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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
| author | shellac |
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| date | Sat, 02 May 2020 07:14:21 -0400 |
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Metadata-Version: 2.1 Name: planemo Version: 0.70.0 Summary: Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/). Home-page: https://github.com/galaxyproject/planemo Author: Galaxy Project and Community Author-email: jmchilton@gmail.com License: AFL Keywords: planemo Platform: UNKNOWN Classifier: Development Status :: 5 - Production/Stable Classifier: Intended Audience :: Developers Classifier: Environment :: Console Classifier: License :: OSI Approved :: Academic Free License (AFL) Classifier: Operating System :: POSIX Classifier: Topic :: Software Development Classifier: Topic :: Software Development :: Code Generators Classifier: Topic :: Software Development :: Testing Classifier: Natural Language :: English Classifier: Programming Language :: Python :: 2 Classifier: Programming Language :: Python :: 2.7 Classifier: Programming Language :: Python :: 3 Classifier: Programming Language :: Python :: 3.5 Classifier: Programming Language :: Python :: 3.6 Classifier: Programming Language :: Python :: 3.7 Classifier: Programming Language :: Python :: 3.8 Description-Content-Type: text/x-rst Requires-Dist: aenum Requires-Dist: BeautifulSoup4 Requires-Dist: bioblend (>=0.13.0) Requires-Dist: Click Requires-Dist: configparser Requires-Dist: cwltool (==1.0.20191225192155) Requires-Dist: docutils Requires-Dist: ephemeris (>=0.10.3) Requires-Dist: galaxy-containers Requires-Dist: galaxy-tool-util (>=20.1.0.dev2) Requires-Dist: galaxy-util (>=20.1.0.dev0) Requires-Dist: glob2 Requires-Dist: gxformat2 (>=0.8.0) Requires-Dist: jinja2 Requires-Dist: lxml Requires-Dist: oyaml Requires-Dist: pyaml Requires-Dist: pyyaml Requires-Dist: six (>=1.7.0) Requires-Dist: virtualenv .. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png :alt: Planemo Logo :align: center :figwidth: 100% :target: https://github.com/galaxyproject/planemo Command-line utilities to assist in developing Galaxy_ and `Common Workflow Language`_ tools. .. image:: https://readthedocs.org/projects/planemo/badge/?version=latest :target: http://planemo.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status .. image:: https://badge.fury.io/py/planemo.svg :target: https://pypi.python.org/pypi/planemo/ :alt: Planemo on the Python Package Index (PyPI) .. image:: https://travis-ci.org/galaxyproject/planemo.png?branch=master :target: https://travis-ci.org/galaxyproject/planemo :alt: Build Status .. image:: https://travis-ci.org/jmchilton/planemo-extended-tests.svg?branch=master :target: https://travis-ci.org/jmchilton/planemo-extended-tests :alt: Build Status of Extended Tests .. image:: https://coveralls.io/repos/galaxyproject/planemo/badge.svg?branch=master :target: https://coveralls.io/r/galaxyproject/planemo?branch=master :alt: Coverage Status * Free software: Academic Free License version 3.0 * Documentation: https://planemo.readthedocs.io. * Code: https://github.com/galaxyproject/planemo Quick Start ----------- ----------------- Obtaining ----------------- For a traditional Python installation of Planemo, first set up a virtualenv for ``planemo`` (this example creates a new one in ``.venv``) and then install with ``pip``. Planemo requires pip 7.0 or newer. :: $ virtualenv .venv; . .venv/bin/activate $ pip install "pip>=7" # Upgrade pip if needed. $ pip install planemo For information on updating Planemo, installing the latest development release, or installing Planemo via `Bioconda <https://github.com/bioconda/bioconda-recipes>`__ - checkout the `installation <http://planemo.readthedocs.io/en/latest/installation.html>`__ documentation. Planemo is also available as a `virtual appliance <https://planemo.readthedocs.io/en/latest/appliance.html>`_ bundled with a preconfigured Galaxy server and set up for Galaxy_ and `Common Workflow Language`_ tool development. You can choose from open virtualization format (OVA_, .ova) or Docker_ appliances. ----------------- Basics - Galaxy ----------------- This quick start will assume you have a directory with one or more Galaxy tool XML files. If no such directory is available, one can be quickly created for demonstrating ``planemo`` as follows ``project_init --template=demo mytools; cd mytools``. Planemo can check tool XML files for common problems and best practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_ (also aliased as ``l``). :: $ planemo lint Like many ``planemo`` commands - by default this will search the current directory and use all tool files it finds. It can be explicitly passed a path to tool files or a directory of tool files. :: $ planemo l randomlines.xml The ``lint`` command takes in additional options related to reporting levels, exit code, etc. These options are described in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_ or (like with all commands) can be accessed by passing ``--help`` to it. :: $ planemo l --help Usage: planemo lint [OPTIONS] TOOL_PATH Once tools are syntactically correct - it is time to test. The ``test`` `command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__ can be used to test a tool or a directory of tools. :: $ planemo test --galaxy_root=../galaxy randomlines.xml If no ``--galaxy_root`` is defined, Planemo will download and configure a disposable Galaxy instance for testing. Planemo will create a HTML output report in the current directory named ``tool_test_output.html`` (override with ``--test_output``). See an `example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_ of such a report for Tophat. Once tools have been linted and tested - the tools can be viewed in a Galaxy interface using the ``serve`` (``s``) `command <http://planemo.readthedocs.org/en/latest/commands.html#serve-command>`__. :: $ planemo serve Like ``test``, ``serve`` requires a Galaxy root and one can be explicitly specified with ``--galaxy_root`` or installed dynamically with ``--install_galaxy``. For more information on building Galaxy tools in general please check out `Building Galaxy Tools Using Planemo`_. ---------------------------------- Basics - Common Workflow Language ---------------------------------- This quick start will assume you have a directory with one or more `Common Workflow Language`_ YAML files. If no such directory is available, one can be quickly created for demonstrating ``planemo`` as follows ``planemo project_init --template=seqtk_complete_cwl mytools; cd mytools``. Planemo can check tools YAML files for common problems and best practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_ (also aliased as ``l``). :: $ planemo lint Like many ``planemo`` commands - by default this will search the current directory and use all tool files it finds. It can be explicitly passed a path to tool files or a directory of tool files. :: $ planemo l seqtk_seq.cwl The ``lint`` command takes in additional options related to reporting levels, exit code, etc. These options are described in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_ or (like with all commands) can be accessed by passing ``--help`` to it. :: $ planemo l --help Usage: planemo lint [OPTIONS] TOOL_PATH Once tools are syntactically correct - it is time to test. The ``test`` `command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__ can be used to test a CWL tool, workflow, or a directories thereof. :: $ planemo test --engine cwltool seqtk_seq.cwl Planemo will create a HTML output report in the current directory named ``tool_test_output.html``. Check out the file ``seqtk_seq_tests.yml`` for an example of Planemo test for a CWL tool. A test consists of any number of jobs (with input descriptions) and corresponding output assertions. Checkout the `Commmon Workflow User Guide`_ for more information on developing CWL tools in general and `Building Common Workflow Language Tools`_ for more information on using Planemo to develop CWL tools. --------- Tool Shed --------- Planemo can help you publish tools to the Galaxy Tool Shed. Check out `Publishing to the Tool Shed`_ for more information. ------ Conda ------ Planemo can help develop tools and Conda packages in unison. Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda>`__ or `CWL <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda-cwl>`__ version of the "Dependencies and Conda" tutorial for more information. ----------------------- Docker and Containers ----------------------- Planemo can help develop tools that run in "Best Practice" containers for scientific workflows. Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-containers>`__ or `CWL <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers-cwl>`__ version of the "Dependencies and Containers" tutorial for more information. .. _Galaxy: http://galaxyproject.org/ .. _GitHub: https://github.com/ .. _Conda: http://conda.pydata.org/ .. _Docker: https://www.docker.com/ .. _Vagrant: https://www.vagrantup.com/ .. _Travis CI: http://travis-ci.org/ .. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam .. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc .. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html .. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html .. _Common Workflow Language: https://www.commonwl.org/ .. _Commmon Workflow User Guide: http://www.commonwl.org/user_guide/ .. _Building Common Workflow Language Tools: http://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html .. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format History ------- .. to_doc --------------------- 0.70.0 (2020-01-29) --------------------- * Temporarily add galaxy-util requirement `Pull Request 991`_ * Make symlinks in tool tree work for planemo test `Pull Request 988`_ * Reduce use of ``shell=True`` in subprocesses `Pull Request 989`_ * Drop planemo database seed option `Pull Request 985`_ * Don't execute ``untar_to()`` subprocesses through the shell `Pull Request 984`_ * Allow setting database_connection for planemo test runs `Pull Request 986`_ * Fix copy-paste mistakes `Pull Request 983`_ * Add planemo list_repos command `Pull Request 982`_ * Make container_register build files with headers and include base_image `Pull Request 980`_ * Replace deprecated galaxy-lib requirement with galaxy-tool-util `Pull Request 978`_ * Close all opened files (thanks to `@bernt-matthias`_). `Pull Request 979`_ * Build single requirement container, log if requirement not in best-practice channels `Pull Request 977`_ * Use tojson jinja2 filter instead of json.dumps `Pull Request 975`_ * Add merge_test_reports command `Pull Request 974`_ * Implement github workflow and fix profile commands if psql unavailable `Pull Request 976`_ * Fix planemo lint --biocontainers if no build number in container `Pull Request 972`_ * Update a training command (thanks to `@hexylena`_). `Pull Request 973`_ * Allow passing through GALAXY_VIRTUAL_ENV variable to venv setup `Pull Request 971`_ * Correct help text (thanks to `@hexylena`_). `Pull Request 970`_ * Remove unneeded html5lib requirement `Pull Request 968`_ --------------------- 0.62.1 (2019-10-14) --------------------- * Init & update submodules when installing and creating packages. Stop distributing eggs (thanks to `@nsoranzo`_). 