Metadata-Version: 1.1
Name: planemo
Version: 0.8.4
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: ===============================
        Planemo
        ===============================
        
        .. image:: https://readthedocs.org/projects/pip/badge/?version=latest
           :target: https://planemo.readthedocs.org
        
        .. image:: https://badge.fury.io/py/planemo.svg
           :target: https://pypi.python.org/pypi/planemo/
        
        .. image:: https://travis-ci.org/galaxyproject/planemo.png?branch=master
           :target: https://travis-ci.org/galaxyproject/planemo
        
        .. image:: https://coveralls.io/repos/galaxyproject/planemo/badge.svg?branch=master
           :target: https://coveralls.io/r/galaxyproject/planemo?branch=master
        
        
        Command-line utilities to assist in building tools for the Galaxy_ project.
        
        * Free software: Academic Free License version 3.0
        * Documentation: https://planemo.readthedocs.org.
        * Code: https://github.com/galaxyproject/planemo
        
        Quick Start
        -----------
        
        This quick start demonstrates using ``planemo`` commands to help
        develop Galaxy tools. Planemo can quickly be installed via
        Homebrew_ or as a more traditional Python project.
        
        To install using Homebrew_ or linuxbrew_:
        
        ::
        
           brew tap galaxyproject/tap
           brew install planemo
        
        For a more traditional Python installation simply setup a virtualenv
        for ``planemo`` (this example creates a new one in ``.venv``) and then
        install with ``pip``.
        
        ::
        
           % virtualenv .venv; . .venv/bin/activate
           % pip install planemo
        
        Planemo is also available a `virtual appliance
        <https://planemo.readthedocs.org/en/latest/appliance.html>`_ for Docker_ or Vagrant_ (bundled
        with a preconfigured Galaxy server optimized for tool development).
        
        This quick start will assume you will have a directory with one or more
        tool XML files. If none is available, one can be quickly create for
        demonstrating ``planemo`` as follows ``mkdir mytools; cd mytools; planemo
        project_init --template=demo``.
        
        Planemo can check tools containing XML 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 other tool files or a directory of tool files. ::
        
            % planemo l randomlines.xml
        
        The ``lint`` command takes in a additional options related to 
        reporting levels, exit code, etc.... These options are descirbed here
        or (like all available commands) be accessed by passing it ``--help``.::
        
            % planemo l --help
            Usage: planemo lint [OPTIONS] TOOL_PATH
            ...
        
        Once tools are syntically 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 directory of tools.::
        
        	% planemo test --galaxy_root=../galaxy-central randomlines.xml
        
        If no ``--galaxy_root`` is defined, ``planemo`` will check for a default in
        `~/.planemo.yml
        <http://planemo.readthedocs.org/en/latest/configuration.html>`_) and finally
        search the tool's parent directories for a Galaxy root directory (developing
        tools under Galaxy ``tools`` directory is a common development workflow).
        Planemo can also download and configure a disposable Galaxy instance just for
        testing by passing it ``-install_galaxy`` instead of a Galaxy root.::
        
        	% planemo t --install_galaxy
        
        **Warning**: The features of Planemo that require a ``--galaxy_root`` will
        only work with Galaxy releases from 2015.
        
        Planemo will create a HTML an output report in the current directory named
        ``tool_test_output.html`` (override with ``--test_output``). `Here <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_ is an
        example 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``.
        
        
        Experimental Features
        ---------------------
        
        Planemo can also be used to explore some more experimental features related to
        Galaxy tooling - including support for `Travis CI`_, Docker_, Homebrew_.
        
        -----------
        Tool Shed
        -----------
        
        For information on using Planemo to publish artifacts to the Galaxy Tool Shed,
        check out the `Publishing to the Tool Shed`_ documentation on reathedocs.org.
        
        -----------
        TravisCI
        -----------
        
        When tools are ready to be published to GitHub_, it may be valuable to setup
        contineous integration to test changes committed and new pull requests.
        `Travis CI`_ is a service providing free testing and deep integration with
        GitHub_.
        
        The ``travis_init`` `command
        <http://planemo.readthedocs.org/en/latest/commands.html#travis_init-
        command>`__ will bootstrap a project with files to ease contineous integration
        testing of tools using a Planemo driven approach inspired by this great `blog
        post <http://bit.ly/gxtravisci>`_ by `Peter Cock
        <https://github.com/peterjc>`_.
        
