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date Sat, 02 May 2020 07:14:21 -0400
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1 Metadata-Version: 2.1
2 Name: planemo
3 Version: 0.70.0
4 Summary: Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
5 Home-page: https://github.com/galaxyproject/planemo
6 Author: Galaxy Project and Community
7 Author-email: jmchilton@gmail.com
8 License: AFL
9 Keywords: planemo
10 Platform: UNKNOWN
11 Classifier: Development Status :: 5 - Production/Stable
12 Classifier: Intended Audience :: Developers
13 Classifier: Environment :: Console
14 Classifier: License :: OSI Approved :: Academic Free License (AFL)
15 Classifier: Operating System :: POSIX
16 Classifier: Topic :: Software Development
17 Classifier: Topic :: Software Development :: Code Generators
18 Classifier: Topic :: Software Development :: Testing
19 Classifier: Natural Language :: English
20 Classifier: Programming Language :: Python :: 2
21 Classifier: Programming Language :: Python :: 2.7
22 Classifier: Programming Language :: Python :: 3
23 Classifier: Programming Language :: Python :: 3.5
24 Classifier: Programming Language :: Python :: 3.6
25 Classifier: Programming Language :: Python :: 3.7
26 Classifier: Programming Language :: Python :: 3.8
27 Description-Content-Type: text/x-rst
28 Requires-Dist: aenum
29 Requires-Dist: BeautifulSoup4
30 Requires-Dist: bioblend (>=0.13.0)
31 Requires-Dist: Click
32 Requires-Dist: configparser
33 Requires-Dist: cwltool (==1.0.20191225192155)
34 Requires-Dist: docutils
35 Requires-Dist: ephemeris (>=0.10.3)
36 Requires-Dist: galaxy-containers
37 Requires-Dist: galaxy-tool-util (>=20.1.0.dev2)
38 Requires-Dist: galaxy-util (>=20.1.0.dev0)
39 Requires-Dist: glob2
40 Requires-Dist: gxformat2 (>=0.8.0)
41 Requires-Dist: jinja2
42 Requires-Dist: lxml
43 Requires-Dist: oyaml
44 Requires-Dist: pyaml
45 Requires-Dist: pyyaml
46 Requires-Dist: six (>=1.7.0)
47 Requires-Dist: virtualenv
48
49 .. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png
50 :alt: Planemo Logo
51 :align: center
52 :figwidth: 100%
53 :target: https://github.com/galaxyproject/planemo
54
55 Command-line utilities to assist in developing Galaxy_ and `Common Workflow Language`_ tools.
56
57 .. image:: https://readthedocs.org/projects/planemo/badge/?version=latest
58 :target: http://planemo.readthedocs.io/en/latest/?badge=latest
59 :alt: Documentation Status
60
61 .. image:: https://badge.fury.io/py/planemo.svg
62 :target: https://pypi.python.org/pypi/planemo/
63 :alt: Planemo on the Python Package Index (PyPI)
64
65 .. image:: https://travis-ci.org/galaxyproject/planemo.png?branch=master
66 :target: https://travis-ci.org/galaxyproject/planemo
67 :alt: Build Status
68
69 .. image:: https://travis-ci.org/jmchilton/planemo-extended-tests.svg?branch=master
70 :target: https://travis-ci.org/jmchilton/planemo-extended-tests
71 :alt: Build Status of Extended Tests
72
73 .. image:: https://coveralls.io/repos/galaxyproject/planemo/badge.svg?branch=master
74 :target: https://coveralls.io/r/galaxyproject/planemo?branch=master
75 :alt: Coverage Status
76
77 * Free software: Academic Free License version 3.0
78 * Documentation: https://planemo.readthedocs.io.
79 * Code: https://github.com/galaxyproject/planemo
80
81
82 Quick Start
83 -----------
84
85 -----------------
86 Obtaining
87 -----------------
88
89 For a traditional Python installation of Planemo, first set up a virtualenv
90 for ``planemo`` (this example creates a new one in ``.venv``) and then
91 install with ``pip``. Planemo requires pip 7.0 or newer.
92
93 ::
94
95 $ virtualenv .venv; . .venv/bin/activate
96 $ pip install "pip>=7" # Upgrade pip if needed.
97 $ pip install planemo
98
99 For information on updating Planemo, installing the latest development release,
100 or installing Planemo via `Bioconda <https://github.com/bioconda/bioconda-recipes>`__
101 - checkout the `installation <http://planemo.readthedocs.io/en/latest/installation.html>`__
102 documentation.
103
104 Planemo is also available as a `virtual appliance
105 <https://planemo.readthedocs.io/en/latest/appliance.html>`_ bundled
106 with a preconfigured Galaxy server and set up for Galaxy_ and
107 `Common Workflow Language`_ tool development.
108 You can choose from open virtualization format (OVA_, .ova) or Docker_
109 appliances.
110
111 -----------------
112 Basics - Galaxy
113 -----------------
114
115 This quick start will assume you have a directory with one or more Galaxy
116 tool XML files. If no such directory is available, one can be quickly created for
117 demonstrating ``planemo`` as follows ``project_init --template=demo mytools; cd mytools``.
118
119 Planemo can check tool XML files for common problems and best
120 practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
121 (also aliased as ``l``).
122
123 ::
124
125 $ planemo lint
126
127 Like many ``planemo`` commands - by default this will search the
128 current directory and use all tool files it finds. It can be explicitly
129 passed a path to tool files or a directory of tool files.
130
131 ::
132
133 $ planemo l randomlines.xml
134
135 The ``lint`` command takes in additional options related to
136 reporting levels, exit code, etc. These options are described
137 in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
138 or (like with all commands) can be accessed by passing ``--help`` to it.
139
140 ::
141
142 $ planemo l --help
143 Usage: planemo lint [OPTIONS] TOOL_PATH
144
145 Once tools are syntactically correct - it is time to test. The ``test``
146 `command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__
147 can be used to test a tool or a directory of tools.
148
149 ::
150
151 $ planemo test --galaxy_root=../galaxy randomlines.xml
152
153 If no ``--galaxy_root`` is defined, Planemo will download and configure
154 a disposable Galaxy instance for testing.
155
156 Planemo will create a HTML output report in the current directory named
157 ``tool_test_output.html`` (override with ``--test_output``). See an
158 `example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>`_
159 of such a report for Tophat.
160
161 Once tools have been linted and tested - the tools can be viewed in a
162 Galaxy interface using the ``serve`` (``s``) `command
163 <http://planemo.readthedocs.org/en/latest/commands.html#serve-command>`__.
164
165 ::
166
167 $ planemo serve
168
169 Like ``test``, ``serve`` requires a Galaxy root and one can be
170 explicitly specified with ``--galaxy_root`` or installed dynamically
171 with ``--install_galaxy``.
172
173 For more information on building Galaxy tools in general please check out
174 `Building Galaxy Tools Using Planemo`_.
175
176 ----------------------------------
177 Basics - Common Workflow Language
178 ----------------------------------
179
180 This quick start will assume you have a directory with one or more `Common Workflow
181 Language`_ YAML files. If no such directory is available, one can be quickly created for
182 demonstrating ``planemo`` as follows ``planemo project_init --template=seqtk_complete_cwl mytools; cd mytools``.
183
184 Planemo can check tools YAML files for common problems and best
185 practices using the ``lint`` `command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
186 (also aliased as ``l``).
187
188 ::
189
190 $ planemo lint
191
192 Like many ``planemo`` commands - by default this will search the
193 current directory and use all tool files it finds. It can be explicitly
194 passed a path to tool files or a directory of tool files.
195
196 ::
197
198 $ planemo l seqtk_seq.cwl
199
200 The ``lint`` command takes in additional options related to
201 reporting levels, exit code, etc. These options are described
202 in the `docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>`_
203 or (like with all commands) can be accessed by passing ``--help`` to it.
204
205 ::
206
207 $ planemo l --help
208 Usage: planemo lint [OPTIONS] TOOL_PATH
209
210 Once tools are syntactically correct - it is time to test. The ``test``
211 `command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>`__
212 can be used to test a CWL tool, workflow, or a directories thereof.
213
214 ::
215
216 $ planemo test --engine cwltool seqtk_seq.cwl
217
218 Planemo will create a HTML output report in the current directory named
219 ``tool_test_output.html``. Check out the file ``seqtk_seq_tests.yml`` for
220 an example of Planemo test for a CWL tool. A test consists of any number of
221 jobs (with input descriptions) and corresponding output assertions.
222
223 Checkout the `Commmon Workflow User Guide`_ for more information on developing
224 CWL tools in general and `Building Common Workflow Language Tools`_ for more
225 information on using Planemo to develop CWL tools.
226
227 ---------
228 Tool Shed
229 ---------
230
231 Planemo can help you publish tools to the Galaxy Tool Shed.
232 Check out `Publishing to the Tool Shed`_ for more information.
233
234 ------
235 Conda
236 ------
237
238 Planemo can help develop tools and Conda packages in unison.
239 Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda>`__ or `CWL
240 <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda-cwl>`__ version of the "Dependencies and Conda" tutorial
241 for more information.
242
243 -----------------------
244 Docker and Containers
245 -----------------------
246
247 Planemo can help develop tools that run in "Best Practice" containers for
248 scientific workflows. Check out the `Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-containers>`__ or `CWL
249 <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers-cwl>`__ version of the "Dependencies and Containers" tutorial for more information.
250
251 .. _Galaxy: http://galaxyproject.org/
252 .. _GitHub: https://github.com/
253 .. _Conda: http://conda.pydata.org/
254 .. _Docker: https://www.docker.com/
255 .. _Vagrant: https://www.vagrantup.com/
256 .. _Travis CI: http://travis-ci.org/
257 .. _`tools-devteam`: https://github.com/galaxyproject/tools-devteam
258 .. _`tools-iuc`: https://github.com/galaxyproject/tools-iuc
259 .. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html
260 .. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html
261 .. _Common Workflow Language: https://www.commonwl.org/
262 .. _Commmon Workflow User Guide: http://www.commonwl.org/user_guide/
263 .. _Building Common Workflow Language Tools: http://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html
264 .. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format
265
266
267
268
269
270 History
271 -------
272
273 .. to_doc
274
275 ---------------------
276 0.70.0 (2020-01-29)
277 ---------------------
278
279 * Temporarily add galaxy-util requirement `Pull Request 991`_
280 * Make symlinks in tool tree work for planemo test `Pull Request 988`_
281 * Reduce use of ``shell=True`` in subprocesses `Pull Request 989`_
282 * Drop planemo database seed option `Pull Request 985`_
283 * Don't execute ``untar_to()`` subprocesses through the shell `Pull Request 984`_
284 * Allow setting database_connection for planemo test runs `Pull Request 986`_
285 * Fix copy-paste mistakes `Pull Request 983`_
286 * Add planemo list_repos command `Pull Request 982`_
287 * Make container_register build files with headers and include base_image `Pull Request 980`_
288 * Replace deprecated galaxy-lib requirement with galaxy-tool-util `Pull Request 978`_
289 * Close all opened files (thanks to `@bernt-matthias`_). `Pull Request 979`_
290 * Build single requirement container, log if requirement not in best-practice channels `Pull Request 977`_
291 * Use tojson jinja2 filter instead of json.dumps `Pull Request 975`_
292 * Add merge_test_reports command `Pull Request 974`_
293 * Implement github workflow and fix profile commands if psql unavailable `Pull Request 976`_
294 * Fix planemo lint --biocontainers if no build number in container `Pull Request 972`_
295 * Update a training command (thanks to `@hexylena`_). `Pull Request 973`_
296 * Allow passing through GALAXY_VIRTUAL_ENV variable to venv setup `Pull Request 971`_
297 * Correct help text (thanks to `@hexylena`_). `Pull Request 970`_
298 * Remove unneeded html5lib requirement `Pull Request 968`_
299
300 ---------------------
301 0.62.1 (2019-10-14)
302 ---------------------
303
304 * Init & update submodules when installing and creating packages. Stop
305 distributing eggs (thanks to `@nsoranzo`_). 1ab8530_
306
307 ---------------------
308 0.62.0 (2019-10-11)
309 ---------------------
310
311 * Use ``unicodify()`` on exceptions and subprocess outputs (thanks to
312 `@nsoranzo`_) `Pull Request 944`_
313 * Do not override ``None`` with empty string (thanks to `@ic4f`_). `Pull Request
314 950`_
315 * Update Docker template for training material generation (thanks to
316 `@bedroesb`_). `Pull Request 958`_
317 * Add support for suite of repos with different owners (thanks to `@nsoranzo`_).