1ab8530_ --------------------- 0.62.0 (2019-10-11) --------------------- * Use ``unicodify()`` on exceptions and subprocess outputs (thanks to `@nsoranzo`_) `Pull Request 944`_ * Do not override ``None`` with empty string (thanks to `@ic4f`_). `Pull Request 950`_ * Update Docker template for training material generation (thanks to `@bedroesb`_). `Pull Request 958`_ * Add support for suite of repos with different owners (thanks to `@nsoranzo`_). `Pull Request 959`_ * Link for collection details updated in the docs (thanks to `@martin-raden`_). `Pull Request 963`_ * Move most tests to Python 3.7, drop Python 3.4 (thanks to `@nsoranzo`_). `Pull Request 964`_ * Remove confusing warning `Pull Request 966`_ --------------------- 0.61.0 (2019-07-08) --------------------- * Training - fix empty repeat + some formatting (thanks to `@bebatut`_). `Pull Request 926`_ * Training - add bibliography to tutorial template (thanks to `@shiltemann`_). `Pull Request 938`_ * Training - support new class definition for input in workflow step (thanks to `@bebatut`_). `Pull Request 943`_ * Various tool tutorial fixes ahead of GCC 2019 (thanks to `@nsoranzo`_). `Pull Request 940`_ * Return validation error if doi is empty (thanks to `@nsoranzo`_). `Pull Request 937`_ --------------------- 0.60.0 (2019-05-31) --------------------- * Return validation error if doi is empty `Pull Request 937`_ * Add junit as test reporter (thanks to `@selten`_). `Pull Request 935`_ * Update galaxy.xsd for new python 3 compatibility attribute (thanks to `@martenson`_). `Pull Request 931`_ * Documentation: add a little warning for <param ... multiple="true"> (thanks to `@bernt-matthias`_). `Pull Request 930`_ --------------------- 0.59.0 (2019-05-09) --------------------- * Add ability to test data manager tools (thanks to `@mvdbeek`_). `Pull Request 912`_ * Update Training for new requirement definition (thanks to `@bebatut`_). `Pull Request 913`_ * Drop amqp workaround (thanks to `@mvdbeek`_). `Pull Request 917`_ * Use ``yaml.safe_load()`` instead of deprecated ``load()`` (thanks to `@nsoranzo`_). `Pull Request 921`_ * Allow converting ``tool_test_report.json`` to xunit (thanks to `@mvdbeek`_). `Pull Request 918`_ * Fix error if testcase.data.job does not exist (thanks to `@mvdbeek`_). `Pull Request 924`_ * Fix deprecated ``getchildren()`` (thanks to `@nsoranzo`_). `Pull Request 925`_ --------------------- 0.58.2 (2019-03-01) --------------------- * Fix display of tool ids in planemo html report (thanks to `@mvdbeek`_). `Pull Request 908`_ * Single quotes for file names (thanks to `@bernt-matthias`_). `Pull Request 909`_ * Fix doc linting (thanks to `@mvdbeek`_). `Pull Request 910`_ * Update TS categories (thanks to `@nsoranzo`_). 07dc6e0_ * Close tag in doc help, to help with copy&paste (thanks to `@blankenberg`_). `Pull Request 914`_ * Update the tool XSD file (thanks to `@bgruening`_). `Pull Request 915`_ --------------------- 0.58.1 (2019-01-03) --------------------- * Update galaxy-lib requirement to 18.9.2 to add Python 3.7 support (thanks to `@nsoranzo`_). `Pull Request 906`_ * Fix command run by `planemo test --skip_venv` (thanks to `@nsoranzo`_). `Pull Request 907`_ --------------------- 0.58.0 (2019-01-01) --------------------- * Remove deprecated ``sudo: false`` from .travis.yml (thanks to `@nsoranzo`_). `Pull Request 902`_ * Do not skip Galaxy client build for ``planemo serve``. Install Galaxy when the directory specified with ``--galaxy_root`` does not exist or is empty. (thanks to `@nsoranzo`_). `Pull Request 895`_, `Issue 845`_ --------------------- 0.57.1 (2018-11-23) --------------------- * Fix username validation for shed linting (thanks to `@martenson`_). `Pull Request 899`_, `Issue 898`_ --------------------- 0.57.0 (2018-11-19) --------------------- * Allow ``workflow_convert`` to convert a native ``.ga`` workflows to format 2 (yaml). `Pull Request 896`_ * New command (``workflow_edit``) to open workflow in a synchronized graphical editor. `Pull Request 894`_ * Conda tutorial fixes (thanks to `@nsoranzo`_). `Pull Request 876`_ * Enable ``--conda_use_local`` option for ``planemo test`` (thanks to `@nsoranzo`_). `Pull Request 876`_ * When testing, skip workflow outputs that do not have a `label` set (thanks to `@bgruening`_). `Pull Request 893`_ * Add ``__repr__`` for ``TestCase`` to improve debugging Planemo (thanks to `@bgruening`_). `Pull Request 892`_ * Increase IO polling interval over time (thanks to `@martenson`_). `Pull Request 891`_ * Sync galaxy xsd and fix tests (thanks to `@mvdbeek`_). `Pull Request 889`_ * Linting fix for ``W605`` (thanks to `@martenson`_). `Pull Request 888`_ * Add icon for repeat parameters in training (thanks to `@bebatut`_). `Pull Request 887`_ --------------------- 0.56.0 (2018-10-30) --------------------- * Allow selection of Python version when starting managed Galaxy (thanks to `@mvdbeek`_). `Pull Request 874`_ * Change the channel priority of conda (again). (thanks to `@bgruening`_). `Pull Request 867`_ * Some small english corrections (thanks to `@hexylena`_). `Pull Request 868`_ * Print the list of excluded paths when running ``ci_find_repos`` (thanks to `@nsoranzo`_). `Pull Request 877`_ * Improved XSD lint reporting. `Pull Request 871`_ * Fix Planemo writing a file called ``gx_venv_None``. `Pull Request 870`_ * Update cwltool and galaxy-lib dependencies for Python 3.7 (thanks to `@nsoranzo`_). `Pull Request 864`_ * Fix to make workflow testing more robust. `Pull Request 882`_ --------------------- 0.55.0 (2018-09-12) --------------------- * Add commands to create Galaxy training materials (thanks to `@bebatut`_). `Pull Request 861`_ * Fix `planemo test` when TEMP env variable contain spaces (thanks to `@nsoranzo`_). `Pull Request 851`_ * Support testing a completely remote galaxy instance (thanks to `@hexylena`_). `Pull Request 856`_ * Allow naming history from command line (thanks to `@hexylena`_). `Pull Request 860`_ * Sync galaxy.xsd from galaxy repo (thanks to `@nsoranzo`_). `Pull Request 866`_ * Fix ServeTestCase.test_shed_serve test (thanks to `@nsoranzo`). bad810a_ --------------------- 0.54.0 (2018-06-06) --------------------- * Better support for testings against different versions of Galaxy efficiently and robustly. `Pull Request 849`_ * New database version (thanks to `@bgruening`_). `Pull Request 847`_ * Hyperlink DOIs against preferred resolver (thanks to `@katrinleinweber`_). `Pull Request 850`_ * Tests for collection inputs to workflows. `Pull Request 843`_ * Bring in Ephemeris sleep function - hopefully makes serve tests a bit more robust. b12b117_ * More tutorial testing, tutorial updates. 016b923_, 324c776_, 2002b49_ * More isolated ``test_shed_upload.py`` tests. 72d2ca7_ * Add filetype support for workflow test inputs (thanks to `@bgruening`_). `Pull Request 842`_ * Add ``--no_shed_install`` option, to prevent shed installs as part of workflow testing. `Pull Request 841`_ * Small docs fix (thanks to `@hexylena`_). `Pull Request 848`_ --------------------- 0.53.0 (2018-05-22) --------------------- * Make Planemo testing easier for CWL tools and workflows in various ways and update tutorials to reflect these simplifications. `Pull Request 837`_ * Test and fix running workflow tests against externally managed Galaxy servers. `Pull Request 833`_, `Pull Request 836`_ * Allow using URIs for inputs of workflow test. `Pull Request 840`_ * Slide Galaxy testing window to include 18.05 and drop 17.09. `Pull Request 838`_ --------------------- 0.52.0 (2018-05-20) --------------------- * Allow optional disabling of Galaxy single user mode. `Pull Request 835`_ * Fix for path pasting options during workflow testing. `Pull Request 834`_ --------------------- 0.51.0 (2018-05-19) --------------------- * Fix essentially all Conda_ and BioContainers_ related functionality to allow parity between CWL_ and existing Galaxy functionality - fixes and enhances many commands including ``lint``, ``conda_install``, ``conda_env``, ``test``, ``run``, and ``mull``. `Pull Request 828`_ * Add two new tutorials for `Conda <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda>`__ and `Container <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers>`__ development with CWL tools that mirrors the existing tutorials for Galaxy tools - including new CWL exercises, answers, and example project templates. 347c622_ * Improve the CWL generated by the ``tool_init`` command to properly deal with ``SoftwareRequirement`` s and generate more idiomatic CWL. `Pull Request 820`_, a5c72e3_ * Add new engine type (``--engine toil``) for testing and running CWL_ tools (requires manually installing Toil_ with ``pip install toil`` in Planemo's environment). `Pull Request 831`_ * Add `documentation <http://planemo.readthedocs.io/en/latest/test_format.html>`__ for the Galaxy Workflow and CWL_ test format files (includes information on configuring various test engines). `Pull Request 832`_ * Better default logging config for CWL development. `Pull Request 830`_ * Various fixes for the ``conda_search`` command. `Pull Request 826`_ * Fix test coverage configuration. `Pull Request 822`_ * Reorganize .travis.yml for clarity. `Pull Request 829`_ * More isolated, robust unit tests that use git_. `Pull Request 827`_, `Pull Request 818`_ * Fix default list of best-practice Conda channels. `Pull Request 825`_ * Refactor tests to speed up quick tests - fewer buggy URLs fetched in "quick" mode. `Pull Request 823`_ * Fix upload configuration of workflow testing to default (overrideable) external Galaxies to not use path pasting. `Pull Request 816`_ * Fix test number parsing for workflow tests. `Pull Request 817`_ --------------------- 0.50.1 (2018-05-11) --------------------- * Fix the process of waiting on Galaxy to boot up for the Docker Galaxy container ``--engine``. --------------------- 0.50.0 (2018-05-10) --------------------- * Fixes and small CLI tweaks to get the Docker Galaxy container working as an ``--engine`` for the run, serve, and test commands. --------------------- 0.49.2 (2018-05-09) --------------------- * Various small fixes for new external Galaxy engine type. --------------------- 0.49.1 (2018-05-06) --------------------- * Fix PyPI_ README rendering for 0.49.0 release changes. --------------------- 0.49.0 (2018-05-06) --------------------- * Implement external Galaxy engine. `Pull Request 781`_ * Restructure serve testing code for reuse. `Pull Request 795`_ * Improve test report handling for JSON generated via galaxy-lib testing script. `Pull Request 799`_ * Improve how various branches of Galaxy are tested. `Pull Request 800`_ * Added documentation for ``GALAXY_MEMORY_MB`` (thanks to `@bernt-matthias`_). `Pull Request 801`_ * Log tool config in verbose logging mode. `Pull Request 802`_ * Replace ``r`` channel with ``conda-forge`` (thanks to `@bgruening`_). `Pull Request 805`_ * Sync ``galaxy.xsd`` with latest Galaxy updates (thanks to `@nsoranzo`_). `Pull Request 806`_ * Use ``requests.get()`` when validating http URLs (thanks to `@nsoranzo`_). `Pull Request 809`_ * Do not consider tools with "deprecated" in the path (thanks to `@bgruening`_). `Pull Request 810`_ * Automatically load tools shipped with Galaxy when testing, running, or serving workflows that reference these tools. `Pull Request 790`_ * Revise README and touch up documentation in general. `Pull Request 787`_ * Various small changes to testing and test framework. `Pull Request 792`_ * Various Python 3 fixes. 