        ::
        
            % planemo travis_init .
            % # setup Ubuntu 12.04 w/tool dependencies
            % vim .travis/setup_custom_dependencies.bash
            % git add .travis.yml .travis
            % git commit -m "Add Travis CI testing infrastructure for tools."
            % git push # and register repository @ http://travis-ci.org/
        
        In this example the file ``.travis/setup_custom_dependencies.bash`` should
        install the dependencies required to test your files on to the Travis user's
        ``PATH``.
        
        This testing approach may only make sense for smaller repositories with a
        handful of tools. For larger repositories, such as `tools-devteam`_ or
        `tools-iuc`_ simply linting tool and tool shed artifacts may be more feasible.
        Check out the ``.travis.yml`` file used by the IUC as `example
        <https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml>`__.
        
        -----------
        Docker
        -----------
        
        Galaxy has `experimental support
        <https://wiki.galaxyproject.org/Admin/Tools/Docker>`_ for running jobs in
        Docker_ containers. Planemo contains tools to assist in development of Docker
        images for Galaxy tools.
        
        A shell can be launched to explore the Docker enviornment referenced by tools 
        that are annotated with publically registered Docker images.::
        
            % $(planemo docker_shell bowtie2.xml)
        
        For Docker containers still in development - a Dockerfile can be associated
        with a tool by sticking it in the tool's directory. Planemo can then build
        and tag a Docker image for this tool and launch a shell into it using the
        following commands.::
        
            % planemo docker_build bowtie2.xml # asssumes Dockerfile in same dir
            % $(planemo docker_shell --from_tag bowtie2.xml)
        
        For more details see the documentation for the `docker_build
        <http://planemo.readthedocs.org/en/latest/commands.html#docker_build-command>`__
        and `docker_shell
        <http://planemo.readthedocs.org/en/latest/commands.html#docker_shell-command>`__
        commands.
        
        -----------
        Brew
        -----------
        
        The Galaxy development team is exploring different options for integrating
        Homebrew_ and linuxbrew_ with Galaxy. One angle is resolving the tool requirements
        using ``brew``. An experimental approach for versioning of brew recipes will be
        used. See full discussion on the homebrew-science issues page here -
        https://github.com/Homebrew/homebrew-science/issues/1191. Information on the
        implementation can be found https://github.com/jmchilton/platform-brew until a
        more permanent project home is setup.
        
        ::
        
            % planemo brew_init # install linuxbrew (only need if not already installed)
            % planemo brew # install dependencies for all tools in directory.
            % planemo brew bowtie2.xml # install dependencies for one tool
            % which bowtie2
            bowtie2 not found
            % . <(planemo brew_env --shell bowtie2.xml) # shell w/brew deps resolved
            (bowtie2) % which bowtie2
            /home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2
            (bowtie2) % exit
            % . <(planemo brew_env bowtie2.xml) # or just source deps in cur env
            % which bowtie2
            /home/john/.linuxbrew/Cellar/bowtie2/2.1.0/bin/bowtie2
        
        For more information see the documentation for the `brew
        <http://planemo.readthedocs.org/en/latest/commands.html#brew-command>`__
        and `brew_env
        <http://planemo.readthedocs.org/en/latest/commands.html#brew_env-command>`__ commands.
        
        .. _Galaxy: (http://galaxyproject.org/)
        .. _GitHub: https://github.com/
        .. _Docker: https://www.docker.com/
        .. _Homebrew: http://brew.sh/
        .. _linuxbrew: https://github.com/Homebrew/linuxbrew
        .. _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
        .. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html
        
        
        
