Pull Request 356`_
        * Add ``--cite_url`` to ``tool_init``. fdb1b51_
        * ``tool_init`` bug fix. f854138_
        * Fix `setup.py`_ for cwltool and bioblend_ changes. 1a157d4_
        * Add option to specify template sqlite database locally. c23569f_
        * Add example IPython notebooks to docs. c8640b6_
        
        ---------------------
        0.18.1 (2015-10-22)
        ---------------------
        
        * Fix issue with test reporting not being populated. 19900a6_
        
        ---------------------
        0.18.0 (2015-10-20)
        ---------------------
        
        * Improvements to ``docker_shell`` usability (thanks to `@kellrott`_).
          `Pull Request 334`_
        * Add docker pull attempt when missing Dockerfile (thanks to `@kellrott`_).
          `Pull Request 333`_
        * Fix bug inferring which files are tool files (thanks to `@erasche`_).
          `Pull Request 335`_, `Issue 313`_
        * Initial work toward automating brew recipe update. 4d6f7d9_, `Issue 329`_
        
        ---------------------
        0.17.0 (2015-10-19)
        ---------------------
        
        * Implement basic XUnit report option for ``shed_update`` (thanks to `@martenson`_).
          `Pull Request 322`_
        * Fix issues with producing test outputs. 572e754_
        * Xunit reporting improvements - refactoring, times, diff output (thanks to `@erasche`_).
          `Pull Request 330`_
        * Implement project governance policy and update developer code of conduct to
          match that of the Galaxy project. `Pull Request 316`_
        * Update filters for account for new ``.txt`` and ``.md`` test outputs
          (thanks to `@erasche`_). `Pull Request 327`_
        * Add verbose logging to galaxy test output handling problems. 5d7db92_
        * Flake8 fixes (thanks to `@martenson`_). 949a36d_
        * Remove uses of deprecated ``mktemp`` Python standard library function
          (thanks to `@erasche`_). `Pull Request 330`_
            
        
        ---------------------
        0.16.0 (2015-10-07)
        ---------------------
        
        * Adding new command ``dependency_script`` to convert Tool Shed dependencies
          into shell scripts - thanks to `@peterjc`_.
          `Pull Request 310`_, f798c7e_, `Issue 303`_
        * Implement profiles in sheds section of the ``~/.planemo.yml``.
          `Pull Request 314`_
        
        ---------------------
        0.15.0 (2015-10-01)
        ---------------------
        
        * Template framework for reporting including new markdown and plain
          text reporting options for testing - thanks to `@erasche`_.
          `Pull Request 304`_
        * XUnit style reporting for ``shed_diff`` command - thanks to
          `@erasche`_. `Pull Request 305`_
        * Add new ``shed_build`` command for building repository tarballs -
          thanks to `@kellrott`_. `Pull Request 297`_
        * Fix exit code handling for ``lint`` commands - thanks to `@mvdbeek`_.
          `Pull Request 292`_    
        * Improved documentation for ``serve`` command - thanks to `@lparsons`_.
          `Pull Request 312`_
        * Tiny backward compatible Python 3 tweaks for `Tool Factory`_ - thanks
          to `@peterjc`_. dad2d9d_
        * Fixed detection of virtual environment in ``Makefile`` - thanks to
          `@lparsons`_. `Pull Request 311`_
        * Updates to Galaxy XSD - thanks to `@mr-c`_. `Pull Request 309`_
        * Allow reading shed key option from an environment variable.
          `Pull Request 307`_
        * Allow specifying host to serve Galaxy using ``-host`` - thanks in
          part to `@chambm`_. `Pull Request 301`_
        * Allow specifying defaults for ``-host`` and ``--port`` in
          ``~/.planemo.yml``. `Pull Request 301`_
        * Improve ``~/.planemo.yml`` sample comments - thanks to `@martenson`_.
          `Pull Request 287`_
        * Update tool shed categories - thanks to `@bgruening`_. `Pull Request 285`_
        * Improved output readibility for ``diff`` command - thanks to `@martenson`_. `Pull Request 284`_
        
        ---------------------
        0.14.0 (2015-08-06)
        ---------------------
        
        * Allow ``-t`` as shorthand for ``--shed_target`` (thanks to Peter Cock).
          `Pull Request 278`_
        * Fix ``tool_init`` command to use ``from_work_dir`` only if file in command
          (thanks to bug report and initial fix outline by Gildas Le Corguillé).
          `Pull Request 277`_
        * Various documentation fixes (thanks in part to Peter Cock and Daniel
          Blankenberg). `Pull Request 256`_, `Pull Request 253`_, `Pull Request 254`_, 
          `Pull Request 255`_, `Pull Request 251`_, `Issue 272`_
        
        ---------------------
        0.13.2 (2015-07-06)
        ---------------------
        
        * Fix project_init for missing files. cb5b906_
        * Various documentation improvements.    
        
        ---------------------
        0.13.1 (2015-07-01)
        ---------------------
        
        * Fix for ``shed_init`` producing non-standard type hints. `Issue 243`_,
          f0610d7_
        * Fix tool linting for parameters that define an ``argument`` but not a
          ``name``. `Issue 245`_, aad1eed_
        * Many doc updates including a tutorial for developing tools in a test-driven
          fashion and instructions for using the planemo appliance through Kitematic
          (with Kitematic screenshots from E. Rasche).
        
        ---------------------
        0.13.0 (2015-06-28)
        ---------------------
        
        * If planemo cannot find a Galaxy root, it will now automatically fetch
          one (specifing ``--galaxy_install`` will still force a fetch).
          `Pull Request 235`_
        * `Docuementation <http://planemo.readthedocs.org/en/latest/appliance.html>`__
          has been updated to reflect new and vastly improved Docker and Vagrant
          virtual appliances are now available, as well as a new VirtualBox OVA
          variant.
        * Update linting for new tool XML features (including ``detect_errors``
          and output collections). `Issue 233`_, 334f2d4_
        * Fix ``shed_test`` help text. `Issue 223`_
        * Fix code typo (thanks to Nicola Soranzo). `Pull Request 230`_
        * Improvements to algorithm used to guess if an XML file is a tool XML file.
          `Issue 231`_
        * Fix configuration file handling bug. `Issue 240`_
        
        ---------------------
        0.12.2 (2015-05-23)
        ---------------------
        
        * Fix ``shed_test`` and ``shed_serve`` for test and local tool sheds.
          f3cafaa_
        
        ---------------------
        0.12.1 (2015-05-21)
        ---------------------
        
        * Fix to ensure the tab completion script is in the Python source tarball
          (required for setting up tab-completion for Homebrew). 6b4e7a6_
        
        ---------------------
        0.12.0 (2015-05-21)
        ---------------------
        
        * Implement a ``--failed`` flag for the ``test`` command to rerun
          previously faied tests. `Pull Request 210`_
        * Implement ``shed_update`` to upload contents and update repository
          metadata. `Pull Request 216`_
        * Implement ``shed_test`` and ``shed_serve`` commands to test and view
          published artifacts in the Tool Shed. `Pull Request 213`_, `Issue 176`_
        * Add shell tab-completion script. 37dcc07_
        * Many more commands allow specifing multiple tool and/or repository targets.
          `Issue 150`_
        * Add -m as alias for --message in planemo shed_upload (thanks to
          Peter Cock). `Pull Request 200`_
        * Add ``--ensure_metadata`` option to ``shed_lint`` to ensure ``.shed.yml``
          files contain many repository. `Pull Request 215`_
        * More developer documentation, additional ``make`` targets including ones
          for setting up git pre-commit hooks. cc8abb6_, `Issue 209`_
        * Small README improvement (thanks to Martin Čech) b53006d_
        * Fixes for shed operation error handling (thanks to Martin Čech).
          `Pull Request 203`_,  `Pull Request 206`_
        * Fix for "smart" ``shed_diff`` not in the repository root directory
          (thanks to Peter Cock). `Pull Request 207`_, `Issue 205`_
        * Recursive ``shed_diff`` with directories not yet in Tool Shed.
          `Pull Request 208`_
        * Improve error handling and reporting for problematic ``--shed_target``
          values. `Issue 217`_
        * Fix typos in lint messages. `Issue 211`_
        
        
        ---------------------
        0.11.1 (2015-05-12)
        ---------------------
        
        * Fix default behavior for ``planemo lint`` to use current directory if
          explicit paths are not supplied. 1e3668a_
        
        ---------------------
        0.11.0 (2015-05-12)
        ---------------------
        
        * More compact syntax for defining multiple custom inclusions in ``.shed.yml``
          files - thanks to Peter Cock. `Issue 180`_, `Pull Request 185`_,
          `Pull Request 196`_
        * Prevent ambigous destinations when defining custom inclusions in
          ``.shed.yml``- thanks to Peter Cock. `Pull Request 186`_
        * ``lint`` now warns if tool ids contain whitespace. `Pull Request 190`_
        * Handle empty tar-balls gracefully on older Python versions - thanks
          to Peter Cock. `Pull Request 187`_
        * Tweak quoting in ``cp`` command - thanks to Peter Cock. 6bcf699_
        * Fix regression causing testing to no longer produce "pretty" test
          results under certain circumstances. `Issue 188`_
        * Fix for recursive ``shed_diff`` folder naming. `Issue 192`_
        * Fix output definitions to ``tool_init`` command. `Issue 189`_
        