318 `Pull Request 959`_
319 * Link for collection details updated in the docs (thanks to `@martin-raden`_).
320 `Pull Request 963`_
321 * Move most tests to Python 3.7, drop Python 3.4 (thanks to `@nsoranzo`_).
322 `Pull Request 964`_
323 * Remove confusing warning `Pull Request 966`_
324
325 ---------------------
326 0.61.0 (2019-07-08)
327 ---------------------
328
329 * Training - fix empty repeat + some formatting (thanks to `@bebatut`_). `Pull
330 Request 926`_
331 * Training - add bibliography to tutorial template (thanks to `@shiltemann`_).
332 `Pull Request 938`_
333 * Training - support new class definition for input in workflow step (thanks to
334 `@bebatut`_). `Pull Request 943`_
335 * Various tool tutorial fixes ahead of GCC 2019 (thanks to `@nsoranzo`_).
336 `Pull Request 940`_
337 * Return validation error if doi is empty (thanks to `@nsoranzo`_).
338 `Pull Request 937`_
339
340 ---------------------
341 0.60.0 (2019-05-31)
342 ---------------------
343
344 * Return validation error if doi is empty `Pull Request 937`_
345 * Add junit as test reporter (thanks to `@selten`_). `Pull Request 935`_
346 * Update galaxy.xsd for new python 3 compatibility attribute (thanks to `@martenson`_). `Pull Request
347 931`_
348 * Documentation: add a little warning for <param ... multiple="true"> (thanks to
349 `@bernt-matthias`_). `Pull Request 930`_
350
351 ---------------------
352 0.59.0 (2019-05-09)
353 ---------------------
354
355 * Add ability to test data manager tools (thanks to `@mvdbeek`_).
356 `Pull Request 912`_
357 * Update Training for new requirement definition (thanks to `@bebatut`_).
358 `Pull Request 913`_
359 * Drop amqp workaround (thanks to `@mvdbeek`_). `Pull Request 917`_
360 * Use ``yaml.safe_load()`` instead of deprecated ``load()`` (thanks to `@nsoranzo`_).
361 `Pull Request 921`_
362 * Allow converting ``tool_test_report.json`` to xunit (thanks to `@mvdbeek`_).
363 `Pull Request 918`_
364 * Fix error if testcase.data.job does not exist (thanks to `@mvdbeek`_).
365 `Pull Request 924`_
366 * Fix deprecated ``getchildren()`` (thanks to `@nsoranzo`_).
367 `Pull Request 925`_
368
369 ---------------------
370 0.58.2 (2019-03-01)
371 ---------------------
372
373 * Fix display of tool ids in planemo html report (thanks to `@mvdbeek`_).
374 `Pull Request 908`_
375 * Single quotes for file names (thanks to `@bernt-matthias`_). `Pull Request
376 909`_
377 * Fix doc linting (thanks to `@mvdbeek`_). `Pull Request 910`_
378 * Update TS categories (thanks to `@nsoranzo`_). 07dc6e0_
379 * Close tag in doc help, to help with copy&paste (thanks to `@blankenberg`_).
380 `Pull Request 914`_
381 * Update the tool XSD file (thanks to `@bgruening`_). `Pull Request 915`_
382
383 ---------------------
384 0.58.1 (2019-01-03)
385 ---------------------
386
387 * Update galaxy-lib requirement to 18.9.2 to add Python 3.7 support (thanks to
388 `@nsoranzo`_). `Pull Request 906`_
389 * Fix command run by `planemo test --skip_venv` (thanks to `@nsoranzo`_).
390 `Pull Request 907`_
391
392 ---------------------
393 0.58.0 (2019-01-01)
394 ---------------------
395
396 * Remove deprecated ``sudo: false`` from .travis.yml (thanks to `@nsoranzo`_).
397 `Pull Request 902`_
398 * Do not skip Galaxy client build for ``planemo serve``. Install Galaxy when the
399 directory specified with ``--galaxy_root`` does not exist or is empty. (thanks
400 to `@nsoranzo`_). `Pull Request 895`_, `Issue 845`_
401
402 ---------------------
403 0.57.1 (2018-11-23)
404 ---------------------
405
406 * Fix username validation for shed linting (thanks to `@martenson`_).
407 `Pull Request 899`_, `Issue 898`_
408
409 ---------------------
410 0.57.0 (2018-11-19)
411 ---------------------
412
413 * Allow ``workflow_convert`` to convert a native ``.ga`` workflows to format 2 (yaml).
414 `Pull Request 896`_
415 * New command (``workflow_edit``) to open workflow in a synchronized graphical editor.
416 `Pull Request 894`_
417 * Conda tutorial fixes (thanks to `@nsoranzo`_). `Pull Request 876`_
418 * Enable ``--conda_use_local`` option for ``planemo test`` (thanks to
419 `@nsoranzo`_). `Pull Request 876`_
420 * When testing, skip workflow outputs that do not have a `label` set (thanks to
421 `@bgruening`_). `Pull Request 893`_
422 * Add ``__repr__`` for ``TestCase`` to improve debugging Planemo
423 (thanks to `@bgruening`_). `Pull Request 892`_
424 * Increase IO polling interval over time (thanks to `@martenson`_).
425 `Pull Request 891`_
426 * Sync galaxy xsd and fix tests (thanks to `@mvdbeek`_).
427 `Pull Request 889`_
428 * Linting fix for ``W605`` (thanks to `@martenson`_). `Pull Request 888`_
429 * Add icon for repeat parameters in training (thanks to `@bebatut`_).
430 `Pull Request 887`_
431
432 ---------------------
433 0.56.0 (2018-10-30)
434 ---------------------
435
436 * Allow selection of Python version when starting managed Galaxy
437 (thanks to `@mvdbeek`_). `Pull Request 874`_
438 * Change the channel priority of conda (again). (thanks to `@bgruening`_).
439 `Pull Request 867`_
440 * Some small english corrections (thanks to `@hexylena`_). `Pull Request 868`_
441 * Print the list of excluded paths when running ``ci_find_repos``
442 (thanks to `@nsoranzo`_). `Pull Request 877`_
443 * Improved XSD lint reporting. `Pull Request 871`_
444 * Fix Planemo writing a file called ``gx_venv_None``. `Pull Request 870`_
445 * Update cwltool and galaxy-lib dependencies for Python 3.7 (thanks to
446 `@nsoranzo`_). `Pull Request 864`_
447 * Fix to make workflow testing more robust.
448 `Pull Request 882`_
449
450 ---------------------
451 0.55.0 (2018-09-12)
452 ---------------------
453
454 * Add commands to create Galaxy training materials (thanks to `@bebatut`_).
455 `Pull Request 861`_
456 * Fix `planemo test` when TEMP env variable contain spaces (thanks to
457 `@nsoranzo`_).
458 `Pull Request 851`_
459 * Support testing a completely remote galaxy instance (thanks to `@hexylena`_).
460 `Pull Request 856`_
461 * Allow naming history from command line (thanks to `@hexylena`_).
462 `Pull Request 860`_
463 * Sync galaxy.xsd from galaxy repo (thanks to `@nsoranzo`_).
464 `Pull Request 866`_
465 * Fix ServeTestCase.test_shed_serve test (thanks to `@nsoranzo`). bad810a_
466
467 ---------------------
468 0.54.0 (2018-06-06)
469 ---------------------
470
471 * Better support for testings against different versions of Galaxy efficiently and robustly.
472 `Pull Request 849`_
473 * New database version (thanks to `@bgruening`_).
474 `Pull Request 847`_
475 * Hyperlink DOIs against preferred resolver (thanks to `@katrinleinweber`_).
476 `Pull Request 850`_
477 * Tests for collection inputs to workflows. `Pull Request 843`_
478 * Bring in Ephemeris sleep function - hopefully makes serve tests a bit more robust.
479 b12b117_
480 * More tutorial testing, tutorial updates.
481 016b923_, 324c776_, 2002b49_
482 * More isolated ``test_shed_upload.py`` tests. 72d2ca7_
483 * Add filetype support for workflow test inputs (thanks to `@bgruening`_).
484 `Pull Request 842`_
485 * Add ``--no_shed_install`` option, to prevent shed installs as part of workflow testing.
486 `Pull Request 841`_
487 * Small docs fix (thanks to `@hexylena`_). `Pull Request 848`_
488
489 ---------------------
490 0.53.0 (2018-05-22)
491 ---------------------
492
493 * Make Planemo testing easier for CWL tools and workflows in various ways and update
494 tutorials to reflect these simplifications. `Pull Request 837`_
495 * Test and fix running workflow tests against externally managed Galaxy servers.
496 `Pull Request 833`_, `Pull Request 836`_
497 * Allow using URIs for inputs of workflow test. `Pull Request 840`_
498 * Slide Galaxy testing window to include 18.05 and drop 17.09. `Pull Request 838`_
499
500 ---------------------
501 0.52.0 (2018-05-20)
502 ---------------------
503
504 * Allow optional disabling of Galaxy single user mode. `Pull Request 835`_
505 * Fix for path pasting options during workflow testing. `Pull Request 834`_
506
507 ---------------------
508 0.51.0 (2018-05-19)
509 ---------------------
510
511 * Fix essentially all Conda_ and BioContainers_ related functionality to allow parity between
512 CWL_ and existing Galaxy functionality - fixes and enhances many commands including ``lint``,
513 ``conda_install``, ``conda_env``, ``test``, ``run``, and ``mull``.
514 `Pull Request 828`_
515 * Add two new tutorials for `Conda
516 <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda>`__
517 and `Container
518 <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers>`__
519 development with CWL tools that mirrors the existing tutorials for Galaxy tools - including new
520 CWL exercises, answers, and example project templates.
521 347c622_
522 * Improve the CWL generated by the ``tool_init`` command to properly deal with
523 ``SoftwareRequirement`` s and generate more idiomatic CWL.
524 `Pull Request 820`_, a5c72e3_
525 * Add new engine type (``--engine toil``) for testing and running CWL_ tools (requires
526 manually installing Toil_ with ``pip install toil`` in Planemo's environment).
527 `Pull Request 831`_
528 * Add `documentation <http://planemo.readthedocs.io/en/latest/test_format.html>`__
529 for the Galaxy Workflow and CWL_ test format files (includes information on configuring
530 various test engines).
531 `Pull Request 832`_
532 * Better default logging config for CWL development. `Pull Request 830`_
533 * Various fixes for the ``conda_search`` command. `Pull Request 826`_
534 * Fix test coverage configuration. `Pull Request 822`_
535 * Reorganize .travis.yml for clarity. `Pull Request 829`_
536 * More isolated, robust unit tests that use git_.
537 `Pull Request 827`_, `Pull Request 818`_
538 * Fix default list of best-practice Conda channels. `Pull Request 825`_
539 * Refactor tests to speed up quick tests - fewer buggy URLs fetched in "quick" mode.
540 `Pull Request 823`_
541 * Fix upload configuration of workflow testing to default (overrideable) external Galaxies
542 to not use path pasting.
543 `Pull Request 816`_
544 * Fix test number parsing for workflow tests. `Pull Request 817`_
545
546 ---------------------
547 0.50.1 (2018-05-11)
548 ---------------------
549
550 * Fix the process of waiting on Galaxy to boot up for the Docker Galaxy container ``--engine``.
551
552 ---------------------
553 0.50.0 (2018-05-10)
554 ---------------------
555
556 * Fixes and small CLI tweaks to get the Docker Galaxy container working as an ``--engine`` for the
557 run, serve, and test commands.
558
559 ---------------------
560 0.49.2 (2018-05-09)
561 ---------------------
562
563 * Various small fixes for new external Galaxy engine type.
564
565 ---------------------
566 0.49.1 (2018-05-06)
567 ---------------------
568
569 * Fix PyPI_ README rendering for 0.49.0 release changes.
570
571 ---------------------
572 0.49.0 (2018-05-06)
573 ---------------------
574
575 * Implement external Galaxy engine. `Pull Request 781`_
576 * Restructure serve testing code for reuse. `Pull Request 795`_
577 * Improve test report handling for JSON generated via galaxy-lib testing
578 script. `Pull Request 799`_
579 * Improve how various branches of Galaxy are tested. `Pull Request 800`_
580 * Added documentation for ``GALAXY_MEMORY_MB`` (thanks to `@bernt-matthias`_).
581 `Pull Request 801`_
582 * Log tool config in verbose logging mode. `Pull Request 802`_
583 * Replace ``r`` channel with ``conda-forge`` (thanks to `@bgruening`_).