        
        History
        -------
        
        .. to_doc
        
        ---------------------
        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 Eric Rasche). `Pull Request 101`_
        * Allow automatic creation of missing repositories  during ``shed_upload``
          with the new ``--force_repository_creation`` flag (thanks to Eric 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
          <http://bioinformatics.oxfordjournals.org/content/early/2012/09/27/bioinformatics.bts573.full.pdf>`_. 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 Eric Rasche). `Pull Request 68`_
        * Fix diff formatting in test reports (thanks to Eric Rasche).
          `Pull Request 63`_
        * Grab updated test database to speed up testing (thanks to approach from
          Eric 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). 36f7cb11_, b9232e55_
        * 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
        .. _b86fe1f: https://github.com/galaxyproject/planemo/commit/b86fe1f
        .. _Pull Request 155: https://github.com/galaxyproject/planemo/pull/155
        .. _Pull Request 164: https://github.com/galaxyproject/planemo/pull/164
        .. _Issue 159: https://github.com/galaxyproject/planemo/issues/159
        .. _Issue 161: https://github.com/galaxyproject/planemo/issues/161
        .. _a2ee135: https://github.com/galaxyproject/planemo/commit/a2ee135
        .. _9ff0d2d: https://github.com/galaxyproject/planemo/commit/9ff0d2d
        .. _Pull Request 151: https://github.com/galaxyproject/planemo/pull/151
        .. _9bf1eab: https://github.com/galaxyproject/planemo/commit/9bf1eab
        .. _Pull Request 143: https://github.com/galaxyproject/planemo/pull/143
        .. _Issue 139: https://github.com/galaxyproject/planemo/issues/139
        .. _Issue 89: https://github.com/galaxyproject/planemo/issues/#89
        .. _Issue 91: https://github.com/galaxyproject/planemo/issues/#91
        .. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e
        .. _36ac6d8: https://github.com/galaxyproject/planemo/commit/36ac6d8
        .. _08de8de: https://github.com/galaxyproject/planemo/commit/08de8de
        .. _4f61025: https://github.com/galaxyproject/planemo/commit/4f61025
        .. _1982076: https://github.com/galaxyproject/planemo/commit/1982076
        .. _Pull Request 129: https://github.com/galaxyproject/planemo/pull/129
        .. _912df02: https://github.com/galaxyproject/planemo/commit/912df02
        .. _Pull Request 130: https://github.com/galaxyproject/planemo/pull/130
        .. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493
        .. _53edd99: https://github.com/galaxyproject/planemo/commit/53edd99
        .. _988de1d: https://github.com/galaxyproject/planemo/commit/988de1d
        .. _Issue 118: https://github.com/galaxyproject/planemo/issues/118
        .. _cc1a447: https://github.com/galaxyproject/planemo/commit/cc1a447
        .. _b7d9e96: https://github.com/galaxyproject/planemo/commit/b7d9e96
        .. _Issue 138: https://github.com/galaxyproject/planemo/issues/#138
        .. _Issue 124: https://github.com/galaxyproject/planemo/issues/#124
        .. _26e3cdb: https://github.com/galaxyproject/planemo/commit/26e3cdb
        .. _63cd431: https://github.com/galaxyproject/planemo/commit/63cd431
        .. _965511d: https://github.com/galaxyproject/planemo/commit/965511d
        .. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9
        .. _343902d: https://github.com/galaxyproject/planemo/commit/343902d
        .. _33294d2: https://github.com/galaxyproject/planemo/commit/33294d2
        .. _4c71299: https://github.com/galaxyproject/planemo/commit/4c71299
        .. _Pull Request 111: https://github.com/galaxyproject/planemo/pull/111
        .. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99
        .. _Pull Request 101: https://github.com/galaxyproject/planemo/pull/101
        .. _Pull Request 102: https://github.com/galaxyproject/planemo/pull/102
        .. _Issue 88: https://github.com/galaxyproject/planemo/issues/88
        .. _182fe57: https://github.com/galaxyproject/planemo/commit/182fe57
        .. _Pull Request 104: https://github.com/galaxyproject/planemo/pull/104
        .. _7c69bf6: https://github.com/galaxyproject/planemo/commit/7c69bf6
        .. _39fedd2: https://github.com/galaxyproject/planemo/commit/39fedd2
        .. _d755fe7: https://github.com/galaxyproject/planemo/commit/d755fe7
        .. _Pull Request 113: https://github.com/galaxyproject/planemo/pull/113
        .. _Pull Request 98: https://github.com/galaxyproject/planemo/pull/98
        .. _0bd4ff0: https://github.com/galaxyproject/planemo/commit/0bd4ff0
        .. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99
        .. _ec6e30f: https://github.com/galaxyproject/planemo/commit/ec6e30f
        .. _8207026: https://github.com/galaxyproject/planemo/commit/8207026
        .. _4823c5e: https://github.com/galaxyproject/planemo/commit/4823c5e
        .. _2e41e0a: https://github.com/galaxyproject/planemo/commit/2e41e0a
        .. _fba3874: https://github.com/galaxyproject/planemo/commit/fba3874
        .. _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 70: https://github.com/galaxyproject/planemo/issues/70
        .. _Pull Request 68: https://github.com/galaxyproject/planemo/pull/68
        .. _Issue 61: https://github.com/galaxyproject/planemo/issues/61
        .. _Pull Request 63: https://github.com/galaxyproject/planemo/pull/63
        .. _Pull Request 56: https://github.com/galaxyproject/planemo/pull/56
        .. _Pull Request 51: https://github.com/galaxyproject/planemo/pull/51
        .. _Pull Request 40: https://github.com/galaxyproject/planemo/pull/40
        .. _Pull Request 29: https://github.com/galaxyproject/planemo/pull/29
        .. _Pull Request 22: https://github.com/galaxyproject/planemo/pull/22
        .. _Pull Request 23: https://github.com/galaxyproject/planemo/pull/23
        .. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33
        .. _Pull Request 6: https://github.com/galaxyproject/planemo/pull/6
        .. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1
        
