planemo 0.33.1

.. 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 building and publishing Galaxy_ tools.

.. 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

* 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.

-----------------
Obtaining Planemo
-----------------

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

Another approach for installing Planemo is to use Homebrew_ or
linuxbrew_. To install Planemo this way use the ``brew`` command as
follows.

::

$ brew tap galaxyproject/tap
$ brew install planemo

For information on updating Planemo, installing the latest development release,
or installing planemo via bioconda - 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 tool development.
You can choose from open virtualization format (OVA_, .ova), Docker_,
or Vagrant_ appliances.

--------------
Planemo Basics
--------------

This quick start will assume you have a directory with one or more
tool XML files. If none is available, one can be quickly created 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 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 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.
Planemo can also download and configure a disposable Galaxy instance for
testing. Pass ``--install_galaxy`` instead of ``--galaxy_root``.

::

$ planemo t --install_galaxy

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``.

---------
Tool Shed
---------

Planemo can help you publish tools to the Galaxy Tool Shed.
Check out `Publishing to the Tool Shed`_.


Experimental Features
---------------------

Planemo can also be used to explore some more experimental features related to
Galaxy tooling - including support for Conda_, `Travis CI`_, Docker_,
`Common Workfow Language`_ (CWL), and Homebrew_.

---------------------
Conda Package Manager
---------------------

Conda_ is package manager that among many other things can be used
to manage Python packages. Please read a few notes regarding the setup:

* Planemo cannot be installed via Conda and then run Galaxy inside
the same Conda environment currently.

* `galaxy-lib <https://github.com/galaxyproject/galaxy-lib>`_ is a
dependency of Planemo and having this on the Python path prevents
correct operation of Galaxy.

* Conda dependency resolution can be used for Galaxy tools,

This allows Galaxy to map conda recipes to ``requirement`` tags on tools

Just install planemo normally via pip into a virtual environment or via brew and
use the appropriate commands and options:

::

$ planemo conda_init
$ planemo conda_install .
$ planemo test --galaxy_branch release_16.04 --conda_dependency_resolution .
$ planemo serve --galaxy_branch release_16.04 --conda_dependency_resolution .

The test and serve commands above require the target Galaxy to be 16.01 or higher.

* Galaxy can also simply run inside an existing conda environment and
rather than using dependency resolution Conda packages can just be picked
up from the ``PATH``.

Note: This isn't a well supported approach yet, and when possible Planemo
and Galaxy should not be installed inside of Conda and the conda dependency
resolution (as described above) should be used to allow tools to find Conda
packages.

To run Galaxy within a Conda environment, Planemo must be installed outside the
Conda environment - via pip into a virtual environment or via homebrew. In the
former case, don't place the virtualenv's ``bin`` directory on your PATH - it
will conflict with Conda. Just reference Planemo directly
``/path/to/planemo_venv/bin/planemo test``.

To run Galaxy from within the environment you will need to install Galaxy
dependencies into the conda environment. Target the development branch of Galaxy
for this since it has "unpinned" dependencies that are easier to fullfill for
conda.

::

(conda-env-test) $ conda install numpy bx-python pysam # install the hard ones using conda
(conda-env-test) $ cd $GALAXY_ROOT
(conda-env-test) $ ./scripts/common_startup.sh --skip-venv --dev-wheels # install remaining ones using pip via Galaxy
(conda-env-test) $ cd /path/to/my/tools
(conda-env-test) $ /path/to/planemo_venv/bin/planemo test --skip_venv .
(conda-env-test) $ /path/to/planemo_venv/bin/planemo serve --skip_venv .

A small `test script <https://github.com/galaxyproject/planemo/blob/master/tests/scripts/conda_test.sh>`__
in the Planemo source tree demonstrates this.

-----------
TravisCI
-----------

When tools are ready to be published to GitHub_, it may be valuable to setup
continuous 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 Containers
-----------------

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.

--------------------------
Common Workflow Language
--------------------------

Planemo includes highly experimental support for running a subset of valid
`Common Workflow Language`_ (CWL) tools using a fork of Galaxy enhanced to run
CWL tools.

::

$ planemo project_init --template cwl_draft3_spec
$ planemo serve --cwl cwl_draft3_spec/cat1-tool.cwl

-----------
Brew
-----------

The Galaxy development team was exploring (the effort has since shifted towards
Conda_) 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/
.. _Conda: http://conda.pydata.org/
.. _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
.. _Common Workfow Language: http://common-workflow-language.github.io
.. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format




History
-------

.. to_doc

---------------------
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 Eric 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 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`_. 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). 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
.. _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
.. _@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