584 `Pull Request 805`_
585 * Sync ``galaxy.xsd`` with latest Galaxy updates (thanks to `@nsoranzo`_).
586 `Pull Request 806`_
587 * Use ``requests.get()`` when validating http URLs (thanks to `@nsoranzo`_).
588 `Pull Request 809`_
589 * Do not consider tools with "deprecated" in the path (thanks to
590 `@bgruening`_). `Pull Request 810`_
591 * Automatically load tools shipped with Galaxy when testing, running, or serving
592 workflows that reference these tools. `Pull Request 790`_
593 * Revise README and touch up documentation in general. `Pull Request 787`_
594 * Various small changes to testing and test framework. `Pull Request 792`_
595 * Various Python 3 fixes. 8cfe9e9_, 41f7df1_
596 * Fixes for Galaxy 18.0X releases.
597 `Pull Request 803`_, dc443d6_
598
599 ---------------------
600 0.48.0 (2018-02-28)
601 ---------------------
602
603 * Run all CI tests against Python 3 (thanks to `@nsoranzo`_).
604 `Pull Request 768`_ and `Pull Request 774`_
605 * Python 3 fix - subprocess with ``universal_newlines=True``
606 (thanks to `@peterjc`_).
607 `Pull Request 764`_
608 * Record CWL_ conformance test results using JUnit xml
609 (thanks to `@mr-c`_).
610 `Pull Request 756`_
611 * Restore run test case for simple Galaxy tools.
612 `Pull Request 769`_
613 * Enhancements to Galaxy profiles and workflow testing.
614 `Pull Request 773`_
615 * Fix resolving & installing shed repositories from workflows for ``test``
616 and ``run`` commands.
617 `Pull Request 776`_
618 * Implement planemo command to convert format 2 workflows into .ga workflows.
619 `Pull Request 771`_
620 * Add a native Galaxy workflow (.ga) testing test.
621 `Pull Request 770`_
622 * Drop Brew support but add more detailed install instructions.
623 `Pull Request 761`_
624 * Clean up CWL_ conformance test execution. `Pull Request 753`_
625 * Assorted small CWL_ and deamon serve fixes. `Pull Request 759`_
626
627
628 ---------------------
629 0.47.0 (2017-11-18)
630 ---------------------
631
632 * Update to the latest Galaxy tool XSD (thanks to `@nsoranzo`_).
633 `Pull Request 747`_
634 * Re-fix problem when shed_update would fail if nothing to update
635 (thanks to `@nsoranzo`_). `Pull Request 747`_
636 * Update instructions for installation via conda (thanks to `@nsoranzo`_) .
637 `Pull Request 743`_
638 * Bug fix for MacOS `chmod` doesn't support `--recursive` flag.
639 (thanks to `@dfornika`_). `Pull Request 739`_
640 * Bug fix to also `socket.error` when linting URLs
641 (thanks to `@nsoranzo`_). `Pull Request 738`_
642 * Disable broken tests. `Pull Request 745`_
643
644 ---------------------
645 0.46.1 (2017-09-26)
646 ---------------------
647
648 * Rev to latest versions of bioblend_ and `galaxy-lib`_ for various fixes
649 related to CWL_.
650
651 ---------------------
652 0.46.0 (2017-09-15)
653 ---------------------
654
655 * Change behavior of ``--docker`` flag, for a few releases it would require
656 Galaxy use a container for every non-upload tool. This breaks various
657 conversion tools for instance and so was reverted.
658 `Pull Request 733`_
659 * Add 'Accept' header when linting doc URLs (thanks to `@nsoranzo`_).
660 `Pull Request 725`_
661 * Fix `--conda_auto_install` help (thanks to `@nsoranzo`_).
662 `Pull Request 727`_
663 * Incremental progress toward CWL support via Galaxy.
664 `Pull Request 729`_, `Pull Request 732`_
665 * Update galaxy-lib to latest version to fix various issues.
666 `Pull Request 730`_
667 * Fix lint detected problems with documentation.
668 `Pull Request 731`_
669
670 ---------------------
671 0.45.0 (2017-09-06)
672 ---------------------
673
674 * Update to the latest `galaxy-lib`_ for Conda fixes. (thanks `@nsoranzo`_)
675 and updated CWL_ utilities. `Pull Request 716`_, `Pull Request 723`_
676 * Update Conda_ channel order to sync with Bioconda_
677 (thanks to `@nsoranzo`_). `Pull Request 715`_
678 * Experimental support running CWL_ workflows through the CWL_ fork of Galaxy.
679 * Mention ``planemo command --help`` in main help
680 (thanks to `@peterjc`_). `Pull Request 709`_
681 * Bugfix handle ``None`` requirement versions when registering containers
682 (thanks to `@bgruening`_). `Pull Request 704`_
683 * Bugfix for dependencies by pinning ruamel.yaml version
684 (thanks to `@mvdbeek`_). `Pull Request 720`_
685
686 ---------------------
687 0.44.0 (2017-06-22)
688 ---------------------
689
690 * Fix and improve Galaxy root option specification options.
691 `Pull Request 701`_, 8a608e0_
692 * Update `planemo mull` to use a default action of `build-and-test` since
693 `build` no longer cleans up itself. ecc1bc2_
694 * Add a command to pre-install Involucro_.
695 `Pull Request 702`_
696
697 ---------------------
698 0.43.0 (2017-06-22)
699 ---------------------
700
701 * Remove stdio from generated tools - just use exit_code for everything.
702 91b6fa0_
703 * Implement some ad-hoc documentation tests. `Pull Request 699`_
704 * A large number of small enhancements and fixes for the documentation and
705 example projects.
706
707 ---------------------
708 0.42.1 (2017-06-16)
709 ---------------------
710
711 * Fix Readme typos (thanks to `@manabuishii`_) 904d77a_
712 * Fix `container_register` to create pull requests against the newly finalized home of the
713 multi-package-containers registry repository.
714 9636682_
715 * Fix `use_global_config` and `use_env_var` for options with unspecified defaults.
716 475104c_
717
718
719 ---------------------
720 0.42.0 (2017-06-15)
721 ---------------------
722
723 * Conda/Container documentation and option naming improvements. `Pull Request
724 684`_
725 * Sync `galaxy.xsd` with latest upstream Galaxy updates (thanks to `@nsoranzo`_).
726 `Pull Request 687`_
727 * Fix `ci_find_repos` command to not filter repos whose only modifications where
728 in subdirs (thanks to `@nsoranzo`_).
729 `Pull Request 688`_
730 * Update `container_register` for mulled version 2 and repository name changes.
731 `Pull Request 689`_
732 * Better pull request messages for the `container_register` command.
733 `Pull Request 690`_
734
735 ---------------------
736 0.41.0 (2017-06-05)
737 ---------------------
738
739 * Fix ``shed_update`` not fail if there is nothing to update
740 (thanks to `@nsoranzo`_). `Issue 494`_, `Pull Request 680`_
741 * Conda documentation and option naming improvements.
742 `Pull Request 683`_
743 * Implement ``container_register`` for tool repositories.
744 `Pull Request 675`_
745 * Fix ``hub`` binary installation for Mac OS X.
746 `Pull Request 682`_
747
748 ---------------------
749 0.40.1 (2017-05-03)
750 ---------------------
751
752 * Fix data manager configuration to not conflict with original Galaxy at
753 ``galaxy_root`` (thanks to `@nsoranzo`_). `Pull Request 662`_
754 * Fix ``filter_paths()`` to not partial match paths when filtering shed repositories
755 (thanks to `@nsoranzo`_). `Pull Request 665`_
756 * Fix description when creating ``.shed.yml`` files (thanks to `@RJMW`_).
757 `Pull Request 664`_
758
759 ---------------------
760 0.40.0 (2017-03-16)
761 ---------------------
762
763 * Implement instructions and project template for GA4GH Tool Execution
764 Challenge Phase 1. 84c4a73_
765 * Eliminate Conda hack forcing ``/tmp`` as temp directory. b4ae44d_
766 * Run dependency script tests in isolated directories. 32f41c9_
767 * Fix OS X bug in ``planemo run`` by reworking it to wait using urllib instead of sockets.
768 3129216_
769
770 ---------------------
771 0.39.0 (2017-03-15)
772 ---------------------
773
774 * Implement documentation and examples for Conda-based dependency development (under
775 "Advanced" topics).
776 `Pull Request 642`_, `Pull Request 643`_
777 * Implement documentation and examples for container-based dependency development (under
778 "Advanced" topics).
779 0a1abfe_
780 * Implement a ``planemo conda_search`` command for searching best practice channels
781 from the command line.
782 `Pull Request 642`_
783 * Allow Planemo to work with locally built Conda packages using the ``--conda_use_local``
784 command.
785 `Pull Request 643`_, `Issue 620`_
786 * Implement an ``open`` (or just ``o``) command to quickly open the last test results
787 (or any file if supplied). `Pull Request 641`_
788 * Linting improvements and fixes due to `galaxy-lib`_ update.
789 * WARN on test output names not found or not matching.
790 * INFO correct information about stdio if profile version is found.
791 * WARN if profile version is incorrect.
792 * INFO profile version
793 * Fix ``assert_command`` not detected as a valid test (fixes `Issue 260`_).
794 * Have ``lint --conda_requirements`` check that at least one actual requirement is found.
795 6638caa_
796 * Allow ``conda_install`` to work with packages as well as just tools.
797 8faf661_
798 * Add ``--global`` option to conda_install to install requirements into global Conda setup
799 instead of using an environment.
800 8faf661_
801 * Implement ``planemo lint --biocontainer`` that checks that a tool has an available BioContainer
802 registered.
803 0a1abfe_
804 * Add more options and more documentation to the ``planemo mull`` command.
805 0a1abfe_
806 * Hack around a bug in Conda 4.2 that makes it so ``planemo mull`` doesn't work out of the box on
807 Mac OS X.
808 0a1abfe_
809 * Allow URIs to be used instead of paths for a couple operations. ce0dc4e_
810 * Implement non-strict CWL parsing option. 4c0f100_
811 * Fixes for changes to cwltool_ and general CWL-relate functionality.
812 3c95b7b_, 06bcf19_, 525de8f_, 9867e56_, 9ab4a0d_
813 * Eliminate deprecated XML-based abstraction from ``planemo.tools``. 04238d3_
814 * Fix ``MANIFEST.in`` entry that was migrated to galaxy-lib. ced5ce2_
815 * Various fixes for the command ``conda_env``. `Pull Request 640`_
816 * Improved command help - both formatting and content. `Pull Request 639`_
817 * Implement a ``--no_dependency_resolution`` option disabling conda dependency
818 resolver.
819 `Pull Request 635`_, `Issue 633`_
820 * Tests for new linting logic. `Pull Request 638`_
821 * Fix bug where tool IDs needs to be lowercase for the shed (thanks to
822 `@bgruening`_).
823 `Pull Request 649`_
824 * Update seqtk version targetted by intro docs. e343b67_
825 * Various other Conda usability improvements. `Pull Request 634`_
826
827 ---------------------
828 0.38.1 (2017-02-06)
829 ---------------------
830
831 * Fix bug with ``shed_lint --urls`` introduced in 0.38.0.
832 84ebc1f_
833
834 ---------------------
835 0.38.0 (2017-02-06)
836 ---------------------
837
838 * Trim down the default amount of logging during testing.
839 `Pull Request 629`_, `Issue 515`_
840 * Improved log messages during shed operations. 08c067c_
841 * Update tool XSD against latest Galaxy.
842 fca4183_, 03c9658_
843 * Fix bug where ``shed_lint --tools`` for a suite lints the same tools multiple
844 times.
845 `Issue 564`_, `Pull Request 628`_
846
847 ---------------------
848 0.37.0 (2017-01-25)
849 ---------------------
850
851 * Update to the latest `galaxy-lib`_ release. This means new installs start with
852 Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes many
853 Conda_ related bugs.
854 * Change defaults so that Conda automatically initializes and performs tool installs
855 by default from within the spawned Galaxy server. The trio of flags
856 ``--conda_dependency_resolution``, ``--conda_auto_install``, and ``--conda_auto_init``
857 are effectively enabled by default now. 4595953_
858 * Use the Galaxy cached dependency manager by default (thanks to `@abretaud`_).
859 `Pull Request 612`_
860 * Test Conda dependency resolution for more versions of Galaxy including the forthcoming
861 release of 17.01.