8cfe9e9_, 41f7df1_ * Fixes for Galaxy 18.0X releases. `Pull Request 803`_, dc443d6_ --------------------- 0.48.0 (2018-02-28) --------------------- * Run all CI tests against Python 3 (thanks to `@nsoranzo`_). `Pull Request 768`_ and `Pull Request 774`_ * Python 3 fix - subprocess with ``universal_newlines=True`` (thanks to `@peterjc`_). `Pull Request 764`_ * Record CWL_ conformance test results using JUnit xml (thanks to `@mr-c`_). `Pull Request 756`_ * Restore run test case for simple Galaxy tools. `Pull Request 769`_ * Enhancements to Galaxy profiles and workflow testing. `Pull Request 773`_ * Fix resolving & installing shed repositories from workflows for ``test`` and ``run`` commands. `Pull Request 776`_ * Implement planemo command to convert format 2 workflows into .ga workflows. `Pull Request 771`_ * Add a native Galaxy workflow (.ga) testing test. `Pull Request 770`_ * Drop Brew support but add more detailed install instructions. `Pull Request 761`_ * Clean up CWL_ conformance test execution. `Pull Request 753`_ * Assorted small CWL_ and deamon serve fixes. `Pull Request 759`_ --------------------- 0.47.0 (2017-11-18) --------------------- * Update to the latest Galaxy tool XSD (thanks to `@nsoranzo`_). `Pull Request 747`_ * Re-fix problem when shed_update would fail if nothing to update (thanks to `@nsoranzo`_). `Pull Request 747`_ * Update instructions for installation via conda (thanks to `@nsoranzo`_) . `Pull Request 743`_ * Bug fix for MacOS `chmod` doesn't support `--recursive` flag. (thanks to `@dfornika`_). `Pull Request 739`_ * Bug fix to also `socket.error` when linting URLs (thanks to `@nsoranzo`_). `Pull Request 738`_ * Disable broken tests. `Pull Request 745`_ --------------------- 0.46.1 (2017-09-26) --------------------- * Rev to latest versions of bioblend_ and `galaxy-lib`_ for various fixes related to CWL_. --------------------- 0.46.0 (2017-09-15) --------------------- * Change behavior of ``--docker`` flag, for a few releases it would require Galaxy use a container for every non-upload tool. This breaks various conversion tools for instance and so was reverted. `Pull Request 733`_ * Add 'Accept' header when linting doc URLs (thanks to `@nsoranzo`_). `Pull Request 725`_ * Fix `--conda_auto_install` help (thanks to `@nsoranzo`_). `Pull Request 727`_ * Incremental progress toward CWL support via Galaxy. `Pull Request 729`_, `Pull Request 732`_ * Update galaxy-lib to latest version to fix various issues. `Pull Request 730`_ * Fix lint detected problems with documentation. `Pull Request 731`_ --------------------- 0.45.0 (2017-09-06) --------------------- * Update to the latest `galaxy-lib`_ for Conda fixes. (thanks `@nsoranzo`_) and updated CWL_ utilities. `Pull Request 716`_, `Pull Request 723`_ * Update Conda_ channel order to sync with Bioconda_ (thanks to `@nsoranzo`_). `Pull Request 715`_ * Experimental support running CWL_ workflows through the CWL_ fork of Galaxy. * Mention ``planemo command --help`` in main help (thanks to `@peterjc`_). `Pull Request 709`_ * Bugfix handle ``None`` requirement versions when registering containers (thanks to `@bgruening`_). `Pull Request 704`_ * Bugfix for dependencies by pinning ruamel.yaml version (thanks to `@mvdbeek`_). `Pull Request 720`_ --------------------- 0.44.0 (2017-06-22) --------------------- * Fix and improve Galaxy root option specification options. `Pull Request 701`_, 8a608e0_ * Update `planemo mull` to use a default action of `build-and-test` since `build` no longer cleans up itself. ecc1bc2_ * Add a command to pre-install Involucro_. `Pull Request 702`_ --------------------- 0.43.0 (2017-06-22) --------------------- * Remove stdio from generated tools - just use exit_code for everything. 91b6fa0_ * Implement some ad-hoc documentation tests. `Pull Request 699`_ * A large number of small enhancements and fixes for the documentation and example projects. --------------------- 0.42.1 (2017-06-16) --------------------- * Fix Readme typos (thanks to `@manabuishii`_) 904d77a_ * Fix `container_register` to create pull requests against the newly finalized home of the multi-package-containers registry repository. 9636682_ * Fix `use_global_config` and `use_env_var` for options with unspecified defaults. 475104c_ --------------------- 0.42.0 (2017-06-15) --------------------- * Conda/Container documentation and option naming improvements. `Pull Request 684`_ * Sync `galaxy.xsd` with latest upstream Galaxy updates (thanks to `@nsoranzo`_). `Pull Request 687`_ * Fix `ci_find_repos` command to not filter repos whose only modifications where in subdirs (thanks to `@nsoranzo`_). `Pull Request 688`_ * Update `container_register` for mulled version 2 and repository name changes. `Pull Request 689`_ * Better pull request messages for the `container_register` command. `Pull Request 690`_ --------------------- 0.41.0 (2017-06-05) --------------------- * Fix ``shed_update`` not fail if there is nothing to update (thanks to `@nsoranzo`_). `Issue 494`_, `Pull Request 680`_ * Conda documentation and option naming improvements. `Pull Request 683`_ * Implement ``container_register`` for tool repositories. `Pull Request 675`_ * Fix ``hub`` binary installation for Mac OS X. `Pull Request 682`_ --------------------- 0.40.1 (2017-05-03) --------------------- * Fix data manager configuration to not conflict with original Galaxy at ``galaxy_root`` (thanks to `@nsoranzo`_). `Pull Request 662`_ * Fix ``filter_paths()`` to not partial match paths when filtering shed repositories (thanks to `@nsoranzo`_). `Pull Request 665`_ * Fix description when creating ``.shed.yml`` files (thanks to `@RJMW`_). `Pull Request 664`_ --------------------- 0.40.0 (2017-03-16) --------------------- * Implement instructions and project template for GA4GH Tool Execution Challenge Phase 1. 84c4a73_ * Eliminate Conda hack forcing ``/tmp`` as temp directory. b4ae44d_ * Run dependency script tests in isolated directories. 32f41c9_ * Fix OS X bug in ``planemo run`` by reworking it to wait using urllib instead of sockets. 3129216_ --------------------- 0.39.0 (2017-03-15) --------------------- * Implement documentation and examples for Conda-based dependency development (under "Advanced" topics). `Pull Request 642`_, `Pull Request 643`_ * Implement documentation and examples for container-based dependency development (under "Advanced" topics). 0a1abfe_ * Implement a ``planemo conda_search`` command for searching best practice channels from the command line. `Pull Request 642`_ * Allow Planemo to work with locally built Conda packages using the ``--conda_use_local`` command. `Pull Request 643`_, `Issue 620`_ * Implement an ``open`` (or just ``o``) command to quickly open the last test results (or any file if supplied). `Pull Request 641`_ * Linting improvements and fixes due to `galaxy-lib`_ update. * WARN on test output names not found or not matching. * INFO correct information about stdio if profile version is found. * WARN if profile version is incorrect. * INFO profile version * Fix ``assert_command`` not detected as a valid test (fixes `Issue 260`_). * Have ``lint --conda_requirements`` check that at least one actual requirement is found. 6638caa_ * Allow ``conda_install`` to work with packages as well as just tools. 8faf661_ * Add ``--global`` option to conda_install to install requirements into global Conda setup instead of using an environment. 8faf661_ * Implement ``planemo lint --biocontainer`` that checks that a tool has an available BioContainer registered. 0a1abfe_ * Add more options and more documentation to the ``planemo mull`` command. 0a1abfe_ * Hack around a bug in Conda 4.2 that makes it so ``planemo mull`` doesn't work out of the box on Mac OS X. 0a1abfe_ * Allow URIs to be used instead of paths for a couple operations. ce0dc4e_ * Implement non-strict CWL parsing option. 4c0f100_ * Fixes for changes to cwltool_ and general CWL-relate functionality. 3c95b7b_, 06bcf19_, 525de8f_, 9867e56_, 9ab4a0d_ * Eliminate deprecated XML-based abstraction from ``planemo.tools``. 04238d3_ * Fix ``MANIFEST.in`` entry that was migrated to galaxy-lib. ced5ce2_ * Various fixes for the command ``conda_env``. `Pull Request 640`_ * Improved command help - both formatting and content. `Pull Request 639`_ * Implement a ``--no_dependency_resolution`` option disabling conda dependency resolver. `Pull Request 635`_, `Issue 633`_ * Tests for new linting logic. `Pull Request 638`_ * Fix bug where tool IDs needs to be lowercase for the shed (thanks to `@bgruening`_). `Pull Request 649`_ * Update seqtk version targetted by intro docs. e343b67_ * Various other Conda usability improvements. `Pull Request 634`_ --------------------- 0.38.1 (2017-02-06) --------------------- * Fix bug with ``shed_lint --urls`` introduced in 0.38.0. 84ebc1f_ --------------------- 0.38.0 (2017-02-06) --------------------- * Trim down the default amount of logging during testing. `Pull Request 629`_, `Issue 515`_ * Improved log messages during shed operations. 08c067c_ * Update tool XSD against latest Galaxy. fca4183_, 03c9658_ * Fix bug where ``shed_lint --tools`` for a suite lints the same tools multiple times. `Issue 564`_, `Pull Request 628`_ --------------------- 0.37.0 (2017-01-25) --------------------- * Update to the latest `galaxy-lib`_ release. This means new installs start with Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes many Conda_ related bugs. * Change defaults so that Conda automatically initializes and performs tool installs by default from within the spawned Galaxy server. The trio of flags ``--conda_dependency_resolution``, ``--conda_auto_install``, and ``--conda_auto_init`` are effectively enabled by default now. 4595953_ * Use the Galaxy cached dependency manager by default (thanks to `@abretaud`_). `Pull Request 612`_ * Test Conda dependency resolution for more versions of Galaxy including the forthcoming release of 17.01. * Update to the latest Galaxy tool XSD for various tool linting fixes. 32acd68_ * Fix pip ignores for ``bioconda_scripts`` (thanks to `@nturaga`_) `Pull Request 614`_ --------------------- 0.36.1 (2016-12-12) --------------------- * Fix move error when using ``project_init``. `Issue 388`_, `Pull Request 610`_ * Improved integration testing for ``test`` command. `Pull Request 609`_ * Update CWL links to v1.0 (thanks to `@mr-c`_). `Pull Request 608`_ --------------------- 0.36.0 (2016-12-11) --------------------- * Bring in latest tool XSD file from Galaxy (thanks to `@peterjc`_). `Pull Request 605`_ * PEP8 fixes for various linting problems (thanks to `@peterjc`_). `Pull Request 606`_ * Update tool syntax URL to new URL (thanks to `@mvdbeek`_). `Pull Request 602`_ --------------------- 0.35.0 (2016-11-14) --------------------- * Native support for building bioconductor tools and recipes (thanks to `@nturaga`_). `Pull Request 570`_ * Fixes for running Galaxy via docker-galaxy-stable (thanks to `@bgruening`_). 50d3c4a_ * Import order linting fixes (thanks to `@bgruening`_). --------------------- 0.34.1 (2016-10-12) --------------------- * Mimic web browser to validate user help URLs fixing `Issue 578`_ (thanks to `@peterjc`_). `Pull Request 591`_ * Fix for Bioconda recipes depending on ``conda-forge`` (thanks to `@nsoranzo`_). `Pull Request 590`_ --------------------- 0.34.0 (2016-10-05) --------------------- * Implement ``mull`` command to build containers for tools based on Conda_ recipes matching requirement definitions. 08cef54_ * Implement ``--mulled_containers`` flag on ``test``, ``serve``, and ``run`` commands to run tools in "mulled" containers. Galaxy will first search locally cache containers (such as ones built with ``mull``), then search the mulled namespace of `quay.io`_, and finally build one on-demand if needed using `galaxy-lib`_ and Involucro_ developed by `@thriqon`_. * Implement ``--conda_requirements`` flag on ``lint`` command to ensure requirements can be resolved in best practice channels. 9da8387_ * Allow ``conda_install`` command over multiple tool paths. 2e4e5fc_ * Update pip_ as part of setting virtual environment in ``Makefile`` target. 19b2ee9_ * Add script to auto-update Bioconda_ recipe for Planemo and open a pull request. f0da66f_ --------------------- 0.33.2 (2016-09-28) --------------------- * Fix HISTORY.rst link problem that prevented correct display of content on PyPI_. --------------------- 0.33.1 (2016-09-28) --------------------- * Fix ``lint --urls`` false positives by being more restrictive with what is considered a URL (fixed by `@hexylena`_ after detailed report from `@peterjc`_). `Issue 573`_, `Pull Request 579`_ --------------------- 0.33.0 (2016-09-23) --------------------- * Enable XSD validation of tools by default (restore old behavior with ``planemo lint --no_xsd``). 