        ---------------------
        0.10.0 (2015-05-06)
        ---------------------
        
        * Extend ``shed_lint`` to check for valid actions in tool_dependencies.xml
          files. 8117e03_
        * Extend ``shed_lint`` to check for required files based on repository type.
          `Issue 156`_
        * Ignore common editor backup files during ``shed_upload``. `Issue 179`_
        * Fix missing file when installing from source via PyPI_. `Issue 181`_
        * Fix ``lint`` to verify ``data`` inputs specify a ``format`` attribute.
          8117e03_
        * Docstring fix thanks to `@peterjc`_. fe7ad46_
        
        
        ---------------------
        0.9.0 (2015-05-03)
        ---------------------
        
        * Add new logo to the README thanks to `@petrkadlec`_ from `puradesign.cz
          <http://puradesign.cz/en>`__ and `@carlfeberhard`_ from the Galaxy Project.
          `Issue 108`_
        * Implement smarter ``shed_diff`` command - it now produces a meaningful
          exit codes and doesn't report differences if these correspond to attributes
          that will be automatically populated by the Tool Shed. `Issue 167`_
        * Use new smarter ``shed_diff`` code to implement a new ``--check_diff``
          option for ``shed_upload`` - to check for meaningful differences before
          updating repositories. `Issue 168`_
        * Record git commit hash during ``shed_upload`` if the ``.shed.yml`` is
          located in a git repository. `Issue 170`_
        * Allow ``shed_`` operations to operate on git URLs directly. `Issue 169`_
        * Fail if missing file inclusion statements encountered during ``.shed.yml``
          repository resolution - bug reported by `@peterjc`_. `Issue 158`_
        * Improved exception handling for tool shed operations including new 
          ``--fail_fast`` command-line option. * `Issue 114`_, `Pull Request 173`_
        * Implement more validation when using the ``shed_init`` command. 1cd0e2d_
        * Add ``-r/--recursive`` option to ``shed_download`` and ``shed_diff`` 
          commands and allow these commands to work with ``.shed.yml`` files defining
          multipe repositories. 40a1f57_
        * Add ``--port`` option to the ``serve`` and ``tool_factory`` commands.
          15804be_
        * Fix problem introduced with `setup.py`_ during the 0.9.0 development cycle
          - thanks to `@peterjc`_. `Pull Request 171`_
        * Fix clone bug introduced during 0.9.0 development cycle - thanks to
          `@bgruening`_. `Pull Request 175`_
        
        ---------------------
        0.8.4 (2015-04-30)
        ---------------------
        
        * Fix for Travis CI testing picking up invalid tests (reported by `@takadonet`_). `Issue 161`_
        * Fix tar ordering for consistency (always sort by name) - thanks to `@peterjc`_.  `Pull Request 164`_, `Issue 159`_
        * Fix exception handling related to tool shed operations - thanks to `@peterjc`_. `Pull Request 155`_, b86fe1f_
        
        ---------------------
        0.8.3 (2015-04-29)
        ---------------------
        
        * Fix bug where ``shed_lint`` was not respecting the ``-r/--recursive`` flag.
          9ff0d2d_
        * Fix bug where planemo was producing tar files incompatible with the Tool
          Shed for package and suite repositories. a2ee135_
        
        ---------------------
        0.8.2 (2015-04-29)
        ---------------------
        
        * Fix bug with ``config_init`` command thanks to `@bgruening`_. `Pull Request 151`_
        * Fix unnessecary ``lint`` warning about ``parallelism`` tag reported by
          `@peterjc`_. 9bf1eab_
        
        ---------------------
        0.8.1 (2015-04-28)
        ---------------------
        
        * Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.
        
        ---------------------
        0.8.0 (2015-04-27)
        ---------------------
        
        * Implement the new ``shed_lint`` command that verifies various aspects of tool
          shed repositories - including XSD_ validation of ``repository_dependencies.xml``
          and ``tool_dependencies.xml`` files, best practices for README files, and the
          contents of ``.shed.yml`` files. This requires the lxml_ library to be available
          to Planemo or the application xmllint_ to be on its ``PATH``. `Pull Request 130`_
          `Issue 89`_ `Issue 91`_ 912df02_ d26929e_ 36ac6d8_
        * Option to enable experimental XSD_ based validation of tools when ``lint``
          is executed with the new ``--xsd`` flag. This validation occurs against the
          unofficial `Galaxy Tool XSD project <https://github.com/JeanFred/Galaxy-XSD>`__
          maintained by `@JeanFred`_. This requires the lxml_ library to be
          available to Planemo or the application xmllint_ to be on its ``PATH``.
          `Pull Request 130`_ 912df02_
        * Allow skipping specific linters when using the ``lint`` command using the new
          ``--skip`` option. 26e3cdb_
        * Implement sophisticated options in ``.shed.yml`` to map a directory to many,
          custom Tool Shed repositories during shed operaitons such ``shed_upload``
          including automatically mapping tools to their own directories and automatically
          building suites repositories. `Pull Request 143`_
        * Make ``shed_upload`` more intelligent when building tar files so that package
          and suite repositories may have README files in source control and they will
          just be filtered out during upload. 53edd99_
        * Implement a new ``shed_init`` command that will help bootstrap ``.shed.yml``
          files in the specified directory. cc1a447_
        * Extend ``shed_init`` to automatically build a ``repository_rependencies.xml``
          file corresponding to a Galaxy workflow (``.ga`` file). `Issue 118`_ 988de1d_
        * In addition to a single file or directory, allow ``lint`` to be passed multiple
          files. 343902d_ `Issue 139`_
        * Add ``-r/--recursive`` option to ``shed_create`` and ``lint`` commands. 63cd431_
          01f2af9_
        * Improved output formatting and option to write diffs to a file for the
          ``shed_diff`` command. 965511d_
        * Fix lint problem when using new Galaxy testing features such as expecting
          job failures and verifing job output. `Issue 138`_
        * Fix typo in ``test`` help thanks to first time contributor `@pvanheus`_.
          `Pull Request 129`_ 1982076_
        * Fix NPE on empty ``help`` element when linting tools. `Issue 124`_
        * Fix ``lint`` warnings when ``configfiles`` are defined in a tool. 1a85493_
        * Fix for empty ``.shed.yml`` files. b7d9e96_
        * Fix the ``test`` command for newer versions of nose_. 33294d2_
        * Update help content and documentation to be clear ``normalize`` should not
          be used to update the contents of tool files at this time. 08de8de_
        * Warn on unknown ``command`` attributes when linting tools (anything but
          ``interpreter``). 4f61025_
        * Various design, documentation (including new documentation on Tool Shed
          `publishing <http://planemo.readthedocs.org/en/latest/publishing.html>`__),
          and testing related improvements (test coverage has risen from 65% to over
          80% during this release cycle).
        
        ---------------------
        0.7.0 (2015-04-13)
        ---------------------
        
        * Implement `shed_create` command to create Tool Shed repositories from
          ``.shed.yml`` files (thanks to E. Rasche). `Pull Request 101`_
        * Allow automatic creation of missing repositories  during ``shed_upload``
          with the new ``--force_repository_creation`` flag (thanks to E. Rasche).
          `Pull Request 102`_
        * Allow specifying files to exclude in ``.shed.yml`` when creating tar files
          for ``shed_upload`` (thanks to Björn Grüning). `Pull Request 99`_
        * Resolve symbolic links when building Tool Shed tar files with
          ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 104`_
        * Add a `Contributor Code of Conduct
          <https://planemo.readthedocs.org/en/latest/conduct.html>`__.
          `Pull Request 113`_
        * Omit ``tool_test_output.json`` from Tool Shed tar file created with
          ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 111`_
        * Update required version of bioblend_ to ``0.5.3``. Fixed `Issue 88`_.
        * Initial work on implementing tests cases for Tool Shed functionality.
          182fe57_
        * Fix incorrect link in HTML test report (thanks to Martin Čech). 4c71299_
        * Download Galaxy from the new, official Github repository. 7c69bf6_
        * Update travis_test to install stable planemo from PyPI_. 39fedd2_
        * Enable caching on ``--install_galaxy`` by default (disable with
          ``--no_cache_galaxy``). d755fe7_
        
        ---------------------
        0.6.0 (2015-03-16)
        ---------------------
        
        * Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc...
        * Fix ``tool_init`` to quote file names (thanks to Peter Cock).  `Pull Request 98`_.
        * Allow ignoring file patterns in ``.shed.yml`` (thanks to Björn Grüning). `Pull Request 99`_
        * Add ``--macros`` flag to ``tool_init`` command to generate a macro file as part of tool generation. ec6e30f_
        * Add linting of tag order for tool XML files. 4823c5e_
        * Add linting of ``stdio`` tags in tool XML files. 8207026_
        * More tests, much higher test coverage. 0bd4ff0_
        
        ---------------------
        0.5.0 (2015-02-22)
        ---------------------
        
        * Implement ``--version`` option. `Issue 78`_
        * Implement ``--no_cleanup`` option for ``test`` and ``serve`` commands to
          persist temp files. 2e41e0a_
        * Fix bug that left temp files undeleted. `Issue 80`_
        * More improvements to release process. fba3874_
        
        ---------------------
        0.4.2 (2015-02-21)
        ---------------------
        
        * Fix `setup.py`_ for installing non-Python data from PyPI_ (required newer
          for ``tool_factory`` command and reStructuredText linting). Thanks to
          Damion Dooley for the bug report. `Issue 83`_
        
        ---------------------
        0.4.1 (2015-02-16)
        ---------------------
        
        * Fix README.rst so it renders properly on PyPI_.
        