862 * Update to the latest Galaxy tool XSD for various tool linting fixes. 32acd68_
863 * Fix pip ignores for ``bioconda_scripts`` (thanks to `@nturaga`_)
864 `Pull Request 614`_
865
866 ---------------------
867 0.36.1 (2016-12-12)
868 ---------------------
869
870 * Fix move error when using ``project_init``.
871 `Issue 388`_, `Pull Request 610`_
872 * Improved integration testing for ``test`` command. `Pull Request 609`_
873 * Update CWL links to v1.0 (thanks to `@mr-c`_).
874 `Pull Request 608`_
875
876 ---------------------
877 0.36.0 (2016-12-11)
878 ---------------------
879
880 * Bring in latest tool XSD file from Galaxy (thanks to `@peterjc`_).
881 `Pull Request 605`_
882 * PEP8 fixes for various linting problems
883 (thanks to `@peterjc`_).
884 `Pull Request 606`_
885 * Update tool syntax URL to new URL (thanks to `@mvdbeek`_).
886 `Pull Request 602`_
887
888 ---------------------
889 0.35.0 (2016-11-14)
890 ---------------------
891
892 * Native support for building bioconductor tools and recipes
893 (thanks to `@nturaga`_). `Pull Request 570`_
894 * Fixes for running Galaxy via docker-galaxy-stable (thanks to
895 `@bgruening`_). 50d3c4a_
896 * Import order linting fixes (thanks to `@bgruening`_).
897
898 ---------------------
899 0.34.1 (2016-10-12)
900 ---------------------
901
902 * Mimic web browser to validate user help URLs fixing `Issue 578`_
903 (thanks to `@peterjc`_). `Pull Request 591`_
904 * Fix for Bioconda recipes depending on ``conda-forge`` (thanks to `@nsoranzo`_).
905 `Pull Request 590`_
906
907
908 ---------------------
909 0.34.0 (2016-10-05)
910 ---------------------
911
912 * Implement ``mull`` command to build containers for tools based on Conda_
913 recipes matching requirement definitions. 08cef54_
914 * Implement ``--mulled_containers`` flag on ``test``, ``serve``, and ``run``
915 commands to run tools in "mulled" containers. Galaxy will first search
916 locally cache containers (such as ones built with ``mull``), then search
917 the mulled namespace of `quay.io`_, and finally build one on-demand if
918 needed using `galaxy-lib`_ and Involucro_ developed by `@thriqon`_.
919 * Implement ``--conda_requirements`` flag on ``lint`` command to ensure requirements
920 can be resolved in best practice channels. 9da8387_
921 * Allow ``conda_install`` command over multiple tool paths. 2e4e5fc_
922 * Update pip_ as part of setting virtual environment in ``Makefile`` target.
923 19b2ee9_
924 * Add script to auto-update Bioconda_ recipe for Planemo and open a pull request.
925 f0da66f_
926
927 ---------------------
928 0.33.2 (2016-09-28)
929 ---------------------
930
931 * Fix HISTORY.rst link problem that prevented correct display of content on PyPI_.
932
933 ---------------------
934 0.33.1 (2016-09-28)
935 ---------------------
936
937 * Fix ``lint --urls`` false positives by being more restrictive with what is considered a URL
938 (fixed by `@hexylena`_ after detailed report from `@peterjc`_).
939 `Issue 573`_, `Pull Request 579`_
940
941 ---------------------
942 0.33.0 (2016-09-23)
943 ---------------------
944
945 * Enable XSD validation of tools by default (restore old behavior with
946 ``planemo lint --no_xsd``). 1ef05d2_
947 * Implement a ``conda_lint`` command to lint Conda_ recipes based
948 on `anaconda-verify`_. 6a6f164_
949 * Implement ``clone`` and ``pull_request`` commands to ease PRs
950 (with documentation fixes from `@martenson`_).
951 e925ba1_, ea5324f_
952 * Update `galaxy.xsd`_ to allow version_command's to have an interpreter
953 attribute. 7cca2e4_
954 * Apply improvement from `@nsoranzo`_ for Planemo's use of
955 `git diff <https://git-scm.com/docs/git-diff>`__.
956 6f91719_
957 * Pull in downstream refactoring of ``tool_init`` code from `@nturaga`_'s
958 Bioconductor_ work. ccdd2d5_
959 * Update to latest `Tool Factory`_ code from `tools-iuc`_. ca88b0c_
960 * Small code cleanups. b6d8294_, d6da3a8_
961 * Fixup docs in ``planemo.xml.validation``.
962 * Allow skipping newly required lxml_ dependency in `setup.py`_. 34538de_
963
964 ---------------------
965 0.32.0 (2016-09-16)
966 ---------------------
967
968 * Enhance ``planemo lint --xsd`` to use a fairly complete and newly official XSD
969 definition. `Pull Request 566`_
970 * Migrate and update documentation related to tool XML macros and handling
971 multiple outputs from the Galaxy wiki (with help from `@bgruening`_, `@mvdbeek`_,
972 and `@nsoranzo`_). `Pull Request 559`_
973 * Documentation fixes (thanks to `@ramezrawas`_). `Pull Request 561`_
974 * Do not fail URL linting in case of too many requests (thanks to `@nsoranzo`_).
975 `Pull Request 565`_
976
977 ---------------------
978 0.31.0 (2016-09-06)
979 ---------------------
980
981 * Implement new commands to ``ci_find_repos`` and ``ci_find_tools`` to ease
982 CI scripting.
983 `Pull Request 555`_
984
985 ---------------------
986 0.30.2 (2016-09-01)
987 ---------------------
988
989 * Fix another problem with Conda_ prefix handling when using
990 ``--conda_dependency_resolution``. f7b6c7e_
991
992 ---------------------
993 0.30.1 (2016-09-01)
994 ---------------------
995
996 * Fix a problem with Conda_ prefix handling when using
997 ``--conda_dependency_resolution``. f7b6c7e_
998 * Fix for quote problem in ``update_planemo_recipe.bash``. 6c03de8_
999 * Fix to restore linting of ``tests/`` directory and fix import order throughout
1000 module. ef4b9f4_
1001
1002 ---------------------
1003 0.30.0 (2016-09-01)
1004 ---------------------
1005
1006 * Update to the latest `galaxy-lib`_ release and change Conda_ semantics to match
1007 recent updates to Galaxy. For the most robust Conda_ usage - use planemo 0.30+
1008 with Galaxy 16.07 or master.
1009 07d94bd_
1010 * Implement the ``--conda_auto_init`` flag for ``conda_install``. ca19910_
1011 * Allow the environment variable ``PLANEMO_CONDA_PREFIX`` to set a default
1012 for ``--conda_prefix``.
1013 24008ab_
1014 * Fixup documentation regarding installs and Conda_. ce44e87_
1015 * Fix and lint Python module import order throughout project.
1016 `Pull Request 550`_
1017 * Use ``cp`` rather than symlink to ``$DOWNLOAD_CACHE`` in the
1018 ``dependency_script`` command (thanks to `@peterjc`_). c2204b3_
1019 * Fixes for the Homebrew recipe updater. c262b6d_
1020
1021 ---------------------
1022 0.29.1 (2016-08-19)
1023 ---------------------
1024
1025 * Improved handling of Python 2.7 specific dependencies.
1026
1027 ---------------------
1028 0.29.0 (2016-08-19)
1029 ---------------------
1030
1031 * Look for sha256sum checksums during shed_lint (thanks to `@peterjc`_).
1032 `Pull Request 539`_
1033 * An assortment fixes and enhancements to the ``dependency_script`` command
1034 (thanks to `@peterjc`_). `Pull Request 541`_, `Pull Request 545`_
1035 * Fix shed_build to respect exclude: in .shed.yml (thanks to `@nsoranzo`_).
1036 `Pull Request 540`_
1037 * Fix linting of tool URLs (thanks to `@nsoranzo`_). `Pull Request 546`_
1038
1039 ---------------------
1040 0.28.0 (2016-08-17)
1041 ---------------------
1042
1043 * Fixes for bioblend_ v0.8.0 (thanks to `@nsoranzo`_). 9fdf490_
1044 * Enable shed repo type update (thanks to `@nsoranzo`_). 3ceaa40_
1045 * Create suite repositories with repository_suite_definition type by default
1046 (thanks to `@nsoranzo`_).
1047 057f4f0_
1048 * Include ``shed_lint`` in script run by ``travis_init`` (thanks to `@peterjc`_).
1049 `Pull Request 528`_
1050 * Minor polish to the ``travis_init`` command (thanks to `@peterjc`_).
1051 `Pull Request 512`_
1052 * Update pip_ and setuptools on TravisCI; fix travis_init (thanks to `@peterjc`_).
1053 `Pull Request 521`_
1054 * Shorten command one line descriptions for main help (thanks to `@peterjc`_).
1055 `Pull Request 510`_
1056 * Use ``planemo test --no_cache_galaxy`` under TravisCI (thanks to `@peterjc`_).
1057 `Pull Request 513`_
1058 * Improve and fix docs ahead of GCC 2016 (thanks to `@martenson`_).
1059 `Pull Request 498`_, 725b232_
1060 * Add description of ``expect_num_outputs`` to planemo FAQ. a066afb_
1061 * Revise planemo tools docs to be more explicit about collection identifiers.
1062 a811e65_
1063 * Add more docs on existing dynamic tool output features. `Pull Request 526`_
1064 * Fix serve command doc (thanks to `@nsoranzo`_). 8c088c6_
1065 * Fix `make lint-readme` (RST link errors) (thanks to `@peterjc`_).
1066 `Pull Request 525`_
1067 * Add union bedgraph example to project templates (for GCC demo example).
1068 d53bcd6_
1069 * Add Flow Cytometry Analysis, Data Export, and Constructive Solid Geometry as
1070 shed categories (thanks to `@bgruening`_, `@gregvonkuster`_, and `@nsoranzo`_).
1071 e890ab5_, 08bb354_, e2398fb_
1072 * Remove duplicated attribute in docs/writing/bwa-mem_v5.xml (thanks to
1073 Paul Stewart `@pstew`_).
1074 `Pull Request 507`_
1075
1076 ---------------------
1077 0.27.0 (2016-06-22)
1078 ---------------------
1079
1080 * Use ephemeris to handle syncing shed tools for workflow actions.
1081 1c6cfbb_
1082 * More planemo testing enhancements for testing artifacts that aren't
1083 Galaxy tools. `Pull Request 491`_
1084 * Implement ``docker_galaxy`` engine type. eb039c0_, `Issue 15`_
1085 * Enhance profiles to be Dockerized Galaxy-aware. `Pull Request 488`_
1086 * Add linter for DOI type citation - thanks to `@mvdbeek`_.
1087 `Pull Request 484`_
1088
1089 ---------------------
1090 0.26.0 (2016-05-20)
1091 ---------------------
1092
1093 * Implement ``Engine`` and ``Runnable`` abstractions - Planemo now has
1094 beta support for testing Galaxy workflows and CWL_ tools with Galaxy and
1095 any CWL_ artifact with cwltool_.
1096 `Pull Request 454`_, 7be1bf5_
1097 * Fix missing command_line in test output json. e38c436_
1098 * More explicit Galaxy ``job_conf.xml`` handling, fixes bugs caused by
1099 ``galaxy_root`` having existing and incompatible ``job_conf.xml`` files
1100 and makes it possible to specify defaults with fixed server name. c4dfd55_
1101 * Introduce profile commands (``profile_create``, ``profile_delete``, and
1102 ``profile_list``) and profile improvements (automatic postgres database
1103 creation support). `Pull Request 480`_, a87899b_
1104 * Rework Galaxy test reporting to use structured data instead of XUnit
1105 data. 4d29bf1_
1106 * Refactor Galaxy configuration toward support for running Galaxy in
1107 docker-galaxy-stable. `Pull Request 479`_
1108
1109 ---------------------
1110 0.25.1 (2016-05-11)
1111 ---------------------
1112
1113 * Tweak dependencies to try to fix cwltool_ related issues - such
1114 as `Issue 475`_.
1115
1116 ---------------------
1117 0.25.0 (2016-05-11)
1118 ---------------------
1119
1120 * Implement Galaxy "profiles" - the ability to configure
1121 perisistent, named environments for ``serve`` and ``test``.
1122 5d08b67_
1123 * Greatly improved ``serve`` command - make ``test-data``
1124 available as an FTP folder, (on 16.07) automatically log
1125 in an admin user, and many more options (such as those
1126 required for "profiles" and a ``--daemon`` mode).
1127 * Two fixes to ensure more consistent, dependable ``test`` output.