1ef05d2_ * Implement a ``conda_lint`` command to lint Conda_ recipes based on `anaconda-verify`_. 6a6f164_ * Implement ``clone`` and ``pull_request`` commands to ease PRs (with documentation fixes from `@martenson`_). e925ba1_, ea5324f_ * Update `galaxy.xsd`_ to allow version_command's to have an interpreter attribute. 7cca2e4_ * Apply improvement from `@nsoranzo`_ for Planemo's use of `git diff <https://git-scm.com/docs/git-diff>`__. 6f91719_ * Pull in downstream refactoring of ``tool_init`` code from `@nturaga`_'s Bioconductor_ work. ccdd2d5_ * Update to latest `Tool Factory`_ code from `tools-iuc`_. ca88b0c_ * Small code cleanups. b6d8294_, d6da3a8_ * Fixup docs in ``planemo.xml.validation``. * Allow skipping newly required lxml_ dependency in `setup.py`_. 34538de_ --------------------- 0.32.0 (2016-09-16) --------------------- * Enhance ``planemo lint --xsd`` to use a fairly complete and newly official XSD definition. `Pull Request 566`_ * Migrate and update documentation related to tool XML macros and handling multiple outputs from the Galaxy wiki (with help from `@bgruening`_, `@mvdbeek`_, and `@nsoranzo`_). `Pull Request 559`_ * Documentation fixes (thanks to `@ramezrawas`_). `Pull Request 561`_ * Do not fail URL linting in case of too many requests (thanks to `@nsoranzo`_). `Pull Request 565`_ --------------------- 0.31.0 (2016-09-06) --------------------- * Implement new commands to ``ci_find_repos`` and ``ci_find_tools`` to ease CI scripting. `Pull Request 555`_ --------------------- 0.30.2 (2016-09-01) --------------------- * Fix another problem with Conda_ prefix handling when using ``--conda_dependency_resolution``. f7b6c7e_ --------------------- 0.30.1 (2016-09-01) --------------------- * Fix a problem with Conda_ prefix handling when using ``--conda_dependency_resolution``. f7b6c7e_ * Fix for quote problem in ``update_planemo_recipe.bash``. 6c03de8_ * Fix to restore linting of ``tests/`` directory and fix import order throughout module. ef4b9f4_ --------------------- 0.30.0 (2016-09-01) --------------------- * Update to the latest `galaxy-lib`_ release and change Conda_ semantics to match recent updates to Galaxy. For the most robust Conda_ usage - use planemo 0.30+ with Galaxy 16.07 or master. 07d94bd_ * Implement the ``--conda_auto_init`` flag for ``conda_install``. ca19910_ * Allow the environment variable ``PLANEMO_CONDA_PREFIX`` to set a default for ``--conda_prefix``. 24008ab_ * Fixup documentation regarding installs and Conda_. ce44e87_ * Fix and lint Python module import order throughout project. `Pull Request 550`_ * Use ``cp`` rather than symlink to ``$DOWNLOAD_CACHE`` in the ``dependency_script`` command (thanks to `@peterjc`_). c2204b3_ * Fixes for the Homebrew recipe updater. c262b6d_ --------------------- 0.29.1 (2016-08-19) --------------------- * Improved handling of Python 2.7 specific dependencies. --------------------- 0.29.0 (2016-08-19) --------------------- * Look for sha256sum checksums during shed_lint (thanks to `@peterjc`_). `Pull Request 539`_ * An assortment fixes and enhancements to the ``dependency_script`` command (thanks to `@peterjc`_). `Pull Request 541`_, `Pull Request 545`_ * Fix shed_build to respect exclude: in .shed.yml (thanks to `@nsoranzo`_). `Pull Request 540`_ * Fix linting of tool URLs (thanks to `@nsoranzo`_). `Pull Request 546`_ --------------------- 0.28.0 (2016-08-17) --------------------- * Fixes for bioblend_ v0.8.0 (thanks to `@nsoranzo`_). 9fdf490_ * Enable shed repo type update (thanks to `@nsoranzo`_). 3ceaa40_ * Create suite repositories with repository_suite_definition type by default (thanks to `@nsoranzo`_). 057f4f0_ * Include ``shed_lint`` in script run by ``travis_init`` (thanks to `@peterjc`_). `Pull Request 528`_ * Minor polish to the ``travis_init`` command (thanks to `@peterjc`_). `Pull Request 512`_ * Update pip_ and setuptools on TravisCI; fix travis_init (thanks to `@peterjc`_). `Pull Request 521`_ * Shorten command one line descriptions for main help (thanks to `@peterjc`_). `Pull Request 510`_ * Use ``planemo test --no_cache_galaxy`` under TravisCI (thanks to `@peterjc`_). `Pull Request 513`_ * Improve and fix docs ahead of GCC 2016 (thanks to `@martenson`_). `Pull Request 498`_, 725b232_ * Add description of ``expect_num_outputs`` to planemo FAQ. a066afb_ * Revise planemo tools docs to be more explicit about collection identifiers. a811e65_ * Add more docs on existing dynamic tool output features. `Pull Request 526`_ * Fix serve command doc (thanks to `@nsoranzo`_). 8c088c6_ * Fix `make lint-readme` (RST link errors) (thanks to `@peterjc`_). `Pull Request 525`_ * Add union bedgraph example to project templates (for GCC demo example). d53bcd6_ * Add Flow Cytometry Analysis, Data Export, and Constructive Solid Geometry as shed categories (thanks to `@bgruening`_, `@gregvonkuster`_, and `@nsoranzo`_). e890ab5_, 08bb354_, e2398fb_ * Remove duplicated attribute in docs/writing/bwa-mem_v5.xml (thanks to Paul Stewart `@pstew`_). `Pull Request 507`_ --------------------- 0.27.0 (2016-06-22) --------------------- * Use ephemeris to handle syncing shed tools for workflow actions. 1c6cfbb_ * More planemo testing enhancements for testing artifacts that aren't Galaxy tools. `Pull Request 491`_ * Implement ``docker_galaxy`` engine type. eb039c0_, `Issue 15`_ * Enhance profiles to be Dockerized Galaxy-aware. `Pull Request 488`_ * Add linter for DOI type citation - thanks to `@mvdbeek`_. `Pull Request 484`_ --------------------- 0.26.0 (2016-05-20) --------------------- * Implement ``Engine`` and ``Runnable`` abstractions - Planemo now has beta support for testing Galaxy workflows and CWL_ tools with Galaxy and any CWL_ artifact with cwltool_. `Pull Request 454`_, 7be1bf5_ * Fix missing command_line in test output json. e38c436_ * More explicit Galaxy ``job_conf.xml`` handling, fixes bugs caused by ``galaxy_root`` having existing and incompatible ``job_conf.xml`` files and makes it possible to specify defaults with fixed server name. c4dfd55_ * Introduce profile commands (``profile_create``, ``profile_delete``, and ``profile_list``) and profile improvements (automatic postgres database creation support). `Pull Request 480`_, a87899b_ * Rework Galaxy test reporting to use structured data instead of XUnit data. 4d29bf1_ * Refactor Galaxy configuration toward support for running Galaxy in docker-galaxy-stable. `Pull Request 479`_ --------------------- 0.25.1 (2016-05-11) --------------------- * Tweak dependencies to try to fix cwltool_ related issues - such as `Issue 475`_. --------------------- 0.25.0 (2016-05-11) --------------------- * Implement Galaxy "profiles" - the ability to configure perisistent, named environments for ``serve`` and ``test``. 5d08b67_ * Greatly improved ``serve`` command - make ``test-data`` available as an FTP folder, (on 16.07) automatically log in an admin user, and many more options (such as those required for "profiles" and a ``--daemon`` mode). * Two fixes to ensure more consistent, dependable ``test`` output. `Pull Request 472`_, f3c6917_ * Add code and documentation for linting (``lint``) and building (``tool_init``) CWL_ tools. a4e6958_, b0b867e_, 4cd571c_ * If needed for Conda_ workaround, shorten ``config_directory`` path (thanks to `@mvdbeek`_). efc5f30_ * Fix ``--no_cache_galaxy`` option (thanks to Gildas Le Corguillé). d8f2038_ * Target draft 3 of CWL_ instead of draft 2. 775bf49_ * Fix ``cwltool`` dependency version - upstream changes broke compatibility. `65b999d`_ * Add documentation section and slides about recent Galaxy tool framework changes (with fix from `@remimarenco`_). 069e7ba_ * Add IUC standards to Planemo docs. 2ae2b49_ * Improve collection-related contents in documentation (thanks in part to `@martenson`_). fea51fc_, 13a5ae7_ * Add documentation on ``GALAXY_SLOTS`` and running planemo on a cluster. 45135ff_, e0acf91_ * Revise command-line handling framework for consistency and extension - allow extra options to be configured as defaults ``~/.planemo.yml`` including ``--job_config_file`` and Conda_ configuration options. e769118_, 26e378e_ * Fix ``tool_init`` commans options typos (thanks to Nitesh Turaga). 826d371_ * Refactor galaxy-related modules into submodules of a new ``planemo.galaxy`` package. 8e96864_ * Fix error message typo (thanks to `@blankenberg`_). b1c8f1d_ * Update documentation for recent command additions. 3f4ab44_ * Rename option ``--galaxy_sqlite_database`` option to ``--galaxy_database_seed`` and fix it so it actually works. f7554d1_ * Add ``--extra_tools`` option to ``serve`` command. 02a08a0_ * Update project testing to include linting documentation (``docs/``), Python import order, and docstrings. a13a120_, 6e1e726_, 95d5cba_ --------------------- 0.24.2 (2016-04-25) --------------------- * Revert "check ``.shed.yml`` owner against credentials during shed creation", test was incorrect and preventing uploads. `Pull Request 425`_, `Issue 246`_ --------------------- 0.24.1 (2016-04-08) --------------------- * Fix test summary report. `Pull Request 429`_ * Improve error reporting when running ``shed_test``. ce8e1be_ * Improved code comments and tests for shed related functionality. 89674cb_ * Rev `galaxy-lib`_ dependency to 16.4.1 to fix wget usage in newer versions of wget. d76b489_ --------------------- 0.24.0 (2016-03-29) --------------------- * Drop support for Python 2.6. 93b7bda_ * A variety of fixes for ``shed_update``. `Pull Request 428`_, `Issue 416`_ * Fix reporting of metadata updates for invalid shed updates. `Pull Request 426`_, `Issue 420`_ * Check ``.shed.yml`` owner against credentials during shed creation. `Pull Request 425`_, `Issue 246`_ * Fix logic error if there is a problem with ``shed_create``. 358a42c_ * Tool documentation improvements. 0298510_, a58a3b8_ --------------------- 0.23.0 (2016-02-15) --------------------- * Fix duplicated attributes with Conda_ resolver (thanks to Björn Grüning). `Pull Request 403`_ * Upgrade to latest version of `galaxy-lib`_ for more linting. * Attempt to better handle conditional dependency on cwltool. --------------------- 0.22.2 (2016-01-14) --------------------- * Fixed bug targetting forthcoming release of Galaxy 16.01. --------------------- 0.22.1 (2016-01-14) --------------------- * Fixed problem with PyPI_ build artifacts due to submodule's not being initialized during previous release. --------------------- 0.22.0 (2016-01-13) --------------------- * Add ``--skip_venv`` to support running Galaxy 16.01 inside of conda environments. 9f3957d_ * Implement conda support. f99f6c1_, ad3b2f0_, 5e0b6d1_ * Update LICENSE for Planemo to match Galaxy. 15d33c7_ * Depend on new `galaxy-lib`_ on PyPI_ instead of previous hacks.... `Pull Request 394`_ * Fix egg caching against master/15.10. 6d0f502_ * Fix bug causing shed publishing of ``.svn`` directories. `Issue 391`_ * Bug fixes for Conda_ support thanks to `@bgruening`_. 63e456c_ * Fix document issues thanks to `@einon`_. `Pull Request 390`_ * Improve client for shed publishing to support newer shed backend being developed by `@hexylena`_. `Pull Request 394`_ * Tool Shed ``repo_id`` change, `@hexylena`_. `Pull Request 398`_ * Various other small changes to testing, project structure, and Python 3 support. --------------------- 0.21.1 (2015-11-29) --------------------- * Fix serious regression to ``test`` command. 94097c7_ * Small fixes to release process. 4e1377c_, 94645ed_ --------------------- 0.21.0 (2015-11-29) --------------------- * If ``virtualenv`` not on ``PATH``, have Planemo create one for Galaxy. 