        ---------------------
        0.4.0 (2015-02-16)
        ---------------------
        
        * Implement ``tool_init`` command for bootstrapping creation of new
          tools (with `tutorial <http://planemo.readthedocs.org/en/latest/writing.html>`_.) 78f8274_
        * Implement ``normalize`` command for reorganizing tool XML and macro
          debugging. e8c1d45_
        * Implement ``tool_factory`` command to spin up Galaxy pre-configured the
          `Tool Factory`_. 9e746b4_
        * Added basic linting of ``command`` blocks. b8d90ab_
        * Improved linting of ``help`` blocks, including verifying valid
          `reStructuredText`. 411a8da_
        * Fix bug related to ``serve`` command not killing Galaxy properly when complete. 53a6766_
        * Have ``serve`` command display tools at the top level instead of in shallow sections. badc25f_
        * Add additional dependencies to ``setup.py`` more functionality works out
          of the box. 85b9614_
        * Fix terrible error message related to bioblend_ being unavailable.
          `Issue 70`_
        * Various smaller documentation and project structure improvements.
        
        ---------------------
        0.3.1 (2015-02-15)
        ---------------------
        
        * Fixes to get PyPI_ workflow working properly.
        
        ---------------------
        0.3.0 (2015-02-13)
        ---------------------
        
        * Add option (``-r``) to the ``shed_upload`` command to recursively upload
          subdirectories (thanks to E. Rasche). `Pull Request 68`_
        * Fix diff formatting in test reports (thanks to E. Rasche).
          `Pull Request 63`_
        * Grab updated test database to speed up testing (thanks to approach from
          E. Rasche and Dannon Baker). `Issue 61`_, dff4f33_
        * Fix test data command-line argument name (was ``test-data`` now it is
          ``test_data``). 834bfb2_
        * Use ``tool_data_table_conf.xml.sample`` file if
          ``tool_data_table_conf.xml.test`` is unavailable. Should allow some
          new tools to be tested without modifying Galaxy's global
          ``tool_data_table_conf.xml`` file. ac4f828_
        
        ---------------------
        0.2.0 (2015-01-13)
        ---------------------
        
        * Improvements to way Planemo loads its own copy of Galaxy modules to prevent
          various conflicts when launching Galaxy from Planemo. `Pull Request 56`_
        * Allow setting various test output options in ``~/.planemo.yml`` and disabling
          JSON output. 21bb463_
        * More experimental Brew and Tool Shed options that should not be considered
          part of Planemo's stable API. See bit.ly/gxbrew1 for more details.
        * Fix ``project_init`` for BSD tar (thanks to Nitesh Turaga for the bug
          report.) a4110a8_
        * Documentation fixes for tool linting command (thanks to Nicola Soranzo).
          `Pull Request 51`_
        
        ---------------------
        0.1.0 (2014-12-16)
        ---------------------
        
        * Moved repository URL to https://github.com/galaxyproject/planemo.
        * Support for publishing to the Tool Shed. `Pull Request 6`_
        * Support for producing diffs (``shed_diff``) between local repositories and
          the Tool Shed (based on scripts by Peter Cock). `Pull Request 33`_
        * Use tool's local test data when available - add option for configuring
          ``test-data`` target. `Pull Request 1`_
        * Support for testing tool features dependent on cached data. 44de95c_
        * Support for generating XUnit tool test reports. 82e8b1f_
        * Prettier HTML reports for tool tests. 05cc9f4_
        * Implement ``share_test`` command for embedding test result links in pull
          requests. `Pull Request 40`_
        * Fix for properly resolving links during Tool Shed publishing (thanks to Dave
          Bouvier). `Pull Request 29`_
        * Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061_
        * Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan
          Blankenberg). a2c13e4_
        * Automate more of Travis CI testing so the scripts added to tool repository
          can be smaller. 20a8680_
        * Documentation fixes for Travis CI (thanks to Peter Cock). `Pull Request 22`_,
          `Pull Request 23`_
        * Various documentation fixes (thanks to Martin Čech). 36f7cb1_, b9232e5_
        * Various smaller fixes for Docker support, tool linting, and documentation.
        
        ---------------------
        0.0.1 (2014-10-04)
        ---------------------
        
        * Initial work on the project - commands for testing, linting, serving Galaxy
          tools - and more experimental features involving Docker and Homebrew. 7d07782_
        