1128 `Pull Request 472`_, f3c6917_
1129 * Add code and documentation for linting (``lint``) and
1130 building (``tool_init``) CWL_ tools. a4e6958_, b0b867e_,
1131 4cd571c_
1132 * If needed for Conda_ workaround, shorten ``config_directory``
1133 path (thanks to `@mvdbeek`_). efc5f30_
1134 * Fix ``--no_cache_galaxy`` option (thanks to Gildas Le
1135 Corguillé). d8f2038_
1136 * Target draft 3 of CWL_ instead of draft 2. 775bf49_
1137 * Fix ``cwltool`` dependency version - upstream changes broke
1138 compatibility. `65b999d`_
1139 * Add documentation section and slides about recent Galaxy
1140 tool framework changes (with fix from `@remimarenco`_). 069e7ba_
1141 * Add IUC standards to Planemo docs. 2ae2b49_
1142 * Improve collection-related contents in documentation
1143 (thanks in part to `@martenson`_).
1144 fea51fc_, 13a5ae7_
1145 * Add documentation on ``GALAXY_SLOTS`` and running planemo
1146 on a cluster. 45135ff_, e0acf91_
1147 * Revise command-line handling framework for consistency and
1148 extension - allow extra options to be configured as
1149 defaults ``~/.planemo.yml`` including ``--job_config_file``
1150 and Conda_ configuration options. e769118_, 26e378e_
1151 * Fix ``tool_init`` commans options typos (thanks to
1152 Nitesh Turaga). 826d371_
1153 * Refactor galaxy-related modules into submodules of a new
1154 ``planemo.galaxy`` package. 8e96864_
1155 * Fix error message typo (thanks to `@blankenberg`_). b1c8f1d_
1156 * Update documentation for recent command additions. 3f4ab44_
1157 * Rename option ``--galaxy_sqlite_database`` option to
1158 ``--galaxy_database_seed`` and fix it so it actually works.
1159 f7554d1_
1160 * Add ``--extra_tools`` option to ``serve`` command. 02a08a0_
1161 * Update project testing to include linting documentation
1162 (``docs/``), Python import order, and docstrings.
1163 a13a120_, 6e1e726_, 95d5cba_
1164
1165
1166 ---------------------
1167 0.24.2 (2016-04-25)
1168 ---------------------
1169
1170 * Revert "check ``.shed.yml`` owner against credentials during shed
1171 creation", test was incorrect and preventing uploads.
1172 `Pull Request 425`_, `Issue 246`_
1173
1174 ---------------------
1175 0.24.1 (2016-04-08)
1176 ---------------------
1177
1178 * Fix test summary report. `Pull Request 429`_
1179 * Improve error reporting when running ``shed_test``. ce8e1be_
1180 * Improved code comments and tests for shed related functionality.
1181 89674cb_
1182 * Rev `galaxy-lib`_ dependency to 16.4.1 to fix wget usage in
1183 newer versions of wget. d76b489_
1184
1185 ---------------------
1186 0.24.0 (2016-03-29)
1187 ---------------------
1188
1189 * Drop support for Python 2.6. 93b7bda_
1190 * A variety of fixes for ``shed_update``.
1191 `Pull Request 428`_, `Issue 416`_
1192 * Fix reporting of metadata updates for invalid shed updates.
1193 `Pull Request 426`_, `Issue 420`_
1194 * Check ``.shed.yml`` owner against credentials during shed creation.
1195 `Pull Request 425`_, `Issue 246`_
1196 * Fix logic error if there is a problem with ``shed_create``. 358a42c_
1197 * Tool documentation improvements. 0298510_, a58a3b8_
1198
1199 ---------------------
1200 0.23.0 (2016-02-15)
1201 ---------------------
1202
1203 * Fix duplicated attributes with Conda_ resolver (thanks
1204 to Björn Grüning). `Pull Request 403`_
1205 * Upgrade to latest version of `galaxy-lib`_ for more linting.
1206 * Attempt to better handle conditional dependency on cwltool.
1207
1208 ---------------------
1209 0.22.2 (2016-01-14)
1210 ---------------------
1211
1212 * Fixed bug targetting forthcoming release of Galaxy 16.01.
1213
1214 ---------------------
1215 0.22.1 (2016-01-14)
1216 ---------------------
1217
1218 * Fixed problem with PyPI_ build artifacts due to submodule's not
1219 being initialized during previous release.
1220
1221 ---------------------
1222 0.22.0 (2016-01-13)
1223 ---------------------
1224
1225 * Add ``--skip_venv`` to support running Galaxy 16.01 inside of
1226 conda environments. 9f3957d_
1227 * Implement conda support. f99f6c1_, ad3b2f0_, 5e0b6d1_
1228 * Update LICENSE for Planemo to match Galaxy. 15d33c7_
1229 * Depend on new `galaxy-lib`_ on PyPI_ instead of previous hacks....
1230 `Pull Request 394`_
1231 * Fix egg caching against master/15.10. 6d0f502_
1232 * Fix bug causing shed publishing of ``.svn`` directories.
1233 `Issue 391`_
1234 * Bug fixes for Conda_ support thanks to `@bgruening`_. 63e456c_
1235 * Fix document issues thanks to `@einon`_.
1236 `Pull Request 390`_
1237 * Improve client for shed publishing to support newer shed backend
1238 being developed by `@hexylena`_. `Pull Request 394`_
1239 * Tool Shed ``repo_id`` change, `@hexylena`_. `Pull Request 398`_
1240 * Various other small changes to testing, project structure, and
1241 Python 3 support.
1242
1243 ---------------------
1244 0.21.1 (2015-11-29)
1245 ---------------------
1246
1247 * Fix serious regression to ``test`` command. 94097c7_
1248 * Small fixes to release process. 4e1377c_, 94645ed_
1249
1250 ---------------------
1251 0.21.0 (2015-11-29)
1252 ---------------------
1253
1254 * If ``virtualenv`` not on ``PATH``, have Planemo create one for Galaxy.
1255 5b97f2e_
1256 * Add documentation section on testing tools installed in an existing
1257 Galaxy instance. 1927168_
1258 * When creating a virtualenv for Galaxy, prefer Python 2.7.
1259 e0577e7_
1260 * Documentation fixes and improvements thanks to `@martenson`_.
1261 0f8cb10_, 01584c5_, b757791_
1262 * Specify a minimum ``six`` version requirement. 1c7ee5b_
1263 * Add script to test a planemo as a wheel. 6514ff5_, `Issue 184`_
1264 * Fix empty macro loading. `Issue 362`_
1265 * Fix an issue when you run ``shed_diff --shed_target local`` thanks
1266 to Gwendoline Andres and Gildas Le Corguillé at ABiMS Roscoff.
1267 `Pull Request 375`_
1268 * Fix ``shed_diff`` printing to stdout if ``-o`` isn't specified.
1269 f3394e7_
1270 * Small ``shed_diff`` improvements to XML diffing and XUnit reporting.
1271 af7448c_, 83e227a_
1272 * More logging of ``shed_diff`` results if ``--verbose`` flagged.
1273 9427b47_
1274 * Add ``test_report`` command for rebuilding reports from structured JSON.
1275 99ee51a_
1276 * Fix option bug with Click 6.0 thanks to `@bgruening`_. 2a7c792_
1277 * Improved error messages for test commands. fdce74c_
1278 * Various fixes for Python 3. 2f66fc3_, 7572e99_, 8eda729_, 764ce01_
1279 * Use newer travis container infrastructure for testing. 6d81a94_
1280 * Test case fixes. 98fdc8c_, 0e4f70a_
1281
1282 ---------------------
1283 0.20.0 (2015-11-11)
1284 ---------------------
1285
1286 * More complete I/O capturing for XUnit. 6409449_
1287 * Check for select parameter without options when linting tools.
1288 `Issue 373`_
1289 * Add ``--cwl_engine`` argument to ``cwl_run`` command. dd94ddc_
1290 * Fixes for select parameter linting. 8b31850_
1291 * Fix to demultiplexing repositories after tool uploads. `Issue 361`_
1292 * Fix to update planemo for Galaxy wheels. 25ef0d5_
1293 * Various fixes for Python 2.6 and Python 3.
1294 c1713d2_, 916f610_, c444855_
1295
1296 ---------------------
1297 0.19.0 (2015-11-03)
1298 ---------------------
1299
1300 * Initial implementation of ``cwl_run`` command that runs a
1301 CWL tool and job file through Galaxy. 49c5c1e_
1302 * Add ``--cwl`` flag to ``serve`` to experimentally serve CWL tools
1303 in Galaxy.
1304 `Pull Request 339`_
1305 * Implement highly experimental ``cwl_script`` command to convert
1306 a CWL job to a bash script. 508dce7_
1307 * Add name to all XUnit reports (thanks to `@hexylena`_).
1308 `Pull Request 343`_
1309 * Capture stdout and stderr for ``shed_diff`` and ``shed_update``
1310 XUnit reports. `Pull Request 344`_
1311 * More tool linting (conditionals) thanks to `@hexylena`_.
1312 `Pull Request 350`_
1313 * UTF-8 fixes when handling XUnit reports. `Pull Request 345`_
1314 * Add `Epigenetics` as Tool Shed category. `Pull Request 351`_
1315 * Merge changes to common modules shared between Galaxy, Planemo, and Pulsar (thanks to `@natefoo`_).
1316 `Pull Request 356`_
1317 * Add ``--cite_url`` to ``tool_init``. fdb1b51_
1318 * ``tool_init`` bug fix. f854138_
1319 * Fix `setup.py`_ for cwltool and bioblend_ changes. 1a157d4_
1320 * Add option to specify template sqlite database locally. c23569f_
1321 * Add example IPython notebooks to docs. c8640b6_
1322
1323 ---------------------
1324 0.18.1 (2015-10-22)
1325 ---------------------
1326
1327 * Fix issue with test reporting not being populated. 19900a6_
1328
1329 ---------------------
1330 0.18.0 (2015-10-20)
1331 ---------------------
1332
1333 * Improvements to ``docker_shell`` usability (thanks to `@kellrott`_).
1334 `Pull Request 334`_
1335 * Add docker pull attempt when missing Dockerfile (thanks to `@kellrott`_).
1336 `Pull Request 333`_
1337 * Fix bug inferring which files are tool files (thanks to `@hexylena`_).
1338 `Pull Request 335`_, `Issue 313`_
1339 * Initial work toward automating brew recipe update. 4d6f7d9_, `Issue 329`_
1340
1341 ---------------------
1342 0.17.0 (2015-10-19)
1343 ---------------------
1344
1345 * Implement basic XUnit report option for ``shed_update`` (thanks to `@martenson`_).
1346 `Pull Request 322`_
1347 * Fix issues with producing test outputs. 572e754_
1348 * Xunit reporting improvements - refactoring, times, diff output (thanks to `@hexylena`_).
1349 `Pull Request 330`_
1350 * Implement project governance policy and update developer code of conduct to
1351 match that of the Galaxy project. `Pull Request 316`_
1352 * Update filters for account for new ``.txt`` and ``.md`` test outputs
1353 (thanks to `@hexylena`_). `Pull Request 327`_
1354 * Add verbose logging to galaxy test output handling problems. 5d7db92_
1355 * Flake8 fixes (thanks to `@martenson`_). 949a36d_
1356 * Remove uses of deprecated ``mktemp`` Python standard library function
1357 (thanks to `@hexylena`_). `Pull Request 330`_
1358
1359 ---------------------
1360 0.16.0 (2015-10-07)
1361 ---------------------
1362
1363 * Adding new command ``dependency_script`` to convert Tool Shed dependencies
1364 into shell scripts - thanks to `@peterjc`_.
1365 `Pull Request 310`_, f798c7e_, `Issue 303`_
1366 * Implement profiles in sheds section of the ``~/.planemo.yml``.
1367 `Pull Request 314`_
1368
1369 ---------------------
1370 0.15.0 (2015-10-01)
1371 ---------------------
1372
1373 * Template framework for reporting including new markdown and plain
1374 text reporting options for testing - thanks to `@hexylena`_.
1375 `Pull Request 304`_
1376 * XUnit style reporting for ``shed_diff`` command - thanks to
1377 `@hexylena`_. `Pull Request 305`_
1378 * Add new ``shed_build`` command for building repository tarballs -
1379 thanks to `@kellrott`_. `Pull Request 297`_
1380 * Fix exit code handling for ``lint`` commands - thanks to `@mvdbeek`_.
1381 `Pull Request 292`_
1382 * Improved documentation for ``serve`` command - thanks to `@lparsons`_.