5b97f2e_ * Add documentation section on testing tools installed in an existing Galaxy instance. 1927168_ * When creating a virtualenv for Galaxy, prefer Python 2.7. e0577e7_ * Documentation fixes and improvements thanks to `@martenson`_. 0f8cb10_, 01584c5_, b757791_ * Specify a minimum ``six`` version requirement. 1c7ee5b_ * Add script to test a planemo as a wheel. 6514ff5_, `Issue 184`_ * Fix empty macro loading. `Issue 362`_ * Fix an issue when you run ``shed_diff --shed_target local`` thanks to Gwendoline Andres and Gildas Le Corguillé at ABiMS Roscoff. `Pull Request 375`_ * Fix ``shed_diff`` printing to stdout if ``-o`` isn't specified. f3394e7_ * Small ``shed_diff`` improvements to XML diffing and XUnit reporting. af7448c_, 83e227a_ * More logging of ``shed_diff`` results if ``--verbose`` flagged. 9427b47_ * Add ``test_report`` command for rebuilding reports from structured JSON. 99ee51a_ * Fix option bug with Click 6.0 thanks to `@bgruening`_. 2a7c792_ * Improved error messages for test commands. fdce74c_ * Various fixes for Python 3. 2f66fc3_, 7572e99_, 8eda729_, 764ce01_ * Use newer travis container infrastructure for testing. 6d81a94_ * Test case fixes. 98fdc8c_, 0e4f70a_ --------------------- 0.20.0 (2015-11-11) --------------------- * More complete I/O capturing for XUnit. 6409449_ * Check for select parameter without options when linting tools. `Issue 373`_ * Add ``--cwl_engine`` argument to ``cwl_run`` command. dd94ddc_ * Fixes for select parameter linting. 8b31850_ * Fix to demultiplexing repositories after tool uploads. `Issue 361`_ * Fix to update planemo for Galaxy wheels. 25ef0d5_ * Various fixes for Python 2.6 and Python 3. c1713d2_, 916f610_, c444855_ --------------------- 0.19.0 (2015-11-03) --------------------- * Initial implementation of ``cwl_run`` command that runs a CWL tool and job file through Galaxy. 49c5c1e_ * Add ``--cwl`` flag to ``serve`` to experimentally serve CWL tools in Galaxy. `Pull Request 339`_ * Implement highly experimental ``cwl_script`` command to convert a CWL job to a bash script. 508dce7_ * Add name to all XUnit reports (thanks to `@hexylena`_). `Pull Request 343`_ * Capture stdout and stderr for ``shed_diff`` and ``shed_update`` XUnit reports. `Pull Request 344`_ * More tool linting (conditionals) thanks to `@hexylena`_. `Pull Request 350`_ * UTF-8 fixes when handling XUnit reports. `Pull Request 345`_ * Add `Epigenetics` as Tool Shed category. `Pull Request 351`_ * Merge changes to common modules shared between Galaxy, Planemo, and Pulsar (thanks to `@natefoo`_). `Pull Request 356`_ * Add ``--cite_url`` to ``tool_init``. fdb1b51_ * ``tool_init`` bug fix. f854138_ * Fix `setup.py`_ for cwltool and bioblend_ changes. 1a157d4_ * Add option to specify template sqlite database locally. c23569f_ * Add example IPython notebooks to docs. c8640b6_ --------------------- 0.18.1 (2015-10-22) --------------------- * Fix issue with test reporting not being populated. 19900a6_ --------------------- 0.18.0 (2015-10-20) --------------------- * Improvements to ``docker_shell`` usability (thanks to `@kellrott`_). `Pull Request 334`_ * Add docker pull attempt when missing Dockerfile (thanks to `@kellrott`_). `Pull Request 333`_ * Fix bug inferring which files are tool files (thanks to `@hexylena`_). `Pull Request 335`_, `Issue 313`_ * Initial work toward automating brew recipe update. 4d6f7d9_, `Issue 329`_ --------------------- 0.17.0 (2015-10-19) --------------------- * Implement basic XUnit report option for ``shed_update`` (thanks to `@martenson`_). `Pull Request 322`_ * Fix issues with producing test outputs. 572e754_ * Xunit reporting improvements - refactoring, times, diff output (thanks to `@hexylena`_). `Pull Request 330`_ * Implement project governance policy and update developer code of conduct to match that of the Galaxy project. `Pull Request 316`_ * Update filters for account for new ``.txt`` and ``.md`` test outputs (thanks to `@hexylena`_). `Pull Request 327`_ * Add verbose logging to galaxy test output handling problems. 5d7db92_ * Flake8 fixes (thanks to `@martenson`_). 949a36d_ * Remove uses of deprecated ``mktemp`` Python standard library function (thanks to `@hexylena`_). `Pull Request 330`_ --------------------- 0.16.0 (2015-10-07) --------------------- * Adding new command ``dependency_script`` to convert Tool Shed dependencies into shell scripts - thanks to `@peterjc`_. `Pull Request 310`_, f798c7e_, `Issue 303`_ * Implement profiles in sheds section of the ``~/.planemo.yml``. `Pull Request 314`_ --------------------- 0.15.0 (2015-10-01) --------------------- * Template framework for reporting including new markdown and plain text reporting options for testing - thanks to `@hexylena`_. `Pull Request 304`_ * XUnit style reporting for ``shed_diff`` command - thanks to `@hexylena`_. `Pull Request 305`_ * Add new ``shed_build`` command for building repository tarballs - thanks to `@kellrott`_. `Pull Request 297`_ * Fix exit code handling for ``lint`` commands - thanks to `@mvdbeek`_. `Pull Request 292`_ * Improved documentation for ``serve`` command - thanks to `@lparsons`_. `Pull Request 312`_ * Tiny backward compatible Python 3 tweaks for `Tool Factory`_ - thanks to `@peterjc`_. dad2d9d_ * Fixed detection of virtual environment in ``Makefile`` - thanks to `@lparsons`_. `Pull Request 311`_ * Updates to Galaxy XSD - thanks to `@mr-c`_. `Pull Request 309`_ * Allow reading shed key option from an environment variable. `Pull Request 307`_ * Allow specifying host to serve Galaxy using ``-host`` - thanks in part to `@chambm`_. `Pull Request 301`_ * Allow specifying defaults for ``-host`` and ``--port`` in ``~/.planemo.yml``. `Pull Request 301`_ * Improve ``~/.planemo.yml`` sample comments - thanks to `@martenson`_. `Pull Request 287`_ * Update tool shed categories - thanks to `@bgruening`_. `Pull Request 285`_ * Improved output readibility for ``diff`` command - thanks to `@martenson`_. `Pull Request 284`_ --------------------- 0.14.0 (2015-08-06) --------------------- * Allow ``-t`` as shorthand for ``--shed_target`` (thanks to Peter Cock). `Pull Request 278`_ * Fix ``tool_init`` command to use ``from_work_dir`` only if file in command (thanks to bug report and initial fix outline by Gildas Le Corguillé). `Pull Request 277`_ * Various documentation fixes (thanks in part to Peter Cock and Daniel Blankenberg). `Pull Request 256`_, `Pull Request 253`_, `Pull Request 254`_, `Pull Request 255`_, `Pull Request 251`_, `Issue 272`_ --------------------- 0.13.2 (2015-07-06) --------------------- * Fix project_init for missing files. cb5b906_ * Various documentation improvements. --------------------- 0.13.1 (2015-07-01) --------------------- * Fix for ``shed_init`` producing non-standard type hints. `Issue 243`_, f0610d7_ * Fix tool linting for parameters that define an ``argument`` but not a ``name``. `Issue 245`_, aad1eed_ * Many doc updates including a tutorial for developing tools in a test-driven fashion and instructions for using the planemo appliance through Kitematic (with Kitematic screenshots from E. Rasche). --------------------- 0.13.0 (2015-06-28) --------------------- * If planemo cannot find a Galaxy root, it will now automatically fetch one (specifing ``--galaxy_install`` will still force a fetch). `Pull Request 235`_ * `Docuementation <http://planemo.readthedocs.org/en/latest/appliance.html>`__ has been updated to reflect new and vastly improved Docker and Vagrant virtual appliances are now available, as well as a new VirtualBox OVA variant. * Update linting for new tool XML features (including ``detect_errors`` and output collections). `Issue 233`_, 334f2d4_ * Fix ``shed_test`` help text. `Issue 223`_ * Fix code typo (thanks to Nicola Soranzo). `Pull Request 230`_ * Improvements to algorithm used to guess if an XML file is a tool XML file. `Issue 231`_ * Fix configuration file handling bug. `Issue 240`_ --------------------- 0.12.2 (2015-05-23) --------------------- * Fix ``shed_test`` and ``shed_serve`` for test and local tool sheds. f3cafaa_ --------------------- 0.12.1 (2015-05-21) --------------------- * Fix to ensure the tab completion script is in the Python source tarball (required for setting up tab-completion for Homebrew). 6b4e7a6_ --------------------- 0.12.0 (2015-05-21) --------------------- * Implement a ``--failed`` flag for the ``test`` command to rerun previously faied tests. `Pull Request 210`_ * Implement ``shed_update`` to upload contents and update repository metadata. `Pull Request 216`_ * Implement ``shed_test`` and ``shed_serve`` commands to test and view published artifacts in the Tool Shed. `Pull Request 213`_, `Issue 176`_ * Add shell tab-completion script. 37dcc07_ * Many more commands allow specifing multiple tool and/or repository targets. `Issue 150`_ * Add -m as alias for --message in planemo shed_upload (thanks to Peter Cock). `Pull Request 200`_ * Add ``--ensure_metadata`` option to ``shed_lint`` to ensure ``.shed.yml`` files contain many repository. `Pull Request 215`_ * More developer documentation, additional ``make`` targets including ones for setting up git pre-commit hooks. cc8abb6_, `Issue 209`_ * Small README improvement (thanks to Martin Čech) b53006d_ * Fixes for shed operation error handling (thanks to Martin Čech). `Pull Request 203`_, `Pull Request 206`_ * Fix for "smart" ``shed_diff`` not in the repository root directory (thanks to Peter Cock). `Pull Request 207`_, `Issue 205`_ * Recursive ``shed_diff`` with directories not yet in Tool Shed. `Pull Request 208`_ * Improve error handling and reporting for problematic ``--shed_target`` values. `Issue 217`_ * Fix typos in lint messages. `Issue 211`_ --------------------- 0.11.1 (2015-05-12) --------------------- * Fix default behavior for ``planemo lint`` to use current directory if explicit paths are not supplied. 1e3668a_ --------------------- 0.11.0 (2015-05-12) --------------------- * More compact syntax for defining multiple custom inclusions in ``.shed.yml`` files - thanks to Peter Cock. `Issue 180`_, `Pull Request 185`_, `Pull Request 196`_ * Prevent ambigous destinations when defining custom inclusions in ``.shed.yml``- thanks to Peter Cock. `Pull Request 186`_ * ``lint`` now warns if tool ids contain whitespace. `Pull Request 190`_ * Handle empty tar-balls gracefully on older Python versions - thanks to Peter Cock. `Pull Request 187`_ * Tweak quoting in ``cp`` command - thanks to Peter Cock. 6bcf699_ * Fix regression causing testing to no longer produce "pretty" test results under certain circumstances. `Issue 188`_ * Fix for recursive ``shed_diff`` folder naming. `Issue 192`_ * Fix output definitions to ``tool_init`` command. `Issue 189`_ --------------------- 0.10.0 (2015-05-06) --------------------- * Extend ``shed_lint`` to check for valid actions in tool_dependencies.xml files. 8117e03_ * Extend ``shed_lint`` to check for required files based on repository type. `Issue 156`_ * Ignore common editor backup files during ``shed_upload``. `Issue 179`_ * Fix missing file when installing from source via PyPI_. `Issue 181`_ * Fix ``lint`` to verify ``data`` inputs specify a ``format`` attribute. 8117e03_ * Docstring fix thanks to `@peterjc`_. fe7ad46_ --------------------- 0.9.0 (2015-05-03) --------------------- * Add new logo to the README thanks to `@petrkadlec`_ from `puradesign.cz <http://puradesign.cz/en>`__ and `@carlfeberhard`_ from the Galaxy Project. `Issue 108`_ * Implement smarter ``shed_diff`` command - it now produces a meaningful exit codes and doesn't report differences if these correspond to attributes that will be automatically populated by the Tool Shed. `Issue 167`_ * Use new smarter ``shed_diff`` code to implement a new ``--check_diff`` option for ``shed_upload`` - to check for meaningful differences before updating repositories. `Issue 168`_ * Record git commit hash during ``shed_upload`` if the ``.shed.yml`` is located in a git repository. `Issue 170`_ * Allow ``shed_`` operations to operate on git URLs directly. `Issue 169`_ * Fail if missing file inclusion statements encountered during ``.shed.yml`` repository resolution - bug reported by `@peterjc`_. `Issue 158`_ * Improved exception handling for tool shed operations including new ``--fail_fast`` command-line option. * `Issue 114`_, `Pull Request 173`_ * Implement more validation when using the ``shed_init`` command. 