        .. github_links
        .. _Pull Request 915: https://github.com/galaxyproject/planemo/pull/915
        .. _Pull Request 914: https://github.com/galaxyproject/planemo/pull/914
        .. _07dc6e0: https://github.com/galaxyproject/planemo/commit/07dc6e0
        .. _Pull Request 910: https://github.com/galaxyproject/planemo/pull/910
        .. _Pull Request 909: https://github.com/galaxyproject/planemo/pull/909
        .. _Pull Request 908: https://github.com/galaxyproject/planemo/pull/908
        .. _Pull Request 907: https://github.com/galaxyproject/planemo/pull/907
        .. _Pull Request 906: https://github.com/galaxyproject/planemo/pull/906
        .. _Pull Request 902: https://github.com/galaxyproject/planemo/pull/902
        .. _Pull Request 895: https://github.com/galaxyproject/planemo/pull/895
        .. _Issue 845: https://github.com/galaxyproject/planemo/issues/845
        .. _Issue 898: https://github.com/galaxyproject/planemo/issues/898
        .. _Pull Request 899: https://github.com/galaxyproject/planemo/pull/899
        .. _Pull Request 896: https://github.com/galaxyproject/planemo/pull/896
        .. _Pull Request 894: https://github.com/galaxyproject/planemo/pull/894
        .. _Pull Request 876: https://github.com/galaxyproject/planemo/pull/876
        .. _Pull Request 893: https://github.com/galaxyproject/planemo/pull/893
        .. _Pull Request 892: https://github.com/galaxyproject/planemo/pull/892
        .. _Pull Request 891: https://github.com/galaxyproject/planemo/pull/891
        .. _Pull Request 889: https://github.com/galaxyproject/planemo/pull/889
        .. _Pull Request 888: https://github.com/galaxyproject/planemo/pull/888
        .. _Pull Request 887: https://github.com/galaxyproject/planemo/pull/887
        .. _Pull Request 882: https://github.com/galaxyproject/planemo/pull/882
        .. _Pull Request 877: https://github.com/galaxyproject/planemo/pull/877
        .. _Pull Request 874: https://github.com/galaxyproject/planemo/pull/874
        .. _Pull Request 871: https://github.com/galaxyproject/planemo/pull/871
        .. _Pull Request 870: https://github.com/galaxyproject/planemo/pull/870
        .. _Pull Request 864: https://github.com/galaxyproject/planemo/pull/864
        .. _Pull Request 867: https://github.com/galaxyproject/planemo/pull/867
        .. _Pull Request 868: https://github.com/galaxyproject/planemo/pull/868
        .. _bad810a: https://github.com/galaxyproject/planemo/commit/bad810a
        .. _Pull Request 851: https://github.com/galaxyproject/planemo/pull/851
        .. _Pull Request 856: https://github.com/galaxyproject/planemo/pull/856
        .. _Pull Request 860: https://github.com/galaxyproject/planemo/pull/860
        .. _Pull Request 866: https://github.com/galaxyproject/planemo/pull/866
        .. _Pull Request 861: https://github.com/galaxyproject/planemo/pull/861
        .. _324c776: https://github.com/galaxyproject/planemo/commit/324c776
        .. _72d2ca7: https://github.com/galaxyproject/planemo/commit/72d2ca7
        .. _b12b117: https://github.com/galaxyproject/planemo/commit/b12b117
        .. _016b923: https://github.com/galaxyproject/planemo/commit/016b923
        .. _2002b49: https://github.com/galaxyproject/planemo/commit/2002b49
        .. _Pull Request 843: https://github.com/galaxyproject/planemo/pull/843
        .. _Pull Request 842: https://github.com/galaxyproject/planemo/pull/842
        .. _Pull Request 841: https://github.com/galaxyproject/planemo/pull/841
        .. _Pull Request 847: https://github.com/galaxyproject/planemo/pull/847
        .. _Pull Request 848: https://github.com/galaxyproject/planemo/pull/848
        .. _Pull Request 849: https://github.com/galaxyproject/planemo/pull/849
        .. _Pull Request 850: https://github.com/galaxyproject/planemo/pull/850
        .. _Pull Request 836: https://github.com/galaxyproject/planemo/pull/836
        .. _Pull Request 833: https://github.com/galaxyproject/planemo/pull/833
        .. _Pull Request 837: https://github.com/galaxyproject/planemo/pull/837
        .. _Pull Request 840: https://github.com/galaxyproject/planemo/pull/840
        .. _Pull Request 838: https://github.com/galaxyproject/planemo/pull/838
        .. _Pull Request 834: https://github.com/galaxyproject/planemo/pull/834
        .. _Pull Request 835: https://github.com/galaxyproject/planemo/pull/835
        .. _347c622: https://github.com/galaxyproject/planemo/commit/347c622
        .. _Pull Request 832: https://github.com/galaxyproject/planemo/pull/832
        .. _Pull Request 831: https://github.com/galaxyproject/planemo/pull/831
        .. _Pull Request 830: https://github.com/galaxyproject/planemo/pull/830
        .. _Pull Request 829: https://github.com/galaxyproject/planemo/pull/829
        .. _Pull Request 828: https://github.com/galaxyproject/planemo/pull/828
        .. _Pull Request 826: https://github.com/galaxyproject/planemo/pull/826
        .. _Pull Request 827: https://github.com/galaxyproject/planemo/pull/827
        .. _Pull Request 825: https://github.com/galaxyproject/planemo/pull/825
        .. _Pull Request 820: https://github.com/galaxyproject/planemo/pull/820
        .. _Pull Request 823: https://github.com/galaxyproject/planemo/pull/823
        .. _Pull Request 822: https://github.com/galaxyproject/planemo/pull/822
        .. _a5c72e3: https://github.com/galaxyproject/planemo/commit/a5c72e3
        .. _Pull Request 818: https://github.com/galaxyproject/planemo/pull/818
        .. _Pull Request 816: https://github.com/galaxyproject/planemo/pull/816
        .. _Pull Request 817: https://github.com/galaxyproject/planemo/pull/817
        .. _Pull Request 795: https://github.com/galaxyproject/planemo/pull/795
        .. _Pull Request 799: https://github.com/galaxyproject/planemo/pull/799
        .. _Pull Request 800: https://github.com/galaxyproject/planemo/pull/800
        .. _Pull Request 781: https://github.com/galaxyproject/planemo/pull/781
        .. _Pull Request 801: https://github.com/galaxyproject/planemo/pull/801
        .. _Pull Request 802: https://github.com/galaxyproject/planemo/pull/802
        .. _Pull Request 803: https://github.com/galaxyproject/planemo/pull/803
        .. _Pull Request 805: https://github.com/galaxyproject/planemo/pull/805
        .. _Pull Request 806: https://github.com/galaxyproject/planemo/pull/806
        .. _Pull Request 809: https://github.com/galaxyproject/planemo/pull/809
        .. _Pull Request 810: https://github.com/galaxyproject/planemo/pull/810
        .. _Pull Request 787: https://github.com/galaxyproject/planemo/pull/787
        .. _Pull Request 792: https://github.com/galaxyproject/planemo/pull/792
        .. _dc443d6: https://github.com/galaxyproject/planemo/commit/dc443d6
        .. _8cfe9e9: https://github.com/galaxyproject/planemo/commit/8cfe9e9
        .. _41f7df1: https://github.com/galaxyproject/planemo/commit/41f7df1
        .. _Pull Request 790: https://github.com/galaxyproject/planemo/pull/790
        .. _Pull Request 776: https://github.com/galaxyproject/planemo/pull/776
        .. _Pull Request 774: https://github.com/galaxyproject/planemo/pull/774
        .. _Pull Request 773: https://github.com/galaxyproject/planemo/pull/773
        .. _Pull Request 771: https://github.com/galaxyproject/planemo/pull/771
        .. _Pull Request 770: https://github.com/galaxyproject/planemo/pull/770
        .. _Pull Request 769: https://github.com/galaxyproject/planemo/pull/769
        .. _Pull Request 768: https://github.com/galaxyproject/planemo/pull/768
        .. _Pull Request 764: https://github.com/galaxyproject/planemo/pull/764
        .. _Pull Request 761: https://github.com/galaxyproject/planemo/pull/761
        .. _Pull Request 759: https://github.com/galaxyproject/planemo/pull/759
        .. _Pull Request 756: https://github.com/galaxyproject/planemo/pull/756
        .. _Pull Request 753: https://github.com/galaxyproject/planemo/pull/753
        .. _Pull Request 747: https://github.com/galaxyproject/planemo/pull/747
        .. _Pull Request 745: https://github.com/galaxyproject/planemo/pull/745
        .. _Pull Request 743: https://github.com/galaxyproject/planemo/pull/743
        .. _Pull Request 739: https://github.com/galaxyproject/planemo/pull/739
        .. _Pull Request 738: https://github.com/galaxyproject/planemo/pull/738
        .. _Pull Request 725: https://github.com/galaxyproject/planemo/pull/725
        .. _Pull Request 727: https://github.com/galaxyproject/planemo/pull/727
        .. _Pull Request 729: https://github.com/galaxyproject/planemo/pull/729
        .. _Pull Request 730: https://github.com/galaxyproject/planemo/pull/730
        .. _Pull Request 731: https://github.com/galaxyproject/planemo/pull/731
        .. _Pull Request 733: https://github.com/galaxyproject/planemo/pull/733
        .. _Pull Request 732: https://github.com/galaxyproject/planemo/pull/732
        .. _Pull Request 704: https://github.com/galaxyproject/planemo/pull/704
        .. _Pull Request 709: https://github.com/galaxyproject/planemo/pull/709
        .. _Pull Request 715: https://github.com/galaxyproject/planemo/pull/715
        .. _Pull Request 716: https://github.com/galaxyproject/planemo/pull/716
        .. _Pull Request 720: https://github.com/galaxyproject/planemo/pull/720
        .. _Pull Request 723: https://github.com/galaxyproject/planemo/pull/723
        .. _8a608e0: https://github.com/galaxyproject/planemo/commit/8a608e0
        .. _ecc1bc2: https://github.com/galaxyproject/planemo/commit/ecc1bc2
        .. _Pull Request 702: https://github.com/galaxyproject/planemo/pull/702
        .. _Pull Request 701: https://github.com/galaxyproject/planemo/pull/701
        .. _Pull Request 699: https://github.com/galaxyproject/planemo/pull/699