1383 `Pull Request 312`_
1384 * Tiny backward compatible Python 3 tweaks for `Tool Factory`_ - thanks
1385 to `@peterjc`_. dad2d9d_
1386 * Fixed detection of virtual environment in ``Makefile`` - thanks to
1387 `@lparsons`_. `Pull Request 311`_
1388 * Updates to Galaxy XSD - thanks to `@mr-c`_. `Pull Request 309`_
1389 * Allow reading shed key option from an environment variable.
1390 `Pull Request 307`_
1391 * Allow specifying host to serve Galaxy using ``-host`` - thanks in
1392 part to `@chambm`_. `Pull Request 301`_
1393 * Allow specifying defaults for ``-host`` and ``--port`` in
1394 ``~/.planemo.yml``. `Pull Request 301`_
1395 * Improve ``~/.planemo.yml`` sample comments - thanks to `@martenson`_.
1396 `Pull Request 287`_
1397 * Update tool shed categories - thanks to `@bgruening`_. `Pull Request 285`_
1398 * Improved output readibility for ``diff`` command - thanks to `@martenson`_. `Pull Request 284`_
1399
1400 ---------------------
1401 0.14.0 (2015-08-06)
1402 ---------------------
1403
1404 * Allow ``-t`` as shorthand for ``--shed_target`` (thanks to Peter Cock).
1405 `Pull Request 278`_
1406 * Fix ``tool_init`` command to use ``from_work_dir`` only if file in command
1407 (thanks to bug report and initial fix outline by Gildas Le Corguillé).
1408 `Pull Request 277`_
1409 * Various documentation fixes (thanks in part to Peter Cock and Daniel
1410 Blankenberg). `Pull Request 256`_, `Pull Request 253`_, `Pull Request 254`_,
1411 `Pull Request 255`_, `Pull Request 251`_, `Issue 272`_
1412
1413 ---------------------
1414 0.13.2 (2015-07-06)
1415 ---------------------
1416
1417 * Fix project_init for missing files. cb5b906_
1418 * Various documentation improvements.
1419
1420 ---------------------
1421 0.13.1 (2015-07-01)
1422 ---------------------
1423
1424 * Fix for ``shed_init`` producing non-standard type hints. `Issue 243`_,
1425 f0610d7_
1426 * Fix tool linting for parameters that define an ``argument`` but not a
1427 ``name``. `Issue 245`_, aad1eed_
1428 * Many doc updates including a tutorial for developing tools in a test-driven
1429 fashion and instructions for using the planemo appliance through Kitematic
1430 (with Kitematic screenshots from E. Rasche).
1431
1432 ---------------------
1433 0.13.0 (2015-06-28)
1434 ---------------------
1435
1436 * If planemo cannot find a Galaxy root, it will now automatically fetch
1437 one (specifing ``--galaxy_install`` will still force a fetch).
1438 `Pull Request 235`_
1439 * `Docuementation <http://planemo.readthedocs.org/en/latest/appliance.html>`__
1440 has been updated to reflect new and vastly improved Docker and Vagrant
1441 virtual appliances are now available, as well as a new VirtualBox OVA
1442 variant.
1443 * Update linting for new tool XML features (including ``detect_errors``
1444 and output collections). `Issue 233`_, 334f2d4_
1445 * Fix ``shed_test`` help text. `Issue 223`_
1446 * Fix code typo (thanks to Nicola Soranzo). `Pull Request 230`_
1447 * Improvements to algorithm used to guess if an XML file is a tool XML file.
1448 `Issue 231`_
1449 * Fix configuration file handling bug. `Issue 240`_
1450
1451 ---------------------
1452 0.12.2 (2015-05-23)
1453 ---------------------
1454
1455 * Fix ``shed_test`` and ``shed_serve`` for test and local tool sheds.
1456 f3cafaa_
1457
1458 ---------------------
1459 0.12.1 (2015-05-21)
1460 ---------------------
1461
1462 * Fix to ensure the tab completion script is in the Python source tarball
1463 (required for setting up tab-completion for Homebrew). 6b4e7a6_
1464
1465 ---------------------
1466 0.12.0 (2015-05-21)
1467 ---------------------
1468
1469 * Implement a ``--failed`` flag for the ``test`` command to rerun
1470 previously faied tests. `Pull Request 210`_
1471 * Implement ``shed_update`` to upload contents and update repository
1472 metadata. `Pull Request 216`_
1473 * Implement ``shed_test`` and ``shed_serve`` commands to test and view
1474 published artifacts in the Tool Shed. `Pull Request 213`_, `Issue 176`_
1475 * Add shell tab-completion script. 37dcc07_
1476 * Many more commands allow specifing multiple tool and/or repository targets.
1477 `Issue 150`_
1478 * Add -m as alias for --message in planemo shed_upload (thanks to
1479 Peter Cock). `Pull Request 200`_
1480 * Add ``--ensure_metadata`` option to ``shed_lint`` to ensure ``.shed.yml``
1481 files contain many repository. `Pull Request 215`_
1482 * More developer documentation, additional ``make`` targets including ones
1483 for setting up git pre-commit hooks. cc8abb6_, `Issue 209`_
1484 * Small README improvement (thanks to Martin Čech) b53006d_
1485 * Fixes for shed operation error handling (thanks to Martin Čech).
1486 `Pull Request 203`_, `Pull Request 206`_
1487 * Fix for "smart" ``shed_diff`` not in the repository root directory
1488 (thanks to Peter Cock). `Pull Request 207`_, `Issue 205`_
1489 * Recursive ``shed_diff`` with directories not yet in Tool Shed.
1490 `Pull Request 208`_
1491 * Improve error handling and reporting for problematic ``--shed_target``
1492 values. `Issue 217`_
1493 * Fix typos in lint messages. `Issue 211`_
1494
1495
1496 ---------------------
1497 0.11.1 (2015-05-12)
1498 ---------------------
1499
1500 * Fix default behavior for ``planemo lint`` to use current directory if
1501 explicit paths are not supplied. 1e3668a_
1502
1503 ---------------------
1504 0.11.0 (2015-05-12)
1505 ---------------------
1506
1507 * More compact syntax for defining multiple custom inclusions in ``.shed.yml``
1508 files - thanks to Peter Cock. `Issue 180`_, `Pull Request 185`_,
1509 `Pull Request 196`_
1510 * Prevent ambigous destinations when defining custom inclusions in
1511 ``.shed.yml``- thanks to Peter Cock. `Pull Request 186`_
1512 * ``lint`` now warns if tool ids contain whitespace. `Pull Request 190`_
1513 * Handle empty tar-balls gracefully on older Python versions - thanks
1514 to Peter Cock. `Pull Request 187`_
1515 * Tweak quoting in ``cp`` command - thanks to Peter Cock. 6bcf699_
1516 * Fix regression causing testing to no longer produce "pretty" test
1517 results under certain circumstances. `Issue 188`_
1518 * Fix for recursive ``shed_diff`` folder naming. `Issue 192`_
1519 * Fix output definitions to ``tool_init`` command. `Issue 189`_
1520
1521 ---------------------
1522 0.10.0 (2015-05-06)
1523 ---------------------
1524
1525 * Extend ``shed_lint`` to check for valid actions in tool_dependencies.xml
1526 files. 8117e03_
1527 * Extend ``shed_lint`` to check for required files based on repository type.
1528 `Issue 156`_
1529 * Ignore common editor backup files during ``shed_upload``. `Issue 179`_
1530 * Fix missing file when installing from source via PyPI_. `Issue 181`_
1531 * Fix ``lint`` to verify ``data`` inputs specify a ``format`` attribute.
1532 8117e03_
1533 * Docstring fix thanks to `@peterjc`_. fe7ad46_
1534
1535
1536 ---------------------
1537 0.9.0 (2015-05-03)
1538 ---------------------
1539
1540 * Add new logo to the README thanks to `@petrkadlec`_ from `puradesign.cz
1541 <http://puradesign.cz/en>`__ and `@carlfeberhard`_ from the Galaxy Project.
1542 `Issue 108`_
1543 * Implement smarter ``shed_diff`` command - it now produces a meaningful
1544 exit codes and doesn't report differences if these correspond to attributes
1545 that will be automatically populated by the Tool Shed. `Issue 167`_
1546 * Use new smarter ``shed_diff`` code to implement a new ``--check_diff``
1547 option for ``shed_upload`` - to check for meaningful differences before
1548 updating repositories. `Issue 168`_
1549 * Record git commit hash during ``shed_upload`` if the ``.shed.yml`` is
1550 located in a git repository. `Issue 170`_
1551 * Allow ``shed_`` operations to operate on git URLs directly. `Issue 169`_
1552 * Fail if missing file inclusion statements encountered during ``.shed.yml``
1553 repository resolution - bug reported by `@peterjc`_. `Issue 158`_
1554 * Improved exception handling for tool shed operations including new
1555 ``--fail_fast`` command-line option. * `Issue 114`_, `Pull Request 173`_
1556 * Implement more validation when using the ``shed_init`` command. 1cd0e2d_
1557 * Add ``-r/--recursive`` option to ``shed_download`` and ``shed_diff``
1558 commands and allow these commands to work with ``.shed.yml`` files defining
1559 multipe repositories. 40a1f57_
1560 * Add ``--port`` option to the ``serve`` and ``tool_factory`` commands.
1561 15804be_
1562 * Fix problem introduced with `setup.py`_ during the 0.9.0 development cycle
1563 - thanks to `@peterjc`_. `Pull Request 171`_
1564 * Fix clone bug introduced during 0.9.0 development cycle - thanks to
1565 `@bgruening`_. `Pull Request 175`_
1566
1567 ---------------------
1568 0.8.4 (2015-04-30)
1569 ---------------------
1570
1571 * Fix for Travis CI testing picking up invalid tests (reported by `@takadonet`_). `Issue 161`_
1572 * Fix tar ordering for consistency (always sort by name) - thanks to `@peterjc`_. `Pull Request 164`_, `Issue 159`_
1573 * Fix exception handling related to tool shed operations - thanks to `@peterjc`_. `Pull Request 155`_, b86fe1f_
1574
1575 ---------------------
1576 0.8.3 (2015-04-29)
1577 ---------------------
1578
1579 * Fix bug where ``shed_lint`` was not respecting the ``-r/--recursive`` flag.
1580 9ff0d2d_
1581 * Fix bug where planemo was producing tar files incompatible with the Tool
1582 Shed for package and suite repositories. a2ee135_
1583
1584 ---------------------
1585 0.8.2 (2015-04-29)
1586 ---------------------
1587
1588 * Fix bug with ``config_init`` command thanks to `@bgruening`_. `Pull Request 151`_
1589 * Fix unnessecary ``lint`` warning about ``parallelism`` tag reported by
1590 `@peterjc`_. 9bf1eab_
1591
1592 ---------------------
1593 0.8.1 (2015-04-28)
1594 ---------------------
1595
1596 * Fixes for the source distribution to allow installation of 0.8.0 via Homebrew.
1597
1598 ---------------------
1599 0.8.0 (2015-04-27)
1600 ---------------------
1601
1602 * Implement the new ``shed_lint`` command that verifies various aspects of tool
1603 shed repositories - including XSD_ validation of ``repository_dependencies.xml``
1604 and ``tool_dependencies.xml`` files, best practices for README files, and the
1605 contents of ``.shed.yml`` files. This requires the lxml_ library to be available
1606 to Planemo or the application xmllint_ to be on its ``PATH``. `Pull Request 130`_
1607 `Issue 89`_ `Issue 91`_ 912df02_ d26929e_ 36ac6d8_
1608 * Option to enable experimental XSD_ based validation of tools when ``lint``
1609 is executed with the new ``--xsd`` flag. This validation occurs against the
1610 unofficial `Galaxy Tool XSD project <https://github.com/JeanFred/Galaxy-XSD>`__
1611 maintained by `@JeanFred`_. This requires the lxml_ library to be
1612 available to Planemo or the application xmllint_ to be on its ``PATH``.