1cd0e2d_ * Add ``-r/--recursive`` option to ``shed_download`` and ``shed_diff`` commands and allow these commands to work with ``.shed.yml`` files defining multipe repositories. 40a1f57_ * Add ``--port`` option to the ``serve`` and ``tool_factory`` commands. 15804be_ * Fix problem introduced with `setup.py`_ during the 0.9.0 development cycle - thanks to `@peterjc`_. `Pull Request 171`_ * Fix clone bug introduced during 0.9.0 development cycle - thanks to `@bgruening`_. `Pull Request 175`_ --------------------- 0.8.4 (2015-04-30) --------------------- * Fix for Travis CI testing picking up invalid tests (reported by `@takadonet`_). `Issue 161`_ * Fix tar ordering for consistency (always sort by name) - thanks to `@peterjc`_. `Pull Request 164`_, `Issue 159`_ * Fix exception handling related to tool shed operations - thanks to `@peterjc`_. `Pull Request 155`_, b86fe1f_ --------------------- 0.8.3 (2015-04-29) --------------------- * Fix bug where ``shed_lint`` was not respecting the ``-r/--recursive`` flag. 9ff0d2d_ * Fix bug where planemo was producing tar files incompatible with the Tool Shed for package and suite repositories. a2ee135_ --------------------- 0.8.2 (2015-04-29) --------------------- * Fix bug with ``config_init`` command thanks to `@bgruening`_. `Pull Request 151`_ * Fix unnessecary ``lint`` warning about ``parallelism`` tag reported by `@peterjc`_. 9bf1eab_ --------------------- 0.8.1 (2015-04-28) --------------------- * Fixes for the source distribution to allow installation of 0.8.0 via Homebrew. --------------------- 0.8.0 (2015-04-27) --------------------- * Implement the new ``shed_lint`` command that verifies various aspects of tool shed repositories - including XSD_ validation of ``repository_dependencies.xml`` and ``tool_dependencies.xml`` files, best practices for README files, and the contents of ``.shed.yml`` files. This requires the lxml_ library to be available to Planemo or the application xmllint_ to be on its ``PATH``. `Pull Request 130`_ `Issue 89`_ `Issue 91`_ 912df02_ d26929e_ 36ac6d8_ * Option to enable experimental XSD_ based validation of tools when ``lint`` is executed with the new ``--xsd`` flag. This validation occurs against the unofficial `Galaxy Tool XSD project <https://github.com/JeanFred/Galaxy-XSD>`__ maintained by `@JeanFred`_. This requires the lxml_ library to be available to Planemo or the application xmllint_ to be on its ``PATH``. `Pull Request 130`_ 912df02_ * Allow skipping specific linters when using the ``lint`` command using the new ``--skip`` option. 26e3cdb_ * Implement sophisticated options in ``.shed.yml`` to map a directory to many, custom Tool Shed repositories during shed operaitons such ``shed_upload`` including automatically mapping tools to their own directories and automatically building suites repositories. `Pull Request 143`_ * Make ``shed_upload`` more intelligent when building tar files so that package and suite repositories may have README files in source control and they will just be filtered out during upload. 53edd99_ * Implement a new ``shed_init`` command that will help bootstrap ``.shed.yml`` files in the specified directory. cc1a447_ * Extend ``shed_init`` to automatically build a ``repository_rependencies.xml`` file corresponding to a Galaxy workflow (``.ga`` file). `Issue 118`_ 988de1d_ * In addition to a single file or directory, allow ``lint`` to be passed multiple files. 343902d_ `Issue 139`_ * Add ``-r/--recursive`` option to ``shed_create`` and ``lint`` commands. 63cd431_ 01f2af9_ * Improved output formatting and option to write diffs to a file for the ``shed_diff`` command. 965511d_ * Fix lint problem when using new Galaxy testing features such as expecting job failures and verifing job output. `Issue 138`_ * Fix typo in ``test`` help thanks to first time contributor `@pvanheus`_. `Pull Request 129`_ 1982076_ * Fix NPE on empty ``help`` element when linting tools. `Issue 124`_ * Fix ``lint`` warnings when ``configfiles`` are defined in a tool. 1a85493_ * Fix for empty ``.shed.yml`` files. b7d9e96_ * Fix the ``test`` command for newer versions of nose_. 33294d2_ * Update help content and documentation to be clear ``normalize`` should not be used to update the contents of tool files at this time. 08de8de_ * Warn on unknown ``command`` attributes when linting tools (anything but ``interpreter``). 4f61025_ * Various design, documentation (including new documentation on Tool Shed `publishing <http://planemo.readthedocs.org/en/latest/publishing.html>`__), and testing related improvements (test coverage has risen from 65% to over 80% during this release cycle). --------------------- 0.7.0 (2015-04-13) --------------------- * Implement `shed_create` command to create Tool Shed repositories from ``.shed.yml`` files (thanks to E. Rasche). `Pull Request 101`_ * Allow automatic creation of missing repositories during ``shed_upload`` with the new ``--force_repository_creation`` flag (thanks to E. Rasche). `Pull Request 102`_ * Allow specifying files to exclude in ``.shed.yml`` when creating tar files for ``shed_upload`` (thanks to Björn Grüning). `Pull Request 99`_ * Resolve symbolic links when building Tool Shed tar files with ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 104`_ * Add a `Contributor Code of Conduct <https://planemo.readthedocs.org/en/latest/conduct.html>`__. `Pull Request 113`_ * Omit ``tool_test_output.json`` from Tool Shed tar file created with ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 111`_ * Update required version of bioblend_ to ``0.5.3``. Fixed `Issue 88`_. * Initial work on implementing tests cases for Tool Shed functionality. 182fe57_ * Fix incorrect link in HTML test report (thanks to Martin Čech). 4c71299_ * Download Galaxy from the new, official Github repository. 7c69bf6_ * Update travis_test to install stable planemo from PyPI_. 39fedd2_ * Enable caching on ``--install_galaxy`` by default (disable with ``--no_cache_galaxy``). d755fe7_ --------------------- 0.6.0 (2015-03-16) --------------------- * Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc... * Fix ``tool_init`` to quote file names (thanks to Peter Cock). `Pull Request 98`_. * Allow ignoring file patterns in ``.shed.yml`` (thanks to Björn Grüning). `Pull Request 99`_ * Add ``--macros`` flag to ``tool_init`` command to generate a macro file as part of tool generation. ec6e30f_ * Add linting of tag order for tool XML files. 4823c5e_ * Add linting of ``stdio`` tags in tool XML files. 8207026_ * More tests, much higher test coverage. 0bd4ff0_ --------------------- 0.5.0 (2015-02-22) --------------------- * Implement ``--version`` option. `Issue 78`_ * Implement ``--no_cleanup`` option for ``test`` and ``serve`` commands to persist temp files. 2e41e0a_ * Fix bug that left temp files undeleted. `Issue 80`_ * More improvements to release process. fba3874_ --------------------- 0.4.2 (2015-02-21) --------------------- * Fix `setup.py`_ for installing non-Python data from PyPI_ (required newer for ``tool_factory`` command and reStructuredText linting). Thanks to Damion Dooley for the bug report. `Issue 83`_ --------------------- 0.4.1 (2015-02-16) --------------------- * Fix README.rst so it renders properly on PyPI_. --------------------- 0.4.0 (2015-02-16) --------------------- * Implement ``tool_init`` command for bootstrapping creation of new tools (with `tutorial <http://planemo.readthedocs.org/en/latest/writing.html>`_.) 78f8274_ * Implement ``normalize`` command for reorganizing tool XML and macro debugging. e8c1d45_ * Implement ``tool_factory`` command to spin up Galaxy pre-configured the `Tool Factory`_. 9e746b4_ * Added basic linting of ``command`` blocks. b8d90ab_ * Improved linting of ``help`` blocks, including verifying valid `reStructuredText`. 411a8da_ * Fix bug related to ``serve`` command not killing Galaxy properly when complete. 53a6766_ * Have ``serve`` command display tools at the top level instead of in shallow sections. badc25f_ * Add additional dependencies to ``setup.py`` more functionality works out of the box. 85b9614_ * Fix terrible error message related to bioblend_ being unavailable. `Issue 70`_ * Various smaller documentation and project structure improvements. --------------------- 0.3.1 (2015-02-15) --------------------- * Fixes to get PyPI_ workflow working properly. --------------------- 0.3.0 (2015-02-13) --------------------- * Add option (``-r``) to the ``shed_upload`` command to recursively upload subdirectories (thanks to E. Rasche). `Pull Request 68`_ * Fix diff formatting in test reports (thanks to E. Rasche). `Pull Request 63`_ * Grab updated test database to speed up testing (thanks to approach from E. Rasche and Dannon Baker). `Issue 61`_, dff4f33_ * Fix test data command-line argument name (was ``test-data`` now it is ``test_data``). 834bfb2_ * Use ``tool_data_table_conf.xml.sample`` file if ``tool_data_table_conf.xml.test`` is unavailable. Should allow some new tools to be tested without modifying Galaxy's global ``tool_data_table_conf.xml`` file. ac4f828_ --------------------- 0.2.0 (2015-01-13) --------------------- * Improvements to way Planemo loads its own copy of Galaxy modules to prevent various conflicts when launching Galaxy from Planemo. `Pull Request 56`_ * Allow setting various test output options in ``~/.planemo.yml`` and disabling JSON output. 21bb463_ * More experimental Brew and Tool Shed options that should not be considered part of Planemo's stable API. See bit.ly/gxbrew1 for more details. * Fix ``project_init`` for BSD tar (thanks to Nitesh Turaga for the bug report.) a4110a8_ * Documentation fixes for tool linting command (thanks to Nicola Soranzo). `Pull Request 51`_ --------------------- 0.1.0 (2014-12-16) --------------------- * Moved repository URL to https://github.com/galaxyproject/planemo. * Support for publishing to the Tool Shed. `Pull Request 6`_ * Support for producing diffs (``shed_diff``) between local repositories and the Tool Shed (based on scripts by Peter Cock). `Pull Request 33`_ * Use tool's local test data when available - add option for configuring ``test-data`` target. `Pull Request 1`_ * Support for testing tool features dependent on cached data. 44de95c_ * Support for generating XUnit tool test reports. 82e8b1f_ * Prettier HTML reports for tool tests. 05cc9f4_ * Implement ``share_test`` command for embedding test result links in pull requests. `Pull Request 40`_ * Fix for properly resolving links during Tool Shed publishing (thanks to Dave Bouvier). `Pull Request 29`_ * Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061_ * Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan Blankenberg). a2c13e4_ * Automate more of Travis CI testing so the scripts added to tool repository can be smaller. 20a8680_ * Documentation fixes for Travis CI (thanks to Peter Cock). `Pull Request 22`_, `Pull Request 23`_ * Various documentation fixes (thanks to Martin Čech). 36f7cb1_, b9232e5_ * Various smaller fixes for Docker support, tool linting, and documentation. --------------------- 0.0.1 (2014-10-04) --------------------- * Initial work on the project - commands for testing, linting, serving Galaxy tools - and more experimental features involving Docker and Homebrew. 