        .. _91b6fa0: https://github.com/galaxyproject/planemo/commit/91b6fa0
        .. _904d77a: https://github.com/galaxyproject/planemo/commit/904d77a
        .. _9636682: https://github.com/galaxyproject/planemo/commit/9636682
        .. _475104c: https://github.com/galaxyproject/planemo/commit/475104c
        .. _Pull Request 684: https://github.com/galaxyproject/planemo/pull/684
        .. _Pull Request 687: https://github.com/galaxyproject/planemo/pull/687
        .. _Pull Request 688: https://github.com/galaxyproject/planemo/pull/688
        .. _Pull Request 689: https://github.com/galaxyproject/planemo/pull/689
        .. _Pull Request 690: https://github.com/galaxyproject/planemo/pull/690
        .. _Issue 494: https://github.com/galaxyproject/planemo/issues/494
        .. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665
        .. _Pull Request 675: https://github.com/galaxyproject/planemo/pull/675
        .. _Pull Request 680: https://github.com/galaxyproject/planemo/pull/680
        .. _Pull Request 682: https://github.com/galaxyproject/planemo/pull/682
        .. _Pull Request 683: https://github.com/galaxyproject/planemo/pull/683
        .. _Pull Request 662: https://github.com/galaxyproject/planemo/pull/662
        .. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665
        .. _Pull Request 664: https://github.com/galaxyproject/planemo/pull/664
        .. _84c4a73: https://github.com/galaxyproject/planemo/commit/84c4a73
        .. _32f41c9: https://github.com/galaxyproject/planemo/commit/32f41c9
        .. _3129216: https://github.com/galaxyproject/planemo/commit/3129216
        .. _b4ae44d: https://github.com/galaxyproject/planemo/commit/b4ae44d
        .. _3c95b7b: https://github.com/galaxyproject/planemo/commit/3c95b7b
        .. _06bcf19: https://github.com/galaxyproject/planemo/commit/06bcf19
        .. _525de8f: https://github.com/galaxyproject/planemo/commit/525de8f
        .. _9867e56: https://github.com/galaxyproject/planemo/commit/9867e56
        .. _ce0dc4e: https://github.com/galaxyproject/planemo/commit/ce0dc4e
        .. _4c0f100: https://github.com/galaxyproject/planemo/commit/4c0f100
        .. _04238d3: https://github.com/galaxyproject/planemo/commit/04238d3
        .. _ced5ce2: https://github.com/galaxyproject/planemo/commit/ced5ce2
        .. _9ab4a0d: https://github.com/galaxyproject/planemo/commit/9ab4a0d
        .. _Pull Request 640: https://github.com/galaxyproject/planemo/pull/640
        .. _0a1abfe: https://github.com/galaxyproject/planemo/commit/0a1abfe
        .. _Pull Request 649: https://github.com/galaxyproject/planemo/pull/649
        .. _Issue 620: https://github.com/galaxyproject/planemo/issues/620
        .. _Pull Request 643: https://github.com/galaxyproject/planemo/pull/643
        .. _Pull Request 642: https://github.com/galaxyproject/planemo/pull/642
        .. _Pull Request 641: https://github.com/galaxyproject/planemo/pull/641
        .. _Pull Request 639: https://github.com/galaxyproject/planemo/pull/639
        .. _Pull Request 635: https://github.com/galaxyproject/planemo/pull/635
        .. _Issue 633: https://github.com/galaxyproject/planemo/issues/633
        .. _Issue 260: https://github.com/galaxyproject/planemo/issues/260
        .. _Pull Request 638: https://github.com/galaxyproject/planemo/pull/638
        .. _6638caa: https://github.com/galaxyproject/planemo/commit/6638caa
        .. _8faf661: https://github.com/galaxyproject/planemo/commit/8faf661
        .. _e343b67: https://github.com/galaxyproject/planemo/commit/e343b67
        .. _Pull Request 634: https://github.com/galaxyproject/planemo/pull/634
        .. _84ebc1f: https://github.com/galaxyproject/planemo/commit/84ebc1f
        .. _03c9658: https://github.com/galaxyproject/planemo/commit/03c9658
        .. _08c067c: https://github.com/galaxyproject/planemo/commit/08c067c
        .. _fca4183: https://github.com/galaxyproject/planemo/commit/fca4183
        .. _Issue 564: https://github.com/galaxyproject/planemo/issues/564
        .. _Pull Request 628: https://github.com/galaxyproject/planemo/pull/628
        .. _Issue 515: https://github.com/galaxyproject/planemo/issues/515
        .. _Pull Request 629: https://github.com/galaxyproject/planemo/pull/629
        .. _Pull Request 614: https://github.com/galaxyproject/planemo/pull/614
        .. _32acd68: https://github.com/galaxyproject/planemo/commit/32acd68
        .. _4595953: https://github.com/galaxyproject/planemo/commit/4595953
        .. _Pull Request 612: https://github.com/galaxyproject/planemo/pull/612
        .. _Issue 388: https://github.com/galaxyproject/planemo/issues/388
        .. _Pull Request 610: https://github.com/galaxyproject/planemo/pull/610
        .. _Pull Request 609: https://github.com/galaxyproject/planemo/pull/609
        .. _Pull Request 608: https://github.com/galaxyproject/planemo/pull/608
        .. _Pull Request 605: https://github.com/galaxyproject/planemo/pull/605
        .. _Pull Request 606: https://github.com/galaxyproject/planemo/pull/606
        .. _Pull Request 602: https://github.com/galaxyproject/planemo/pull/602
        .. _Pull Request 570: https://github.com/galaxyproject/planemo/pull/570
        .. _9228416: https://github.com/galaxyproject/planemo/commit/9228416
        .. _50d3c4a: https://github.com/galaxyproject/planemo/commit/50d3c4a
        .. _Issue 578: https://github.com/galaxyproject/planemo/issues/578
        .. _Pull Request 591: https://github.com/galaxyproject/planemo/pull/591
        .. _Pull Request 590: https://github.com/galaxyproject/planemo/pull/590
        .. _f0da66f: https://github.com/galaxyproject/planemo/commit/f0da66f
        .. _19b2ee9: https://github.com/galaxyproject/planemo/commit/19b2ee9
        .. _9da8387: https://github.com/galaxyproject/planemo/commit/9da8387
        .. _08cef54: https://github.com/galaxyproject/planemo/commit/08cef54
        .. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc
        .. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc
        .. _Issue 573: https://github.com/galaxyproject/planemo/issues/573
        .. _Pull Request 579: https://github.com/galaxyproject/planemo/pull/579
        .. _ccdd2d5: https://github.com/galaxyproject/planemo/commit/ccdd2d5
        .. _e925ba1: https://github.com/galaxyproject/planemo/commit/e925ba1
        .. _ea5324f: https://github.com/galaxyproject/planemo/commit/ea5324f
        .. _ca88b0c: https://github.com/galaxyproject/planemo/commit/ca88b0c
        .. _b6d8294: https://github.com/galaxyproject/planemo/commit/b6d8294
        .. _6a6f164: https://github.com/galaxyproject/planemo/commit/6a6f164
        .. _d6da3a8: https://github.com/galaxyproject/planemo/commit/d6da3a8
        .. _1ef05d2: https://github.com/galaxyproject/planemo/commit/1ef05d2
        .. _7cca2e4: https://github.com/galaxyproject/planemo/commit/7cca2e4
        .. _34538de: https://github.com/galaxyproject/planemo/commit/34538de
        .. _6f91719: https://github.com/galaxyproject/planemo/commit/6f91719
        .. _Pull Request 566: https://github.com/galaxyproject/planemo/pull/566
        .. _Pull Request 559: https://github.com/galaxyproject/planemo/pull/559
        .. _Pull Request 561: https://github.com/galaxyproject/planemo/pull/561
        .. _Pull Request 565: https://github.com/galaxyproject/planemo/pull/565
        .. _Pull Request 555: https://github.com/galaxyproject/planemo/pull/555
        .. _a8e797b: https://github.com/galaxyproject/planemo/commit/a8e797b
        .. _6c03de8: https://github.com/galaxyproject/planemo/commit/6c03de8
        .. _ef4b9f4: https://github.com/galaxyproject/planemo/commit/ef4b9f4
        .. _f7b6c7e: https://github.com/galaxyproject/planemo/commit/f7b6c7e
        .. _07d94bd: https://github.com/galaxyproject/planemo/commit/07d94bd
        .. _ca19910: https://github.com/galaxyproject/planemo/commit/ca19910
        .. _24008ab: https://github.com/galaxyproject/planemo/commit/24008ab
        .. _ce44e87: https://github.com/galaxyproject/planemo/commit/ce44e87
        .. _Pull Request 550: https://github.com/galaxyproject/planemo/pull/550
        .. _c2204b3: https://github.com/galaxyproject/planemo/commit/c2204b3
        .. _c262b6d: https://github.com/galaxyproject/planemo/commit/c262b6d
        .. _Pull Request 539: https://github.com/galaxyproject/planemo/pull/539
        .. _Pull Request 541: https://github.com/galaxyproject/planemo/pull/541
        .. _Pull Request 540: https://github.com/galaxyproject/planemo/pull/540
        .. _Pull Request 545: https://github.com/galaxyproject/planemo/pull/545
        .. _Pull Request 546: https://github.com/galaxyproject/planemo/pull/546
        .. _3ceaa40: https://github.com/galaxyproject/planemo/commit/3ceaa40
        .. _057f4f0: https://github.com/galaxyproject/planemo/commit/057f4f0
        .. _9fdf490: https://github.com/galaxyproject/planemo/commit/9fdf490
        .. _8c088c6: https://github.com/galaxyproject/planemo/commit/8c088c6
        .. _e2398fb: https://github.com/galaxyproject/planemo/commit/e2398fb
        .. _Pull Request 526: https://github.com/galaxyproject/planemo/pull/526
        .. _Pull Request 528: https://github.com/galaxyproject/planemo/pull/528
        .. _Pull Request 525: https://github.com/galaxyproject/planemo/pull/525
        .. _a811e65: https://github.com/galaxyproject/planemo/commit/a811e65
        .. _Pull Request 521: https://github.com/galaxyproject/planemo/pull/521
        .. _a066afb: https://github.com/galaxyproject/planemo/commit/a066afb
        .. _Pull Request 512: https://github.com/galaxyproject/planemo/pull/512
        .. _08bb354: https://github.com/galaxyproject/planemo/commit/08bb354
        .. _Pull Request 513: https://github.com/galaxyproject/planemo/pull/513