1613 `Pull Request 130`_ 912df02_
1614 * Allow skipping specific linters when using the ``lint`` command using the new
1615 ``--skip`` option. 26e3cdb_
1616 * Implement sophisticated options in ``.shed.yml`` to map a directory to many,
1617 custom Tool Shed repositories during shed operaitons such ``shed_upload``
1618 including automatically mapping tools to their own directories and automatically
1619 building suites repositories. `Pull Request 143`_
1620 * Make ``shed_upload`` more intelligent when building tar files so that package
1621 and suite repositories may have README files in source control and they will
1622 just be filtered out during upload. 53edd99_
1623 * Implement a new ``shed_init`` command that will help bootstrap ``.shed.yml``
1624 files in the specified directory. cc1a447_
1625 * Extend ``shed_init`` to automatically build a ``repository_rependencies.xml``
1626 file corresponding to a Galaxy workflow (``.ga`` file). `Issue 118`_ 988de1d_
1627 * In addition to a single file or directory, allow ``lint`` to be passed multiple
1628 files. 343902d_ `Issue 139`_
1629 * Add ``-r/--recursive`` option to ``shed_create`` and ``lint`` commands. 63cd431_
1630 01f2af9_
1631 * Improved output formatting and option to write diffs to a file for the
1632 ``shed_diff`` command. 965511d_
1633 * Fix lint problem when using new Galaxy testing features such as expecting
1634 job failures and verifing job output. `Issue 138`_
1635 * Fix typo in ``test`` help thanks to first time contributor `@pvanheus`_.
1636 `Pull Request 129`_ 1982076_
1637 * Fix NPE on empty ``help`` element when linting tools. `Issue 124`_
1638 * Fix ``lint`` warnings when ``configfiles`` are defined in a tool. 1a85493_
1639 * Fix for empty ``.shed.yml`` files. b7d9e96_
1640 * Fix the ``test`` command for newer versions of nose_. 33294d2_
1641 * Update help content and documentation to be clear ``normalize`` should not
1642 be used to update the contents of tool files at this time. 08de8de_
1643 * Warn on unknown ``command`` attributes when linting tools (anything but
1644 ``interpreter``). 4f61025_
1645 * Various design, documentation (including new documentation on Tool Shed
1646 `publishing <http://planemo.readthedocs.org/en/latest/publishing.html>`__),
1647 and testing related improvements (test coverage has risen from 65% to over
1648 80% during this release cycle).
1649
1650 ---------------------
1651 0.7.0 (2015-04-13)
1652 ---------------------
1653
1654 * Implement `shed_create` command to create Tool Shed repositories from
1655 ``.shed.yml`` files (thanks to E. Rasche). `Pull Request 101`_
1656 * Allow automatic creation of missing repositories during ``shed_upload``
1657 with the new ``--force_repository_creation`` flag (thanks to E. Rasche).
1658 `Pull Request 102`_
1659 * Allow specifying files to exclude in ``.shed.yml`` when creating tar files
1660 for ``shed_upload`` (thanks to Björn Grüning). `Pull Request 99`_
1661 * Resolve symbolic links when building Tool Shed tar files with
1662 ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 104`_
1663 * Add a `Contributor Code of Conduct
1664 <https://planemo.readthedocs.org/en/latest/conduct.html>`__.
1665 `Pull Request 113`_
1666 * Omit ``tool_test_output.json`` from Tool Shed tar file created with
1667 ``shed_upload`` (thanks to Dave Bouvier). `Pull Request 111`_
1668 * Update required version of bioblend_ to ``0.5.3``. Fixed `Issue 88`_.
1669 * Initial work on implementing tests cases for Tool Shed functionality.
1670 182fe57_
1671 * Fix incorrect link in HTML test report (thanks to Martin Čech). 4c71299_
1672 * Download Galaxy from the new, official Github repository. 7c69bf6_
1673 * Update travis_test to install stable planemo from PyPI_. 39fedd2_
1674 * Enable caching on ``--install_galaxy`` by default (disable with
1675 ``--no_cache_galaxy``). d755fe7_
1676
1677 ---------------------
1678 0.6.0 (2015-03-16)
1679 ---------------------
1680
1681 * Many enhancements to the tool building documentation - descriptions of macros, collections, simple and conditional parameters, etc...
1682 * Fix ``tool_init`` to quote file names (thanks to Peter Cock). `Pull Request 98`_.
1683 * Allow ignoring file patterns in ``.shed.yml`` (thanks to Björn Grüning). `Pull Request 99`_
1684 * Add ``--macros`` flag to ``tool_init`` command to generate a macro file as part of tool generation. ec6e30f_
1685 * Add linting of tag order for tool XML files. 4823c5e_
1686 * Add linting of ``stdio`` tags in tool XML files. 8207026_
1687 * More tests, much higher test coverage. 0bd4ff0_
1688
1689 ---------------------
1690 0.5.0 (2015-02-22)
1691 ---------------------
1692
1693 * Implement ``--version`` option. `Issue 78`_
1694 * Implement ``--no_cleanup`` option for ``test`` and ``serve`` commands to
1695 persist temp files. 2e41e0a_
1696 * Fix bug that left temp files undeleted. `Issue 80`_
1697 * More improvements to release process. fba3874_
1698
1699 ---------------------
1700 0.4.2 (2015-02-21)
1701 ---------------------
1702
1703 * Fix `setup.py`_ for installing non-Python data from PyPI_ (required newer
1704 for ``tool_factory`` command and reStructuredText linting). Thanks to
1705 Damion Dooley for the bug report. `Issue 83`_
1706
1707 ---------------------
1708 0.4.1 (2015-02-16)
1709 ---------------------
1710
1711 * Fix README.rst so it renders properly on PyPI_.
1712
1713 ---------------------
1714 0.4.0 (2015-02-16)
1715 ---------------------
1716
1717 * Implement ``tool_init`` command for bootstrapping creation of new
1718 tools (with `tutorial <http://planemo.readthedocs.org/en/latest/writing.html>`_.) 78f8274_
1719 * Implement ``normalize`` command for reorganizing tool XML and macro
1720 debugging. e8c1d45_
1721 * Implement ``tool_factory`` command to spin up Galaxy pre-configured the
1722 `Tool Factory`_. 9e746b4_
1723 * Added basic linting of ``command`` blocks. b8d90ab_
1724 * Improved linting of ``help`` blocks, including verifying valid
1725 `reStructuredText`. 411a8da_
1726 * Fix bug related to ``serve`` command not killing Galaxy properly when complete. 53a6766_
1727 * Have ``serve`` command display tools at the top level instead of in shallow sections. badc25f_
1728 * Add additional dependencies to ``setup.py`` more functionality works out
1729 of the box. 85b9614_
1730 * Fix terrible error message related to bioblend_ being unavailable.
1731 `Issue 70`_
1732 * Various smaller documentation and project structure improvements.
1733
1734 ---------------------
1735 0.3.1 (2015-02-15)
1736 ---------------------
1737
1738 * Fixes to get PyPI_ workflow working properly.
1739
1740 ---------------------
1741 0.3.0 (2015-02-13)
1742 ---------------------
1743
1744 * Add option (``-r``) to the ``shed_upload`` command to recursively upload
1745 subdirectories (thanks to E. Rasche). `Pull Request 68`_
1746 * Fix diff formatting in test reports (thanks to E. Rasche).
1747 `Pull Request 63`_
1748 * Grab updated test database to speed up testing (thanks to approach from
1749 E. Rasche and Dannon Baker). `Issue 61`_, dff4f33_
1750 * Fix test data command-line argument name (was ``test-data`` now it is
1751 ``test_data``). 834bfb2_
1752 * Use ``tool_data_table_conf.xml.sample`` file if
1753 ``tool_data_table_conf.xml.test`` is unavailable. Should allow some
1754 new tools to be tested without modifying Galaxy's global
1755 ``tool_data_table_conf.xml`` file. ac4f828_
1756
1757 ---------------------
1758 0.2.0 (2015-01-13)
1759 ---------------------
1760
1761 * Improvements to way Planemo loads its own copy of Galaxy modules to prevent
1762 various conflicts when launching Galaxy from Planemo. `Pull Request 56`_
1763 * Allow setting various test output options in ``~/.planemo.yml`` and disabling
1764 JSON output. 21bb463_
1765 * More experimental Brew and Tool Shed options that should not be considered
1766 part of Planemo's stable API. See bit.ly/gxbrew1 for more details.
1767 * Fix ``project_init`` for BSD tar (thanks to Nitesh Turaga for the bug
1768 report.) a4110a8_
1769 * Documentation fixes for tool linting command (thanks to Nicola Soranzo).
1770 `Pull Request 51`_
1771
1772 ---------------------
1773 0.1.0 (2014-12-16)
1774 ---------------------
1775
1776 * Moved repository URL to https://github.com/galaxyproject/planemo.
1777 * Support for publishing to the Tool Shed. `Pull Request 6`_
1778 * Support for producing diffs (``shed_diff``) between local repositories and
1779 the Tool Shed (based on scripts by Peter Cock). `Pull Request 33`_
1780 * Use tool's local test data when available - add option for configuring
1781 ``test-data`` target. `Pull Request 1`_
1782 * Support for testing tool features dependent on cached data. 44de95c_
1783 * Support for generating XUnit tool test reports. 82e8b1f_
1784 * Prettier HTML reports for tool tests. 05cc9f4_
1785 * Implement ``share_test`` command for embedding test result links in pull
1786 requests. `Pull Request 40`_
1787 * Fix for properly resolving links during Tool Shed publishing (thanks to Dave
1788 Bouvier). `Pull Request 29`_
1789 * Fix for citation linter (thanks to Michael Crusoe for the bug report). af39061_
1790 * Fix tool scanning for tool files with fewer than 10 lines (thanks to Dan
1791 Blankenberg). a2c13e4_
1792 * Automate more of Travis CI testing so the scripts added to tool repository
1793 can be smaller. 20a8680_
1794 * Documentation fixes for Travis CI (thanks to Peter Cock). `Pull Request 22`_,
1795 `Pull Request 23`_
1796 * Various documentation fixes (thanks to Martin Čech). 36f7cb1_, b9232e5_
1797 * Various smaller fixes for Docker support, tool linting, and documentation.