        .. _3499ca0: https://github.com/galaxyproject/planemo/commit/3499ca0a15affcaf8ac9efc55880da40b0626679
        .. _85b9614: https://github.com/galaxyproject/planemo/commit/85b961465f46351507f80ddc3758349535060502
        .. _53a6766: https://github.com/galaxyproject/planemo/commit/53a6766cdebdddc976189f6dc6a264bb4105c4bf
        .. _badc25f: https://github.com/galaxyproject/planemo/commit/badc25fca495b61457ffb2e027f3fe9cf17c798f
        .. _411a8da: https://github.com/galaxyproject/planemo/commit/411a8da21c92ba37c7ad95bfce9928d9b8fd998e
        .. _b8d90ab: https://github.com/galaxyproject/planemo/commit/b8d90abab8bf53ae2e7cca4317223c01af9ab68c
        .. _e8c1d45: https://github.com/galaxyproject/planemo/commit/e8c1d45f0c9a11bcf69ec2967836c3b8f432dd97
        .. _78f8274: https://github.com/galaxyproject/planemo/commit/78f82747996e4a28f96c85ad72efe5e54c8c74bd
        .. _9e746b4: https://github.com/galaxyproject/planemo/commit/9e746b455e3b15219878cddcdeda722979639401
        .. _ac4f828: https://github.com/galaxyproject/planemo/commit/ac4f82898f7006799142503a33c3978428660ce7
        .. _834bfb2: https://github.com/galaxyproject/planemo/commit/834bfb2929d367892a3abe9c0b88d5a0277d7905
        .. _dff4f33: https://github.com/galaxyproject/planemo/commit/dff4f33c750a8dbe651c38e149a26dd42e706a82
        .. _a4110a8: https://github.com/galaxyproject/planemo/commit/a4110a85a770988e5cd3c31ccc9475717897d59c
        .. _21bb463: https://github.com/galaxyproject/planemo/commit/21bb463ad6c321bcb669603049a5e89a69766ad9
        .. _af39061: https://github.com/galaxyproject/planemo/commit/af390612004dab636d8696839bb723d39f97c85d
        .. _20a8680: https://github.com/galaxyproject/planemo/commit/20a86807cb7ea87db2dbc0197ae08a40df3ab2bc
        .. _44de95c: https://github.com/galaxyproject/planemo/commit/44de95c0d7087a5822941959f9a062f6382e329b
        .. _82e8b1f: https://github.com/galaxyproject/planemo/commit/82e8b1f17eae526aeb341cb4fffb8d09d73bb419
        .. _05cc9f4: https://github.com/galaxyproject/planemo/commit/05cc9f485ee87bc344e3f43bb1cfd025a16a6247
        .. _32c6e7f: https://github.com/galaxyproject/planemo/commit/32c6e7f78bb8f04d27615cfd8948b0b89f27b4e6
        .. _7d07782: https://github.com/galaxyproject/planemo/commit/7d077828559c9c9c352ac814f9e3b86b1b3a2a9f
        .. _a2c13e4: https://github.com/galaxyproject/planemo/commit/a2c13e46259e3be35de1ecaae858ba818bb94734
        .. _36f7cb11: https://github.com/galaxyproject/planemo/commit/36f7cb114f77731f90860d513a930e10ce5c1ba5
        .. _b9232e55: https://github.com/galaxyproject/planemo/commit/b9232e55e713abbd1d9ce8b0b34cbec6c701dc17
        
        .. _bioblend: https://github.com/galaxyproject/bioblend/
        .. _XSD: http://www.w3schools.com/schema/
        .. _lxml: http://lxml.de/
        .. _xmllint: http://xmlsoft.org/xmllint.html
        .. _nose: https://nose.readthedocs.org/en/latest/
        
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 :: 2.6
Classifier: Programming Language :: Python :: 2.7