        .. _Pull Request 510: https://github.com/galaxyproject/planemo/pull/510
        .. _e890ab5: https://github.com/galaxyproject/planemo/commit/e890ab5
        .. _Pull Request 507: https://github.com/galaxyproject/planemo/pull/507
        .. _d53bcd6: https://github.com/galaxyproject/planemo/commit/d53bcd6
        .. _725b232: https://github.com/galaxyproject/planemo/commit/725b232
        .. _Pull Request 498: https://github.com/galaxyproject/planemo/pull/498
        .. _01584c5: https://github.com/galaxyproject/planemo/commit/01584c5
        .. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9
        .. _0298510: https://github.com/galaxyproject/planemo/commit/0298510
        .. _02a08a0: https://github.com/galaxyproject/planemo/commit/02a08a0
        .. _05cc9f4: https://github.com/galaxyproject/planemo/commit/05cc9f485ee87bc344e3f43bb1cfd025a16a6247
        .. _069e7ba: https://github.com/galaxyproject/planemo/commit/069e7ba
        .. _08de8de: https://github.com/galaxyproject/planemo/commit/08de8de
        .. _0bd4ff0: https://github.com/galaxyproject/planemo/commit/0bd4ff0
        .. _0e4f70a: https://github.com/galaxyproject/planemo/commit/0e4f70a
        .. _0f8cb10: https://github.com/galaxyproject/planemo/commit/0f8cb10
        .. _13a5ae7: https://github.com/galaxyproject/planemo/commit/13a5ae7
        .. _15804be: https://github.com/galaxyproject/planemo/commit/15804be
        .. _15d33c7: https://github.com/galaxyproject/planemo/commit/15d33c7
        .. _182fe57: https://github.com/galaxyproject/planemo/commit/182fe57
        .. _1927168: https://github.com/galaxyproject/planemo/commit/1927168
        .. _1982076: https://github.com/galaxyproject/planemo/commit/1982076
        .. _19900a6: https://github.com/galaxyproject/planemo/commit/19900a6
        .. _1a157d4: https://github.com/galaxyproject/planemo/commit/1a157d4
        .. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493
        .. _1c6cfbb: https://github.com/galaxyproject/planemo/commit/1c6cfbb
        .. _1c7ee5b: https://github.com/galaxyproject/planemo/commit/1c7ee5b
        .. _1cd0e2d: https://github.com/galaxyproject/planemo/commit/1cd0e2d
        .. _1e3668a: https://github.com/galaxyproject/planemo/commit/1e3668a
        .. _2052db0: https://github.com/galaxyproject/planemo/commit/2052db0
        .. _20a8680: https://github.com/galaxyproject/planemo/commit/20a86807cb7ea87db2dbc0197ae08a40df3ab2bc
        .. _21bb463: https://github.com/galaxyproject/planemo/commit/21bb463ad6c321bcb669603049a5e89a69766ad9
        .. _25ef0d5: https://github.com/galaxyproject/planemo/commit/25ef0d5
        .. _26e378e: https://github.com/galaxyproject/planemo/commit/26e378e
        .. _26e3cdb: https://github.com/galaxyproject/planemo/commit/26e3cdb
        .. _2a7c792: https://github.com/galaxyproject/planemo/commit/2a7c792
        .. _2ae2b49: https://github.com/galaxyproject/planemo/commit/2ae2b49
        .. _2e41e0a: https://github.com/galaxyproject/planemo/commit/2e41e0a
        .. _2f66fc3: https://github.com/galaxyproject/planemo/commit/2f66fc3
        .. _30a9c3f: https://github.com/galaxyproject/planemo/commit/30a9c3f
        .. _32c6e7f: https://github.com/galaxyproject/planemo/commit/32c6e7f78bb8f04d27615cfd8948b0b89f27b4e6
        .. _33294d2: https://github.com/galaxyproject/planemo/commit/33294d2
        .. _334f2d4: https://github.com/galaxyproject/planemo/commit/334f2d4
        .. _343902d: https://github.com/galaxyproject/planemo/commit/343902d
        .. _3499ca0: https://github.com/galaxyproject/planemo/commit/3499ca0a15affcaf8ac9efc55880da40b0626679
        .. _358a42c: https://github.com/galaxyproject/planemo/commit/358a42c
        .. _36ac6d8: https://github.com/galaxyproject/planemo/commit/36ac6d8
        .. _36f7cb1: https://github.com/galaxyproject/planemo/commit/36f7cb114f77731f90860d513a930e10ce5c1ba5
        .. _37dcc07: https://github.com/galaxyproject/planemo/commit/37dcc07
        .. _39fedd2: https://github.com/galaxyproject/planemo/commit/39fedd2
        .. _3f4ab44: https://github.com/galaxyproject/planemo/commit/3f4ab44
        .. _40a1f57: https://github.com/galaxyproject/planemo/commit/40a1f57
        .. _411a8da: https://github.com/galaxyproject/planemo/commit/411a8da21c92ba37c7ad95bfce9928d9b8fd998e
        .. _44de95c: https://github.com/galaxyproject/planemo/commit/44de95c0d7087a5822941959f9a062f6382e329b
        .. _45135ff: https://github.com/galaxyproject/planemo/commit/45135ff
        .. _4823c5e: https://github.com/galaxyproject/planemo/commit/4823c5e
        .. _49c5c1e: https://github.com/galaxyproject/planemo/commit/49c5c1e
        .. _4c71299: https://github.com/galaxyproject/planemo/commit/4c71299
        .. _4cd571c: https://github.com/galaxyproject/planemo/commit/4cd571c
        .. _4d29bf1: https://github.com/galaxyproject/planemo/commit/4d29bf1
        .. _4d6f7d9: https://github.com/galaxyproject/planemo/commit/4d6f7d9
        .. _4e1377c: https://github.com/galaxyproject/planemo/commit/4e1377c
        .. _4f61025: https://github.com/galaxyproject/planemo/commit/4f61025
        .. _508dce7: https://github.com/galaxyproject/planemo/commit/508dce7
        .. _53a6766: https://github.com/galaxyproject/planemo/commit/53a6766cdebdddc976189f6dc6a264bb4105c4bf
        .. _53edd99: https://github.com/galaxyproject/planemo/commit/53edd99
        .. _552059f: https://github.com/galaxyproject/planemo/commit/552059f
        .. _572e754: https://github.com/galaxyproject/planemo/commit/572e754
        .. _5b97f2e: https://github.com/galaxyproject/planemo/commit/5b97f2e
        .. _5d08b67: https://github.com/galaxyproject/planemo/commit/5d08b67
        .. _5d7db92: https://github.com/galaxyproject/planemo/commit/5d7db92
        .. _5e0b6d1: https://github.com/galaxyproject/planemo/commit/5e0b6d1
        .. _63cd431: https://github.com/galaxyproject/planemo/commit/63cd431
        .. _63e456c: https://github.com/galaxyproject/planemo/commit/63e456c
        .. _6409449: https://github.com/galaxyproject/planemo/commit/6409449
        .. _6514ff5: https://github.com/galaxyproject/planemo/commit/6514ff5
        .. _65b999d: https://github.com/galaxyproject/planemo/commit/65b999d21bacc133a80ecf5f61e0728afec66ccc
        .. _6b4e7a6: https://github.com/galaxyproject/planemo/commit/6b4e7a6
        .. _6bcf699: https://github.com/galaxyproject/planemo/commit/6bcf699
        .. _6d0f502: https://github.com/galaxyproject/planemo/commit/6d0f502
        .. _6d81a94: https://github.com/galaxyproject/planemo/commit/6d81a94
        .. _6e1e726: https://github.com/galaxyproject/planemo/commit/6e1e726
        .. _7572e99: https://github.com/galaxyproject/planemo/commit/7572e99
        .. _764ce01: https://github.com/galaxyproject/planemo/commit/764ce01
        .. _775bf49: https://github.com/galaxyproject/planemo/commit/775bf49
        .. _776773c: https://github.com/galaxyproject/planemo/commit/776773c
        .. _78f8274: https://github.com/galaxyproject/planemo/commit/78f82747996e4a28f96c85ad72efe5e54c8c74bd
        .. _7be1bf5: https://github.com/galaxyproject/planemo/commit/7be1bf5
        .. _7c69bf6: https://github.com/galaxyproject/planemo/commit/7c69bf6
        .. _7d07782: https://github.com/galaxyproject/planemo/commit/7d077828559c9c9c352ac814f9e3b86b1b3a2a9f
        .. _8117e03: https://github.com/galaxyproject/planemo/commit/8117e03
        .. _8207026: https://github.com/galaxyproject/planemo/commit/8207026
        .. _826d371: https://github.com/galaxyproject/planemo/commit/826d371
        .. _82e8b1f: https://github.com/galaxyproject/planemo/commit/82e8b1f17eae526aeb341cb4fffb8d09d73bb419
        .. _834bfb2: https://github.com/galaxyproject/planemo/commit/834bfb2929d367892a3abe9c0b88d5a0277d7905
        .. _83e227a: https://github.com/galaxyproject/planemo/commit/83e227a
        .. _85b9614: https://github.com/galaxyproject/planemo/commit/85b961465f46351507f80ddc3758349535060502
        .. _89674cb: https://github.com/galaxyproject/planemo/commit/89674cb
        .. _8b31850: https://github.com/galaxyproject/planemo/commit/8b31850
        .. _8e96864: https://github.com/galaxyproject/planemo/commit/8e96864
        .. _8eda729: https://github.com/galaxyproject/planemo/commit/8eda729
        .. _912df02: https://github.com/galaxyproject/planemo/commit/912df02
        .. _916f610: https://github.com/galaxyproject/planemo/commit/916f610
        .. _93b7bda: https://github.com/galaxyproject/planemo/commit/93b7bda
        .. _94097c7: https://github.com/galaxyproject/planemo/commit/94097c7
        .. _9427b47: https://github.com/galaxyproject/planemo/commit/9427b47
        .. _94645ed: https://github.com/galaxyproject/planemo/commit/94645ed
        .. _949a36d: https://github.com/galaxyproject/planemo/commit/949a36d
        .. _95d5cba: https://github.com/galaxyproject/planemo/commit/95d5cba
        .. _965511d: https://github.com/galaxyproject/planemo/commit/965511d
        .. _988de1d: https://github.com/galaxyproject/planemo/commit/988de1d
        .. _98fdc8c: https://github.com/galaxyproject/planemo/commit/98fdc8c
        .. _99ee51a: https://github.com/galaxyproject/planemo/commit/99ee51a
        .. _9bf1eab: https://github.com/galaxyproject/planemo/commit/9bf1eab
        .. _9e746b4: https://github.com/galaxyproject/planemo/commit/9e746b455e3b15219878cddcdeda722979639401
        .. _9f3957d: https://github.com/galaxyproject/planemo/commit/9f3957d
        .. _9ff0d2d: https://github.com/galaxyproject/planemo/commit/9ff0d2d
        .. _CWL: http://www.commonwl.org/
        .. _Issue 108: https://github.com/galaxyproject/planemo/issues/108
        .. _Issue 114: https://github.com/galaxyproject/planemo/issues/114
        .. _Issue 118: https://github.com/galaxyproject/planemo/issues/118