7d07782_ .. github_links .. _Pull Request 991: https://github.com/galaxyproject/planemo/pull/991 .. _Pull Request 988: https://github.com/galaxyproject/planemo/pull/988 .. _Pull Request 989: https://github.com/galaxyproject/planemo/pull/989 .. _Pull Request 985: https://github.com/galaxyproject/planemo/pull/985 .. _Pull Request 984: https://github.com/galaxyproject/planemo/pull/984 .. _Pull Request 986: https://github.com/galaxyproject/planemo/pull/986 .. _Pull Request 983: https://github.com/galaxyproject/planemo/pull/983 .. _Pull Request 982: https://github.com/galaxyproject/planemo/pull/982 .. _Pull Request 980: https://github.com/galaxyproject/planemo/pull/980 .. _Pull Request 978: https://github.com/galaxyproject/planemo/pull/978 .. _Pull Request 979: https://github.com/galaxyproject/planemo/pull/979 .. _Pull Request 977: https://github.com/galaxyproject/planemo/pull/977 .. _Pull Request 975: https://github.com/galaxyproject/planemo/pull/975 .. _Pull Request 974: https://github.com/galaxyproject/planemo/pull/974 .. _Pull Request 976: https://github.com/galaxyproject/planemo/pull/976 .. _Pull Request 972: https://github.com/galaxyproject/planemo/pull/972 .. _Pull Request 973: https://github.com/galaxyproject/planemo/pull/973 .. _Pull Request 971: https://github.com/galaxyproject/planemo/pull/971 .. _Pull Request 970: https://github.com/galaxyproject/planemo/pull/970 .. _Pull Request 968: https://github.com/galaxyproject/planemo/pull/968 .. _1ab8530: https://github.com/galaxyproject/planemo/commit/1ab8530 .. _Pull Request 966: https://github.com/galaxyproject/planemo/pull/966 .. _Pull Request 964: https://github.com/galaxyproject/planemo/pull/964 .. _Pull Request 963: https://github.com/galaxyproject/planemo/pull/963 .. _Pull Request 959: https://github.com/galaxyproject/planemo/pull/959 .. _Pull Request 958: https://github.com/galaxyproject/planemo/pull/958 .. _Pull Request 950: https://github.com/galaxyproject/planemo/pull/950 .. _Pull Request 944: https://github.com/galaxyproject/planemo/pull/944 .. _Pull Request 926: https://github.com/galaxyproject/planemo/pull/926 .. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937 .. _Pull Request 938: https://github.com/galaxyproject/planemo/pull/938 .. _Pull Request 943: https://github.com/galaxyproject/planemo/pull/943 .. _Pull Request 940: https://github.com/galaxyproject/planemo/pull/940 .. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937 .. _Pull Request 935: https://github.com/galaxyproject/planemo/pull/935 .. _Pull Request 931: https://github.com/galaxyproject/planemo/pull/931 .. _Pull Request 930: https://github.com/galaxyproject/planemo/pull/930 .. _Pull Request 913: https://github.com/galaxyproject/planemo/pull/913 .. _Pull Request 917: https://github.com/galaxyproject/planemo/pull/917 .. _Pull Request 921: https://github.com/galaxyproject/planemo/pull/921 .. _Pull Request 918: https://github.com/galaxyproject/planemo/pull/918 .. _Pull Request 924: https://github.com/galaxyproject/planemo/pull/924 .. _Pull Request 925: https://github.com/galaxyproject/planemo/pull/925 .. _Pull Request 912: https://github.com/galaxyproject/planemo/pull/912 .. _Pull Request 915: https://github.com/galaxyproject/planemo/pull/915 .. _Pull Request 914: https://github.com/galaxyproject/planemo/pull/914 .. _07dc6e0: https://github.com/galaxyproject/planemo/commit/07dc6e0 .. _Pull Request 910: https://github.com/galaxyproject/planemo/pull/910 .. _Pull Request 909: https://github.com/galaxyproject/planemo/pull/909 .. _Pull Request 908: https://github.com/galaxyproject/planemo/pull/908 .. _Pull Request 907: https://github.com/galaxyproject/planemo/pull/907 .. _Pull Request 906: https://github.com/galaxyproject/planemo/pull/906 .. _Pull Request 902: https://github.com/galaxyproject/planemo/pull/902 .. _Pull Request 895: https://github.com/galaxyproject/planemo/pull/895 .. _Issue 845: https://github.com/galaxyproject/planemo/issues/845 .. _Issue 898: https://github.com/galaxyproject/planemo/issues/898 .. _Pull Request 899: https://github.com/galaxyproject/planemo/pull/899 .. _Pull Request 896: https://github.com/galaxyproject/planemo/pull/896 .. _Pull Request 894: https://github.com/galaxyproject/planemo/pull/894 .. _Pull Request 876: https://github.com/galaxyproject/planemo/pull/876 .. _Pull Request 893: https://github.com/galaxyproject/planemo/pull/893 .. _Pull Request 892: https://github.com/galaxyproject/planemo/pull/892 .. _Pull Request 891: https://github.com/galaxyproject/planemo/pull/891 .. _Pull Request 889: https://github.com/galaxyproject/planemo/pull/889 .. _Pull Request 888: https://github.com/galaxyproject/planemo/pull/888 .. _Pull Request 887: https://github.com/galaxyproject/planemo/pull/887 .. _Pull Request 882: https://github.com/galaxyproject/planemo/pull/882 .. _Pull Request 877: https://github.com/galaxyproject/planemo/pull/877 .. _Pull Request 874: https://github.com/galaxyproject/planemo/pull/874 .. _Pull Request 871: https://github.com/galaxyproject/planemo/pull/871 .. _Pull Request 870: https://github.com/galaxyproject/planemo/pull/870 .. _Pull Request 864: https://github.com/galaxyproject/planemo/pull/864 .. _Pull Request 867: https://github.com/galaxyproject/planemo/pull/867 .. _Pull Request 868: https://github.com/galaxyproject/planemo/pull/868 .. _bad810a: https://github.com/galaxyproject/planemo/commit/bad810a .. _Pull Request 851: https://github.com/galaxyproject/planemo/pull/851 .. _Pull Request 856: https://github.com/galaxyproject/planemo/pull/856 .. _Pull Request 860: https://github.com/galaxyproject/planemo/pull/860 .. _Pull Request 866: https://github.com/galaxyproject/planemo/pull/866 .. _Pull Request 861: https://github.com/galaxyproject/planemo/pull/861 .. _324c776: https://github.com/galaxyproject/planemo/commit/324c776 .. _72d2ca7: https://github.com/galaxyproject/planemo/commit/72d2ca7 .. _b12b117: https://github.com/galaxyproject/planemo/commit/b12b117 .. _016b923: https://github.com/galaxyproject/planemo/commit/016b923 .. _2002b49: https://github.com/galaxyproject/planemo/commit/2002b49 .. _Pull Request 843: https://github.com/galaxyproject/planemo/pull/843 .. _Pull Request 842: https://github.com/galaxyproject/planemo/pull/842 .. _Pull Request 841: https://github.com/galaxyproject/planemo/pull/841 .. _Pull Request 847: https://github.com/galaxyproject/planemo/pull/847 .. _Pull Request 848: https://github.com/galaxyproject/planemo/pull/848 .. _Pull Request 849: https://github.com/galaxyproject/planemo/pull/849 .. _Pull Request 850: https://github.com/galaxyproject/planemo/pull/850 .. _Pull Request 836: https://github.com/galaxyproject/planemo/pull/836 .. _Pull Request 833: https://github.com/galaxyproject/planemo/pull/833 .. _Pull Request 837: https://github.com/galaxyproject/planemo/pull/837 .. _Pull Request 840: https://github.com/galaxyproject/planemo/pull/840 .. _Pull Request 838: https://github.com/galaxyproject/planemo/pull/838 .. _Pull Request 834: https://github.com/galaxyproject/planemo/pull/834 .. _Pull Request 835: https://github.com/galaxyproject/planemo/pull/835 .. _347c622: https://github.com/galaxyproject/planemo/commit/347c622 .. _Pull Request 832: https://github.com/galaxyproject/planemo/pull/832 .. _Pull Request 831: https://github.com/galaxyproject/planemo/pull/831 .. _Pull Request 830: https://github.com/galaxyproject/planemo/pull/830 .. _Pull Request 829: https://github.com/galaxyproject/planemo/pull/829 .. _Pull Request 828: https://github.com/galaxyproject/planemo/pull/828 .. _Pull Request 826: https://github.com/galaxyproject/planemo/pull/826 .. _Pull Request 827: https://github.com/galaxyproject/planemo/pull/827 .. _Pull Request 825: https://github.com/galaxyproject/planemo/pull/825 .. _Pull Request 820: https://github.com/galaxyproject/planemo/pull/820 .. _Pull Request 823: https://github.com/galaxyproject/planemo/pull/823 .. _Pull Request 822: https://github.com/galaxyproject/planemo/pull/822 .. _a5c72e3: https://github.com/galaxyproject/planemo/commit/a5c72e3 .. _Pull Request 818: https://github.com/galaxyproject/planemo/pull/818 .. _Pull Request 816: https://github.com/galaxyproject/planemo/pull/816 .. _Pull Request 817: https://github.com/galaxyproject/planemo/pull/817 .. _Pull Request 795: https://github.com/galaxyproject/planemo/pull/795 .. _Pull Request 799: https://github.com/galaxyproject/planemo/pull/799 .. _Pull Request 800: https://github.com/galaxyproject/planemo/pull/800 .. _Pull Request 781: https://github.com/galaxyproject/planemo/pull/781 .. _Pull Request 801: https://github.com/galaxyproject/planemo/pull/801 .. _Pull Request 802: https://github.com/galaxyproject/planemo/pull/802 .. _Pull Request 803: https://github.com/galaxyproject/planemo/pull/803 .. _Pull Request 805: https://github.com/galaxyproject/planemo/pull/805 .. _Pull Request 806: https://github.com/galaxyproject/planemo/pull/806 .. _Pull Request 809: https://github.com/galaxyproject/planemo/pull/809 .. _Pull Request 810: https://github.com/galaxyproject/planemo/pull/810 .. _Pull Request 787: https://github.com/galaxyproject/planemo/pull/787 .. _Pull Request 792: https://github.com/galaxyproject/planemo/pull/792 .. _dc443d6: https://github.com/galaxyproject/planemo/commit/dc443d6 .. _8cfe9e9: https://github.com/galaxyproject/planemo/commit/8cfe9e9 .. _41f7df1: https://github.com/galaxyproject/planemo/commit/41f7df1 .. _Pull Request 790: https://github.com/galaxyproject/planemo/pull/790 .. _Pull Request 776: https://github.com/galaxyproject/planemo/pull/776 .. _Pull Request 774: https://github.com/galaxyproject/planemo/pull/774 .. _Pull Request 773: https://github.com/galaxyproject/planemo/pull/773 .. _Pull Request 771: https://github.com/galaxyproject/planemo/pull/771 .. _Pull Request 770: https://github.com/galaxyproject/planemo/pull/770 .. _Pull Request 769: https://github.com/galaxyproject/planemo/pull/769 .. _Pull Request 768: https://github.com/galaxyproject/planemo/pull/768 .. _Pull Request 764: https://github.com/galaxyproject/planemo/pull/764 .. _Pull Request 761: https://github.com/galaxyproject/planemo/pull/761 .. _Pull Request 759: https://github.com/galaxyproject/planemo/pull/759 .. _Pull Request 756: https://github.com/galaxyproject/planemo/pull/756 .. _Pull Request 753: https://github.com/galaxyproject/planemo/pull/753 .. _Pull Request 747: https://github.com/galaxyproject/planemo/pull/747 .. _Pull Request 745: https://github.com/galaxyproject/planemo/pull/745 .. _Pull Request 743: https://github.com/galaxyproject/planemo/pull/743 .. _Pull Request 739: https://github.com/galaxyproject/planemo/pull/739 .. _Pull Request 738: https://github.com/galaxyproject/planemo/pull/738 .. _Pull Request 725: https://github.com/galaxyproject/planemo/pull/725 .. _Pull Request 727: https://github.com/galaxyproject/planemo/pull/727 .. _Pull Request 729: https://github.com/galaxyproject/planemo/pull/729 .. _Pull Request 730: https://github.com/galaxyproject/planemo/pull/730 .. _Pull Request 731: https://github.com/galaxyproject/planemo/pull/731 .. _Pull Request 733: https://github.com/galaxyproject/planemo/pull/733 .. _Pull Request 732: https://github.com/galaxyproject/planemo/pull/732 .. _Pull Request 704: https://github.com/galaxyproject/planemo/pull/704 .. _Pull Request 709: https://github.com/galaxyproject/planemo/pull/709 .. _Pull Request 715: https://github.com/galaxyproject/planemo/pull/715 .. _Pull Request 716: https://github.com/galaxyproject/planemo/pull/716 .. _Pull Request 720: https://github.com/galaxyproject/planemo/pull/720 .. _Pull Request 723: https://github.com/galaxyproject/planemo/pull/723 .. _8a608e0: https://github.com/galaxyproject/planemo/commit/8a608e0 .. _ecc1bc2: https://github.com/galaxyproject/planemo/commit/ecc1bc2 .. _Pull Request 702: https://github.com/galaxyproject/planemo/pull/702 .. _Pull Request 701: https://github.com/galaxyproject/planemo/pull/701 .. _Pull Request 699: https://github.com/galaxyproject/planemo/pull/699 .. _91b6fa0: https://github.com/galaxyproject/planemo/commit/91b6fa0 .. _904d77a: https://github.com/galaxyproject/planemo/commit/904d77a .. _9636682: https://github.com/galaxyproject/planemo/commit/9636682 .. _475104c: https://github.com/galaxyproject/planemo/commit/475104c .. _Pull Request 684: https://github.com/galaxyproject/planemo/pull/684 .. _Pull Request 687: https://github.com/galaxyproject/planemo/pull/687 .. _Pull Request 688: https://github.com/galaxyproject/planemo/pull/688 .. _Pull Request 689: https://github.com/galaxyproject/planemo/pull/689 .. _Pull Request 690: https://github.com/galaxyproject/planemo/pull/690 .. _Issue 494: https://github.com/galaxyproject/planemo/issues/494 .. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665 .. _Pull Request 675: https://github.com/galaxyproject/planemo/pull/675 .. _Pull Request 680: https://github.com/galaxyproject/planemo/pull/680 .. _Pull Request 682: https://github.com/galaxyproject/planemo/pull/682 .. _Pull Request 683: https://github.com/galaxyproject/planemo/pull/683 .. _Pull Request 662: https://github.com/galaxyproject/planemo/pull/662 .. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665 .. _Pull Request 664: https://github.com/galaxyproject/planemo/pull/664 .. _84c4a73: https://github.com/galaxyproject/planemo/commit/84c4a73 .. _32f41c9: https://github.com/galaxyproject/planemo/commit/32f41c9 .. _3129216: https://github.com/galaxyproject/planemo/commit/3129216 .. _b4ae44d: https://github.com/galaxyproject/planemo/commit/b4ae44d .. _3c95b7b: https://github.com/galaxyproject/planemo/commit/3c95b7b .. _06bcf19: https://github.com/galaxyproject/planemo/commit/06bcf19 .. _525de8f: https://github.com/galaxyproject/planemo/commit/525de8f .. _9867e56: https://github.com/galaxyproject/planemo/commit/9867e56 .. _ce0dc4e: https://github.com/galaxyproject/planemo/commit/ce0dc4e .. _4c0f100: https://github.com/galaxyproject/planemo/commit/4c0f100 .. _04238d3: https://github.com/galaxyproject/planemo/commit/04238d3 .. _ced5ce2: https://github.com/galaxyproject/planemo/commit/ced5ce2 .. _9ab4a0d: https://github.com/galaxyproject/planemo/commit/9ab4a0d .. _Pull Request 640: https://github.com/galaxyproject/planemo/pull/640 .. _0a1abfe: https://github.com/galaxyproject/planemo/commit/0a1abfe .. _Pull Request 649: https://github.com/galaxyproject/planemo/pull/649 .. _Issue 620: https://github.com/galaxyproject/planemo/issues/620 .. _Pull Request 643: https://github.com/galaxyproject/planemo/pull/643 .. _Pull Request 642: https://github.com/galaxyproject/planemo/pull/642 .. _Pull Request 641: https://github.com/galaxyproject/planemo/pull/641 .. _Pull Request 639: https://github.com/galaxyproject/planemo/pull/639 .. _Pull Request 635: https://github.com/galaxyproject/planemo/pull/635 .. _Issue 633: https://github.com/galaxyproject/planemo/issues/633 .. _Issue 260: https://github.com/galaxyproject/planemo/issues/260 .. _Pull Request 638: https://github.com/galaxyproject/planemo/pull/638 .. _6638caa: https://github.com/galaxyproject/planemo/commit/6638caa .. _8faf661: https://github.com/galaxyproject/planemo/commit/8faf661 .. _e343b67: https://github.com/galaxyproject/planemo/commit/e343b67 .. _Pull Request 634: https://github.com/galaxyproject/planemo/pull/634 .. _84ebc1f: https://github.com/galaxyproject/planemo/commit/84ebc1f .. _03c9658: https://github.com/galaxyproject/planemo/commit/03c9658 .. _08c067c: https://github.com/galaxyproject/planemo/commit/08c067c .. _fca4183: https://github.com/galaxyproject/planemo/commit/fca4183 .. _Issue 564: https://github.com/galaxyproject/planemo/issues/564 .. _Pull Request 628: https://github.com/galaxyproject/planemo/pull/628 .. _Issue 515: https://github.com/galaxyproject/planemo/issues/515 .. _Pull Request 629: https://github.com/galaxyproject/planemo/pull/629 .. _Pull Request 614: https://github.com/galaxyproject/planemo/pull/614 .. _32acd68: https://github.com/galaxyproject/planemo/commit/32acd68 .. _4595953: https://github.com/galaxyproject/planemo/commit/4595953 .. _Pull Request 612: https://github.com/galaxyproject/planemo/pull/612 .. _Issue 388: https://github.com/galaxyproject/planemo/issues/388 .. _Pull Request 610: https://github.com/galaxyproject/planemo/pull/610 .. _Pull Request 609: https://github.com/galaxyproject/planemo/pull/609 .. _Pull Request 608: https://github.com/galaxyproject/planemo/pull/608 .. _Pull Request 605: https://github.com/galaxyproject/planemo/pull/605 .. _Pull Request 606: https://github.com/galaxyproject/planemo/pull/606 .. _Pull Request 602: https://github.com/galaxyproject/planemo/pull/602 .. _Pull Request 570: https://github.com/galaxyproject/planemo/pull/570 .. _9228416: https://github.com/galaxyproject/planemo/commit/9228416 .. _50d3c4a: https://github.com/galaxyproject/planemo/commit/50d3c4a .. _Issue 578: https://github.com/galaxyproject/planemo/issues/578 .. _Pull Request 591: https://github.com/galaxyproject/planemo/pull/591 .. _Pull Request 590: https://github.com/galaxyproject/planemo/pull/590 .. _f0da66f: https://github.com/galaxyproject/planemo/commit/f0da66f .. _19b2ee9: https://github.com/galaxyproject/planemo/commit/19b2ee9 .. _9da8387: https://github.com/galaxyproject/planemo/commit/9da8387 .. _08cef54: https://github.com/galaxyproject/planemo/commit/08cef54 .. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc .. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc .. _Issue 573: https://github.com/galaxyproject/planemo/issues/573 .. _Pull Request 579: https://github.com/galaxyproject/planemo/pull/579 .. _ccdd2d5: https://github.com/galaxyproject/planemo/commit/ccdd2d5 .. _e925ba1: https://github.com/galaxyproject/planemo/commit/e925ba1 .. _ea5324f: https://github.com/galaxyproject/planemo/commit/ea5324f .. _ca88b0c: https://github.com/galaxyproject/planemo/commit/ca88b0c .. _b6d8294: https://github.com/galaxyproject/planemo/commit/b6d8294 .. _6a6f164: https://github.com/galaxyproject/planemo/commit/6a6f164 .. _d6da3a8: https://github.com/galaxyproject/planemo/commit/d6da3a8 .. _1ef05d2: https://github.com/galaxyproject/planemo/commit/1ef05d2 .. _7cca2e4: https://github.com/galaxyproject/planemo/commit/7cca2e4 .. _34538de: https://github.com/galaxyproject/planemo/commit/34538de .. _6f91719: https://github.com/galaxyproject/planemo/commit/6f91719 .. _Pull Request 566: https://github.com/galaxyproject/planemo/pull/566 .. _Pull Request 559: https://github.com/galaxyproject/planemo/pull/559 .. _Pull Request 561: https://github.com/galaxyproject/planemo/pull/561 .. _Pull Request 565: https://github.com/galaxyproject/planemo/pull/565 .. _Pull Request 555: https://github.com/galaxyproject/planemo/pull/555 .. _a8e797b: https://github.com/galaxyproject/planemo/commit/a8e797b .. _6c03de8: https://github.com/galaxyproject/planemo/commit/6c03de8 .. _ef4b9f4: https://github.com/galaxyproject/planemo/commit/ef4b9f4 .. _f7b6c7e: https://github.com/galaxyproject/planemo/commit/f7b6c7e .. _07d94bd: https://github.com/galaxyproject/planemo/commit/07d94bd .. _ca19910: https://github.com/galaxyproject/planemo/commit/ca19910 .. _24008ab: https://github.com/galaxyproject/planemo/commit/24008ab .. _ce44e87: https://github.com/galaxyproject/planemo/commit/ce44e87 .. _Pull Request 550: https://github.com/galaxyproject/planemo/pull/550 .. _c2204b3: https://github.com/galaxyproject/planemo/commit/c2204b3 .. _c262b6d: https://github.com/galaxyproject/planemo/commit/c262b6d .. _Pull Request 539: https://github.com/galaxyproject/planemo/pull/539 .. _Pull Request 541: https://github.com/galaxyproject/planemo/pull/541 .. _Pull Request 540: https://github.com/galaxyproject/planemo/pull/540 .. _Pull Request 545: https://github.com/galaxyproject/planemo/pull/545 .. _Pull Request 546: https://github.com/galaxyproject/planemo/pull/546 .. _3ceaa40: https://github.com/galaxyproject/planemo/commit/3ceaa40 .. _057f4f0: https://github.com/galaxyproject/planemo/commit/057f4f0 .. _9fdf490: https://github.com/galaxyproject/planemo/commit/9fdf490 .. _8c088c6: https://github.com/galaxyproject/planemo/commit/8c088c6 .. _e2398fb: https://github.com/galaxyproject/planemo/commit/e2398fb .. _Pull Request 526: https://github.com/galaxyproject/planemo/pull/526 .. _Pull Request 528: https://github.com/galaxyproject/planemo/pull/528 .. _Pull Request 525: https://github.com/galaxyproject/planemo/pull/525 .. _a811e65: https://github.com/galaxyproject/planemo/commit/a811e65 .. _Pull Request 521: https://github.com/galaxyproject/planemo/pull/521 .. _a066afb: https://github.com/galaxyproject/planemo/commit/a066afb .. _Pull Request 512: https://github.com/galaxyproject/planemo/pull/512 .. _08bb354: https://github.com/galaxyproject/planemo/commit/08bb354 .. _Pull Request 513: https://github.com/galaxyproject/planemo/pull/513 .. _Pull Request 510: https://github.com/galaxyproject/planemo/pull/510 .. _e890ab5: https://github.com/galaxyproject/planemo/commit/e890ab5 .. _Pull Request 507: https://github.com/galaxyproject/planemo/pull/507 .. _d53bcd6: https://github.com/galaxyproject/planemo/commit/d53bcd6 .. _725b232: https://github.com/galaxyproject/planemo/commit/725b232 .. _Pull Request 498: https://github.com/galaxyproject/planemo/pull/498 .. _01584c5: https://github.com/galaxyproject/planemo/commit/01584c5 .. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9 .. _0298510: https://github.com/galaxyproject/planemo/commit/0298510 .. _02a08a0: https://github.com/galaxyproject/planemo/commit/02a08a0 .. _05cc9f4: https://github.com/galaxyproject/planemo/commit/05cc9f485ee87bc344e3f43bb1cfd025a16a6247 .. _069e7ba: https://github.com/galaxyproject/planemo/commit/069e7ba .. _08de8de: https://github.com/galaxyproject/planemo/commit/08de8de .. _0bd4ff0: https://github.com/galaxyproject/planemo/commit/0bd4ff0 .. _0e4f70a: https://github.com/galaxyproject/planemo/commit/0e4f70a .. _0f8cb10: https://github.com/galaxyproject/planemo/commit/0f8cb10 .. _13a5ae7: https://github.com/galaxyproject/planemo/commit/13a5ae7 .. _15804be: https://github.com/galaxyproject/planemo/commit/15804be .. _15d33c7: https://github.com/galaxyproject/planemo/commit/15d33c7 .. _182fe57: https://github.com/galaxyproject/planemo/commit/182fe57 .. _1927168: https://github.com/galaxyproject/planemo/commit/1927168 .. _1982076: https://github.com/galaxyproject/planemo/commit/1982076 .. _19900a6: https://github.com/galaxyproject/planemo/commit/19900a6 .. _1a157d4: https://github.com/galaxyproject/planemo/commit/1a157d4 .. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493 .. _1c6cfbb: https://github.com/galaxyproject/planemo/commit/1c6cfbb .. _1c7ee5b: https://github.com/galaxyproject/planemo/commit/1c7ee5b .. _1cd0e2d: https://github.com/galaxyproject/planemo/commit/1cd0e2d .. _1e3668a: https://github.com/galaxyproject/planemo/commit/1e3668a .. _2052db0: 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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: 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_@blankenberg: https://github.com/blankenberg .. _@JeanFred: https://github.com/JeanFred .. _@gregvonkuster: https://github.com/gregvonkuster .. _@remimarenco: https://github.com/remimarenco .. _@thriqon: https://github.com/thriqon .. _@RJMW: https://github.com/RJMW .. _@manabuishii: https://github.com/manabuishii .. _@dfornika: https://github.com/dfornika .. _@bernt-matthias: https://github.com/bernt-matthias .. _@katrinleinweber: https://github.com/katrinleinweber .. _@bebatut: https://github.com/bebatut .. _@selten: https://github.com/selten .. _@shiltemann: https://github.com/shiltemann .. _@bedroesb: https://github.com/bedroesb .. _@ic4f: https://github.com/ic4f .. _@martin-raden: https://github.com/martin-raden