        .. _Issue 124: https://github.com/galaxyproject/planemo/issues/#124
        .. _Issue 138: https://github.com/galaxyproject/planemo/issues/#138
        .. _Issue 139: https://github.com/galaxyproject/planemo/issues/139
        .. _Issue 150: https://github.com/galaxyproject/planemo/issues/150
        .. _Issue 156: https://github.com/galaxyproject/planemo/issues/156
        .. _Issue 158: https://github.com/galaxyproject/planemo/issues/158
        .. _Issue 159: https://github.com/galaxyproject/planemo/issues/159
        .. _Issue 15: https://github.com/galaxyproject/planemo/issues/15
        .. _Issue 161: https://github.com/galaxyproject/planemo/issues/161
        .. _Issue 167: https://github.com/galaxyproject/planemo/issues/167
        .. _Issue 168: https://github.com/galaxyproject/planemo/issues/168
        .. _Issue 169: https://github.com/galaxyproject/planemo/issues/169
        .. _Issue 170: https://github.com/galaxyproject/planemo/issues/170
        .. _Issue 176: https://github.com/galaxyproject/planemo/issues/176
        .. _Issue 179: https://github.com/galaxyproject/planemo/issues/179
        .. _Issue 180: https://github.com/galaxyproject/planemo/issues/180
        .. _Issue 181: https://github.com/galaxyproject/planemo/issues/181
        .. _Issue 184: https://github.com/galaxyproject/planemo/issues/184
        .. _Issue 186: https://github.com/galaxyproject/planemo/issues/186
        .. _Issue 188: https://github.com/galaxyproject/planemo/issues/188
        .. _Issue 189: https://github.com/galaxyproject/planemo/issues/189
        .. _Issue 192: https://github.com/galaxyproject/planemo/issues/192
        .. _Issue 205: https://github.com/galaxyproject/planemo/issues/205
        .. _Issue 206: https://github.com/galaxyproject/planemo/issues/206
        .. _Issue 209: https://github.com/galaxyproject/planemo/issues/209
        .. _Issue 211: https://github.com/galaxyproject/planemo/issues/211
        .. _Issue 217: https://github.com/galaxyproject/planemo/issues/217
        .. _Issue 223: https://github.com/galaxyproject/planemo/issues/223
        .. _Issue 231: https://github.com/galaxyproject/planemo/issues/231
        .. _Issue 233: https://github.com/galaxyproject/planemo/issues/233
        .. _Issue 240: https://github.com/galaxyproject/planemo/issues/240
        .. _Issue 243: https://github.com/galaxyproject/planemo/issues/243
        .. _Issue 245: https://github.com/galaxyproject/planemo/issues/245
        .. _Issue 246: https://github.com/galaxyproject/planemo/issues/246
        .. _Issue 272: https://github.com/galaxyproject/planemo/issues/272
        .. _Issue 303: https://github.com/galaxyproject/planemo/issues/303
        .. _Issue 313: https://github.com/galaxyproject/planemo/issues/313
        .. _Issue 329: https://github.com/galaxyproject/planemo/issues/329
        .. _Issue 333: https://github.com/galaxyproject/planemo/issues/333
        .. _Issue 361: https://github.com/galaxyproject/planemo/issues/361
        .. _Issue 362: https://github.com/galaxyproject/planemo/issues/362
        .. _Issue 373: https://github.com/galaxyproject/planemo/issues/373
        .. _Issue 391: https://github.com/galaxyproject/planemo/issues/391
        .. _Issue 416: https://github.com/galaxyproject/planemo/issues/416
        .. _Issue 420: https://github.com/galaxyproject/planemo/issues/420
        .. _Issue 475: https://github.com/galaxyproject/planemo/issues/475
        .. _Issue 61: https://github.com/galaxyproject/planemo/issues/61
        .. _Issue 70: https://github.com/galaxyproject/planemo/issues/70
        .. _Issue 78: https://github.com/galaxyproject/planemo/issues/78
        .. _Issue 80: https://github.com/galaxyproject/planemo/issues/80
        .. _Issue 83: https://github.com/galaxyproject/planemo/issues/83
        .. _Issue 88: https://github.com/galaxyproject/planemo/issues/88
        .. _Issue 89: https://github.com/galaxyproject/planemo/issues/#89
        .. _Issue 91: https://github.com/galaxyproject/planemo/issues/#91
        .. _Pull Request 101: https://github.com/galaxyproject/planemo/pull/101
        .. _Pull Request 102: https://github.com/galaxyproject/planemo/pull/102
        .. _Pull Request 104: https://github.com/galaxyproject/planemo/pull/104
        .. _Pull Request 111: https://github.com/galaxyproject/planemo/pull/111
        .. _Pull Request 113: https://github.com/galaxyproject/planemo/pull/113
        .. _Pull Request 129: https://github.com/galaxyproject/planemo/pull/129
        .. _Pull Request 130: https://github.com/galaxyproject/planemo/pull/130
        .. _Pull Request 143: https://github.com/galaxyproject/planemo/pull/143
        .. _Pull Request 151: https://github.com/galaxyproject/planemo/pull/151
        .. _Pull Request 155: https://github.com/galaxyproject/planemo/pull/155
        .. _Pull Request 164: https://github.com/galaxyproject/planemo/pull/164
        .. _Pull Request 171: https://github.com/galaxyproject/planemo/pull/171
        .. _Pull Request 173: https://github.com/galaxyproject/planemo/pull/173
        .. _Pull Request 175: https://github.com/galaxyproject/planemo/pull/175
        .. _Pull Request 185: https://github.com/galaxyproject/planemo/pull/185
        .. _Pull Request 186: https://github.com/galaxyproject/planemo/pull/186
        .. _Pull Request 187: https://github.com/galaxyproject/planemo/pull/187
        .. _Pull Request 190: https://github.com/galaxyproject/planemo/pull/190
        .. _Pull Request 196: https://github.com/galaxyproject/planemo/pull/196
        .. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1
        .. _Pull Request 200: https://github.com/galaxyproject/planemo/pull/200
        .. _Pull Request 203: https://github.com/galaxyproject/planemo/pull/203
        .. _Pull Request 206: https://github.com/galaxyproject/planemo/pull/206
        .. _Pull Request 207: https://github.com/galaxyproject/planemo/pull/207
        .. _Pull Request 208: https://github.com/galaxyproject/planemo/pull/208
        .. _Pull Request 210: https://github.com/galaxyproject/planemo/pull/210
        .. _Pull Request 213: https://github.com/galaxyproject/planemo/pull/213
        .. _Pull Request 215: https://github.com/galaxyproject/planemo/pull/215
        .. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216
        .. _Pull Request 22: https://github.com/galaxyproject/planemo/pull/22
        .. _Pull Request 230: https://github.com/galaxyproject/planemo/pull/230
        .. _Pull Request 235: https://github.com/galaxyproject/planemo/pull/235
        .. _Pull Request 23: https://github.com/galaxyproject/planemo/pull/23
        .. _Pull Request 251: https://github.com/galaxyproject/planemo/pull/251
        .. _Pull Request 253: https://github.com/galaxyproject/planemo/pull/253
        .. _Pull Request 254: https://github.com/galaxyproject/planemo/pull/254
        .. _Pull Request 255: https://github.com/galaxyproject/planemo/pull/255
        .. _Pull Request 256: https://github.com/galaxyproject/planemo/pull/256
        .. _Pull Request 277: https://github.com/galaxyproject/planemo/pull/277
        .. _Pull Request 278: https://github.com/galaxyproject/planemo/pull/278
        .. _Pull Request 284: https://github.com/galaxyproject/planemo/pull/284
        .. _Pull Request 285: https://github.com/galaxyproject/planemo/pull/285
        .. _Pull Request 287: https://github.com/galaxyproject/planemo/pull/287
        .. _Pull Request 292: https://github.com/galaxyproject/planemo/pull/292
        .. _Pull Request 297: https://github.com/galaxyproject/planemo/pull/297
        .. _Pull Request 29: https://github.com/galaxyproject/planemo/pull/29
        .. _Pull Request 301: https://github.com/galaxyproject/planemo/pull/301
        .. _Pull Request 304: https://github.com/galaxyproject/planemo/pull/304
        .. _Pull Request 305: https://github.com/galaxyproject/planemo/pull/305
        .. _Pull Request 307: https://github.com/galaxyproject/planemo/pull/307
        .. _Pull Request 309: https://github.com/galaxyproject/planemo/pull/309
        .. _Pull Request 310: https://github.com/galaxyproject/planemo/pull/310
        .. _Pull Request 311: https://github.com/galaxyproject/planemo/pull/311
        .. _Pull Request 312: https://github.com/galaxyproject/planemo/pull/312
        .. _Pull Request 314: https://github.com/galaxyproject/planemo/pull/314
        .. _Pull Request 316: https://github.com/galaxyproject/planemo/pull/316
        .. _Pull Request 322: https://github.com/galaxyproject/planemo/pull/322
        .. _Pull Request 327: https://github.com/galaxyproject/planemo/pull/327
        .. _Pull Request 330: https://github.com/galaxyproject/planemo/pull/330
        .. _Pull Request 333: https://github.com/galaxyproject/planemo/pull/333
        .. _Pull Request 334: https://github.com/galaxyproject/planemo/pull/334
        .. _Pull Request 335: https://github.com/galaxyproject/planemo/pull/335
        .. _Pull Request 339: https://github.com/galaxyproject/planemo/pull/339
        .. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33
        .. _Pull Request 343: https://github.com/galaxyproject/planemo/pull/343
        .. _Pull Request 344: https://github.com/galaxyproject/planemo/pull/344
        .. _Pull Request 345: https://github.com/galaxyproject/planemo/pull/345
        .. _Pull Request 350: https://github.com/galaxyproject/planemo/pull/350
        .. _Pull Request 351: https://github.com/galaxyproject/planemo/pull/351
        .. _Pull Request 356: https://github.com/galaxyproject/planemo/pull/356
        .. _Pull Request 375: https://github.com/galaxyproject/planemo/pull/375
        .. _Pull Request 390: https://github.com/galaxyproject/planemo/pull/390
        .. _Pull Request 394: https://github.com/galaxyproject/planemo/pull/394
        .. _Pull Request 398: https://github.com/galaxyproject/planemo/pull/398
        .. _Pull Request 403: https://github.com/galaxyproject/planemo/pull/403
        .. _Pull Request 40: https://github.com/galaxyproject/planemo/pull/40
        .. _Pull Request 425: https://github.com/galaxyproject/planemo/pull/425
        .. _Pull Request 426: https://github.com/galaxyproject/planemo/pull/426
        .. _Pull Request 428: https://github.com/galaxyproject/planemo/pull/428
        .. _Pull Request 429: https://github.com/galaxyproject/planemo/pull/429
        .. _Pull Request 454: https://github.com/galaxyproject/planemo/pull/454
        .. _Pull Request 472: https://github.com/galaxyproject/planemo/pull/472
        .. _Pull Request 479: https://github.com/galaxyproject/planemo/pull/479
        .. _Pull Request 480: https://github.com/galaxyproject/planemo/pull/480
        .. _Pull Request 484: https://github.com/galaxyproject/planemo/pull/484
        .. _Pull Request 488: https://github.com/galaxyproject/planemo/pull/488
        .. _Pull Request 491: https://github.com/galaxyproject/planemo/pull/491
        .. _Pull Request 51: https://github.com/galaxyproject/planemo/pull/51
        .. _Pull Request 56: https://github.com/galaxyproject/planemo/pull/56
        .. _Pull Request 63: https://github.com/galaxyproject/planemo/pull/63
        .. _Pull Request 68: https://github.com/galaxyproject/planemo/pull/68
        .. _Pull Request 6: https://github.com/galaxyproject/planemo/pull/6
        .. _Pull Request 98: https://github.com/galaxyproject/planemo/pull/98
        .. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99
        .. _XSD: http://www.w3schools.com/schema/
        .. _a13a120: https://github.com/galaxyproject/planemo/commit/a13a120
        .. _a2c13e4: https://github.com/galaxyproject/planemo/commit/a2c13e46259e3be35de1ecaae858ba818bb94734
        .. _a2ee135: https://github.com/galaxyproject/planemo/commit/a2ee135
        .. _a4110a8: https://github.com/galaxyproject/planemo/commit/a4110a85a770988e5cd3c31ccc9475717897d59c
        .. _a4e6958: https://github.com/galaxyproject/planemo/commit/a4e6958
        .. _a58a3b8: https://github.com/galaxyproject/planemo/commit/a58a3b8
        .. _a87899b: https://github.com/galaxyproject/planemo/commit/a87899b
        .. _aad1eed: https://github.com/galaxyproject/planemo/commit/aad1eed
        .. _ac4f828: https://github.com/galaxyproject/planemo/commit/ac4f82898f7006799142503a33c3978428660ce7
        .. _ad3b2f0: https://github.com/galaxyproject/planemo/commit/ad3b2f0
        .. _af39061: https://github.com/galaxyproject/planemo/commit/af390612004dab636d8696839bb723d39f97c85d
        .. _af7448c: https://github.com/galaxyproject/planemo/commit/af7448c
        .. _b0b867e: https://github.com/galaxyproject/planemo/commit/b0b867e
        .. _b1c8f1d: https://github.com/galaxyproject/planemo/commit/b1c8f1d
        .. _b53006d: https://github.com/galaxyproject/planemo/commit/b53006d
        .. _b757791: https://github.com/galaxyproject/planemo/commit/b757791
        .. _b7d9e96: https://github.com/galaxyproject/planemo/commit/b7d9e96
        .. _b86fe1f: https://github.com/galaxyproject/planemo/commit/b86fe1f
        .. _b8d90ab: https://github.com/galaxyproject/planemo/commit/b8d90abab8bf53ae2e7cca4317223c01af9ab68c
        .. _b9232e5: https://github.com/galaxyproject/planemo/commit/b9232e55e713abbd1d9ce8b0b34cbec6c701dc17
        .. _badc25f: https://github.com/galaxyproject/planemo/commit/badc25fca495b61457ffb2e027f3fe9cf17c798f
        .. _bioblend: https://github.com/galaxyproject/bioblend/
        .. _c1713d2: https://github.com/galaxyproject/planemo/commit/c1713d2
        .. _c23569f: https://github.com/galaxyproject/planemo/commit/c23569f
        .. _c444855: https://github.com/galaxyproject/planemo/commit/c444855
        .. _c4dfd55: https://github.com/galaxyproject/planemo/commit/c4dfd55
        .. _c8640b6: https://github.com/galaxyproject/planemo/commit/c8640b6
        .. _cb5b906: https://github.com/galaxyproject/planemo/commit/cb5b906
        .. _cc1a447: https://github.com/galaxyproject/planemo/commit/cc1a447
        .. _cc8abb6: https://github.com/galaxyproject/planemo/commit/cc8abb6
        .. _ce8e1be: https://github.com/galaxyproject/planemo/commit/ce8e1be
        .. _cwltool: https://github.com/common-workflow-language/cwltool/.. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e
        .. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e
        .. _d755fe7: https://github.com/galaxyproject/planemo/commit/d755fe7
        .. _d76b489: https://github.com/galaxyproject/planemo/commit/d76b489
        .. _d8f2038: https://github.com/galaxyproject/planemo/commit/d8f2038
        .. _dad2d9d: https://github.com/galaxyproject/planemo/commit/dad2d9d
        .. _dd94ddc: https://github.com/galaxyproject/planemo/commit/dd94ddc
        .. _dff4f33: https://github.com/galaxyproject/planemo/commit/dff4f33c750a8dbe651c38e149a26dd42e706a82
        .. _e0577e7: https://github.com/galaxyproject/planemo/commit/e0577e7
        .. _e0acf91: https://github.com/galaxyproject/planemo/commit/e0acf91
        .. _e38c436: https://github.com/galaxyproject/planemo/commit/e38c436
        .. _e769118: https://github.com/galaxyproject/planemo/commit/e769118
        .. _e8c1d45: https://github.com/galaxyproject/planemo/commit/e8c1d45f0c9a11bcf69ec2967836c3b8f432dd97
        .. _eb039c0: https://github.com/galaxyproject/planemo/commit/eb039c0
        .. _ec6e30f: https://github.com/galaxyproject/planemo/commit/ec6e30f
        .. _efc5f30: https://github.com/galaxyproject/planemo/commit/efc5f30
        .. _f0610d7: https://github.com/galaxyproject/planemo/commit/f0610d7
        .. _f3394e7: https://github.com/galaxyproject/planemo/commit/f3394e7
        .. _f3c6917: https://github.com/galaxyproject/planemo/commit/f3c6917
        .. _f3cafaa: https://github.com/galaxyproject/planemo/commit/f3cafaa
        .. _f7554d1: https://github.com/galaxyproject/planemo/commit/f7554d1
        .. _f798c7e: https://github.com/galaxyproject/planemo/commit/f798c7e
        .. _f854138: https://github.com/galaxyproject/planemo/commit/f854138
        .. _f99f6c1: https://github.com/galaxyproject/planemo/commit/f99f6c1
        .. _fba3874: https://github.com/galaxyproject/planemo/commit/fba3874
        .. _fdb1b51: https://github.com/galaxyproject/planemo/commit/fdb1b51
        .. _fdce74c: https://github.com/galaxyproject/planemo/commit/fdce74c
        .. _fe7ad46: https://github.com/galaxyproject/planemo/commit/fe7ad46
        .. _fea51fc: https://github.com/galaxyproject/planemo/commit/fea51fc
        .. _lxml: http://lxml.de/
        .. _nose: https://nose.readthedocs.org/en/latest/
        .. _xmllint: http://xmlsoft.org/xmllint.html
        .. _Conda: http://conda.pydata.org/
        .. _Tool Factory: http://bioinformatics.oxfordjournals.org/content/early/2012/09/27/bioinformatics.bts573.full.pdf
        .. _git: https://git-scm.com/
        .. _anaconda-verify: https://github.com/ContinuumIO/anaconda-verify
        .. _galaxy.xsd: https://github.com/galaxyproject/planemo/blob/master/planemo/xml/xsd/tool/galaxy.xsd
        .. _setup.py: https://github.com/galaxyproject/planemo/blob/master/setup.py
        .. _Bioconductor: https://www.bioconductor.org/
        .. _tools-iuc: https://github.com/galaxyproject/tools-iuc
        .. _PyPI: https://pypi.python.org/pypi
        .. _Involucro: https://github.com/involucro/involucro
        .. _Bioconda: https://bioconda.github.io/
        .. _pip: https://pip.pypa.io/en/stable/
        .. _BioContainers: http://biocontainers.pro/
        .. _Toil: https://github.com/BD2KGenomics/toil
        .. _quay.io: https://quay.io/
        .. _galaxy-lib: https://github.com/galaxyproject/galaxy-lib
        .. _@abretaud: https://github.com/abretaud
        .. _@erasche: https://github.com/erasche
        .. _@peterjc: https://github.com/peterjc
        .. _@mr-c: https://github.com/mr-c
        .. _@martenson: https://github.com/martenson
        .. _@nsoranzo: https://github.com/nsoranzo
        .. _@nturaga: https://github.com/nturaga
        .. _@bgruening: https://github.com/bgruening
        .. _@carlfeberhard: https://github.com/carlfeberhard
        .. _@lparsons: https://github.com/lparsons
        .. _@kellrott: https://github.com/kellrott
        .. _@mvdbeek: https://github.com/mvdbeek
        .. _@natefoo: https://github.com/natefoo
        .. _@pstew: https://github.com/pstew
        .. _@ramezrawas: https://github.com/ramezrawas
        .. _@chambm: https://github.com/chambm
        .. _@takadonet: https://github.com/takadonet
        .. _@petrkadlec: https://github.com/petrkadlec
        .. _@pvanheus: https://github.com/pvanheus
        .. _@einon: https://github.com/einon
        .. _@blankenberg: https://github.com/blankenberg
        .. _@JeanFred: https://github.com/JeanFred
        .. _@gregvonkuster: https://github.com/gregvonkuster
        .. _@remimarenco: https://github.com/remimarenco
        .. _@thriqon: https://github.com/thriqon
        .. _@RJMW: https://github.com/RJMW
        .. _@manabuishii: https://github.com/manabuishii
        .. _@dfornika: https://github.com/dfornika
        .. _@bernt-matthias: https://github.com/bernt-matthias
        .. _@katrinleinweber: https://github.com/katrinleinweber
        .. _@bebatut: https://github.com/bebatut
        
Keywords: planemo
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: Academic Free License (AFL)
Classifier: Operating System :: POSIX
Classifier: Topic :: Software Development
Classifier: Topic :: Software Development :: Code Generators
Classifier: Topic :: Software Development :: Testing
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