1798
1799 ---------------------
1800 0.0.1 (2014-10-04)
1801 ---------------------
1802
1803 * Initial work on the project - commands for testing, linting, serving Galaxy
1804 tools - and more experimental features involving Docker and Homebrew. 7d07782_
1805
1806 .. github_links
1807 .. _Pull Request 991: https://github.com/galaxyproject/planemo/pull/991
1808 .. _Pull Request 988: https://github.com/galaxyproject/planemo/pull/988
1809 .. _Pull Request 989: https://github.com/galaxyproject/planemo/pull/989
1810 .. _Pull Request 985: https://github.com/galaxyproject/planemo/pull/985
1811 .. _Pull Request 984: https://github.com/galaxyproject/planemo/pull/984
1812 .. _Pull Request 986: https://github.com/galaxyproject/planemo/pull/986
1813 .. _Pull Request 983: https://github.com/galaxyproject/planemo/pull/983
1814 .. _Pull Request 982: https://github.com/galaxyproject/planemo/pull/982
1815 .. _Pull Request 980: https://github.com/galaxyproject/planemo/pull/980
1816 .. _Pull Request 978: https://github.com/galaxyproject/planemo/pull/978
1817 .. _Pull Request 979: https://github.com/galaxyproject/planemo/pull/979
1818 .. _Pull Request 977: https://github.com/galaxyproject/planemo/pull/977
1819 .. _Pull Request 975: https://github.com/galaxyproject/planemo/pull/975
1820 .. _Pull Request 974: https://github.com/galaxyproject/planemo/pull/974
1821 .. _Pull Request 976: https://github.com/galaxyproject/planemo/pull/976
1822 .. _Pull Request 972: https://github.com/galaxyproject/planemo/pull/972
1823 .. _Pull Request 973: https://github.com/galaxyproject/planemo/pull/973
1824 .. _Pull Request 971: https://github.com/galaxyproject/planemo/pull/971
1825 .. _Pull Request 970: https://github.com/galaxyproject/planemo/pull/970
1826 .. _Pull Request 968: https://github.com/galaxyproject/planemo/pull/968
1827 .. _1ab8530: https://github.com/galaxyproject/planemo/commit/1ab8530
1828 .. _Pull Request 966: https://github.com/galaxyproject/planemo/pull/966
1829 .. _Pull Request 964: https://github.com/galaxyproject/planemo/pull/964
1830 .. _Pull Request 963: https://github.com/galaxyproject/planemo/pull/963
1831 .. _Pull Request 959: https://github.com/galaxyproject/planemo/pull/959
1832 .. _Pull Request 958: https://github.com/galaxyproject/planemo/pull/958
1833 .. _Pull Request 950: https://github.com/galaxyproject/planemo/pull/950
1834 .. _Pull Request 944: https://github.com/galaxyproject/planemo/pull/944
1835 .. _Pull Request 926: https://github.com/galaxyproject/planemo/pull/926
1836 .. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937
1837 .. _Pull Request 938: https://github.com/galaxyproject/planemo/pull/938
1838 .. _Pull Request 943: https://github.com/galaxyproject/planemo/pull/943
1839 .. _Pull Request 940: https://github.com/galaxyproject/planemo/pull/940
1840 .. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937
1841 .. _Pull Request 935: https://github.com/galaxyproject/planemo/pull/935
1842 .. _Pull Request 931: https://github.com/galaxyproject/planemo/pull/931
1843 .. _Pull Request 930: https://github.com/galaxyproject/planemo/pull/930
1844 .. _Pull Request 913: https://github.com/galaxyproject/planemo/pull/913
1845 .. _Pull Request 917: https://github.com/galaxyproject/planemo/pull/917
1846 .. _Pull Request 921: https://github.com/galaxyproject/planemo/pull/921
1847 .. _Pull Request 918: https://github.com/galaxyproject/planemo/pull/918
1848 .. _Pull Request 924: https://github.com/galaxyproject/planemo/pull/924
1849 .. _Pull Request 925: https://github.com/galaxyproject/planemo/pull/925
1850 .. _Pull Request 912: https://github.com/galaxyproject/planemo/pull/912
1851 .. _Pull Request 915: https://github.com/galaxyproject/planemo/pull/915
1852 .. _Pull Request 914: https://github.com/galaxyproject/planemo/pull/914
1853 .. _07dc6e0: https://github.com/galaxyproject/planemo/commit/07dc6e0
1854 .. _Pull Request 910: https://github.com/galaxyproject/planemo/pull/910
1855 .. _Pull Request 909: https://github.com/galaxyproject/planemo/pull/909
1856 .. _Pull Request 908: https://github.com/galaxyproject/planemo/pull/908
1857 .. _Pull Request 907: https://github.com/galaxyproject/planemo/pull/907
1858 .. _Pull Request 906: https://github.com/galaxyproject/planemo/pull/906
1859 .. _Pull Request 902: https://github.com/galaxyproject/planemo/pull/902
1860 .. _Pull Request 895: https://github.com/galaxyproject/planemo/pull/895
1861 .. _Issue 845: https://github.com/galaxyproject/planemo/issues/845
1862 .. _Issue 898: https://github.com/galaxyproject/planemo/issues/898
1863 .. _Pull Request 899: https://github.com/galaxyproject/planemo/pull/899
1864 .. _Pull Request 896: https://github.com/galaxyproject/planemo/pull/896
1865 .. _Pull Request 894: https://github.com/galaxyproject/planemo/pull/894
1866 .. _Pull Request 876: https://github.com/galaxyproject/planemo/pull/876
1867 .. _Pull Request 893: https://github.com/galaxyproject/planemo/pull/893
1868 .. _Pull Request 892: https://github.com/galaxyproject/planemo/pull/892
1869 .. _Pull Request 891: https://github.com/galaxyproject/planemo/pull/891
1870 .. _Pull Request 889: https://github.com/galaxyproject/planemo/pull/889
1871 .. _Pull Request 888: https://github.com/galaxyproject/planemo/pull/888
1872 .. _Pull Request 887: https://github.com/galaxyproject/planemo/pull/887
1873 .. _Pull Request 882: https://github.com/galaxyproject/planemo/pull/882
1874 .. _Pull Request 877: https://github.com/galaxyproject/planemo/pull/877
1875 .. _Pull Request 874: https://github.com/galaxyproject/planemo/pull/874
1876 .. _Pull Request 871: https://github.com/galaxyproject/planemo/pull/871
1877 .. _Pull Request 870: https://github.com/galaxyproject/planemo/pull/870
1878 .. _Pull Request 864: https://github.com/galaxyproject/planemo/pull/864
1879 .. _Pull Request 867: https://github.com/galaxyproject/planemo/pull/867
1880 .. _Pull Request 868: https://github.com/galaxyproject/planemo/pull/868
1881 .. _bad810a: https://github.com/galaxyproject/planemo/commit/bad810a
1882 .. _Pull Request 851: https://github.com/galaxyproject/planemo/pull/851
1883 .. _Pull Request 856: https://github.com/galaxyproject/planemo/pull/856
1884 .. _Pull Request 860: https://github.com/galaxyproject/planemo/pull/860
1885 .. _Pull Request 866: https://github.com/galaxyproject/planemo/pull/866
1886 .. _Pull Request 861: https://github.com/galaxyproject/planemo/pull/861
1887 .. _324c776: https://github.com/galaxyproject/planemo/commit/324c776
1888 .. _72d2ca7: https://github.com/galaxyproject/planemo/commit/72d2ca7
1889 .. _b12b117: https://github.com/galaxyproject/planemo/commit/b12b117
1890 .. _016b923: https://github.com/galaxyproject/planemo/commit/016b923
1891 .. _2002b49: https://github.com/galaxyproject/planemo/commit/2002b49
1892 .. _Pull Request 843: https://github.com/galaxyproject/planemo/pull/843
1893 .. _Pull Request 842: https://github.com/galaxyproject/planemo/pull/842
1894 .. _Pull Request 841: https://github.com/galaxyproject/planemo/pull/841
1895 .. _Pull Request 847: https://github.com/galaxyproject/planemo/pull/847
1896 .. _Pull Request 848: https://github.com/galaxyproject/planemo/pull/848
1897 .. _Pull Request 849: https://github.com/galaxyproject/planemo/pull/849
1898 .. _Pull Request 850: https://github.com/galaxyproject/planemo/pull/850
1899 .. _Pull Request 836: https://github.com/galaxyproject/planemo/pull/836
1900 .. _Pull Request 833: https://github.com/galaxyproject/planemo/pull/833
1901 .. _Pull Request 837: https://github.com/galaxyproject/planemo/pull/837
1902 .. _Pull Request 840: https://github.com/galaxyproject/planemo/pull/840
1903 .. _Pull Request 838: https://github.com/galaxyproject/planemo/pull/838
1904 .. _Pull Request 834: https://github.com/galaxyproject/planemo/pull/834
1905 .. _Pull Request 835: https://github.com/galaxyproject/planemo/pull/835
1906 .. _347c622: https://github.com/galaxyproject/planemo/commit/347c622
1907 .. _Pull Request 832: https://github.com/galaxyproject/planemo/pull/832
1908 .. _Pull Request 831: https://github.com/galaxyproject/planemo/pull/831
1909 .. _Pull Request 830: https://github.com/galaxyproject/planemo/pull/830
1910 .. _Pull Request 829: https://github.com/galaxyproject/planemo/pull/829
1911 .. _Pull Request 828: https://github.com/galaxyproject/planemo/pull/828
1912 .. _Pull Request 826: https://github.com/galaxyproject/planemo/pull/826
1913 .. _Pull Request 827: https://github.com/galaxyproject/planemo/pull/827
1914 .. _Pull Request 825: https://github.com/galaxyproject/planemo/pull/825
1915 .. _Pull Request 820: https://github.com/galaxyproject/planemo/pull/820
1916 .. _Pull Request 823: https://github.com/galaxyproject/planemo/pull/823
1917 .. _Pull Request 822: https://github.com/galaxyproject/planemo/pull/822
1918 .. _a5c72e3: https://github.com/galaxyproject/planemo/commit/a5c72e3
1919 .. _Pull Request 818: https://github.com/galaxyproject/planemo/pull/818
1920 .. _Pull Request 816: https://github.com/galaxyproject/planemo/pull/816
1921 .. _Pull Request 817: https://github.com/galaxyproject/planemo/pull/817
1922 .. _Pull Request 795: https://github.com/galaxyproject/planemo/pull/795
1923 .. _Pull Request 799: https://github.com/galaxyproject/planemo/pull/799
1924 .. _Pull Request 800: https://github.com/galaxyproject/planemo/pull/800
1925 .. _Pull Request 781: https://github.com/galaxyproject/planemo/pull/781
1926 .. _Pull Request 801: https://github.com/galaxyproject/planemo/pull/801
1927 .. _Pull Request 802: https://github.com/galaxyproject/planemo/pull/802
1928 .. _Pull Request 803: https://github.com/galaxyproject/planemo/pull/803
1929 .. _Pull Request 805: https://github.com/galaxyproject/planemo/pull/805
1930 .. _Pull Request 806: https://github.com/galaxyproject/planemo/pull/806
1931 .. _Pull Request 809: https://github.com/galaxyproject/planemo/pull/809
1932 .. _Pull Request 810: https://github.com/galaxyproject/planemo/pull/810
1933 .. _Pull Request 787: https://github.com/galaxyproject/planemo/pull/787
1934 .. _Pull Request 792: https://github.com/galaxyproject/planemo/pull/792
1935 .. _dc443d6: https://github.com/galaxyproject/planemo/commit/dc443d6
1936 .. _8cfe9e9: https://github.com/galaxyproject/planemo/commit/8cfe9e9
1937 .. _41f7df1: https://github.com/galaxyproject/planemo/commit/41f7df1
1938 .. _Pull Request 790: https://github.com/galaxyproject/planemo/pull/790
1939 .. _Pull Request 776: https://github.com/galaxyproject/planemo/pull/776
1940 .. _Pull Request 774: https://github.com/galaxyproject/planemo/pull/774
1941 .. _Pull Request 773: https://github.com/galaxyproject/planemo/pull/773
1942 .. _Pull Request 771: https://github.com/galaxyproject/planemo/pull/771
1943 .. _Pull Request 770: https://github.com/galaxyproject/planemo/pull/770
1944 .. _Pull Request 769: https://github.com/galaxyproject/planemo/pull/769
1945 .. _Pull Request 768: https://github.com/galaxyproject/planemo/pull/768
1946 .. _Pull Request 764: https://github.com/galaxyproject/planemo/pull/764
1947 .. _Pull Request 761: https://github.com/galaxyproject/planemo/pull/761
1948 .. _Pull Request 759: https://github.com/galaxyproject/planemo/pull/759
1949 .. _Pull Request 756: https://github.com/galaxyproject/planemo/pull/756
1950 .. _Pull Request 753: https://github.com/galaxyproject/planemo/pull/753
1951 .. _Pull Request 747: https://github.com/galaxyproject/planemo/pull/747
1952 .. _Pull Request 745: https://github.com/galaxyproject/planemo/pull/745
1953 .. _Pull Request 743: https://github.com/galaxyproject/planemo/pull/743
1954 .. _Pull Request 739: https://github.com/galaxyproject/planemo/pull/739
1955 .. _Pull Request 738: https://github.com/galaxyproject/planemo/pull/738
1956 .. _Pull Request 725: https://github.com/galaxyproject/planemo/pull/725
1957 .. _Pull Request 727: https://github.com/galaxyproject/planemo/pull/727
1958 .. _Pull Request 729: https://github.com/galaxyproject/planemo/pull/729
1959 .. _Pull Request 730: https://github.com/galaxyproject/planemo/pull/730
1960 .. _Pull Request 731: https://github.com/galaxyproject/planemo/pull/731
1961 .. _Pull Request 733: https://github.com/galaxyproject/planemo/pull/733
1962 .. _Pull Request 732: https://github.com/galaxyproject/planemo/pull/732
1963 .. _Pull Request 704: https://github.com/galaxyproject/planemo/pull/704
1964 .. _Pull Request 709: https://github.com/galaxyproject/planemo/pull/709
1965 .. _Pull Request 715: https://github.com/galaxyproject/planemo/pull/715
1966 .. _Pull Request 716: https://github.com/galaxyproject/planemo/pull/716
1967 .. _Pull Request 720: https://github.com/galaxyproject/planemo/pull/720
1968 .. _Pull Request 723: https://github.com/galaxyproject/planemo/pull/723
1969 .. _8a608e0: https://github.com/galaxyproject/planemo/commit/8a608e0
1970 .. _ecc1bc2: https://github.com/galaxyproject/planemo/commit/ecc1bc2
1971 .. _Pull Request 702: https://github.com/galaxyproject/planemo/pull/702
1972 .. _Pull Request 701: https://github.com/galaxyproject/planemo/pull/701
1973 .. _Pull Request 699: https://github.com/galaxyproject/planemo/pull/699
1974 .. _91b6fa0: https://github.com/galaxyproject/planemo/commit/91b6fa0
1975 .. _904d77a: https://github.com/galaxyproject/planemo/commit/904d77a
1976 .. _9636682: https://github.com/galaxyproject/planemo/commit/9636682
1977 .. _475104c: https://github.com/galaxyproject/planemo/commit/475104c
1978 .. _Pull Request 684: https://github.com/galaxyproject/planemo/pull/684
1979 .. _Pull Request 687: https://github.com/galaxyproject/planemo/pull/687
1980 .. _Pull Request 688: https://github.com/galaxyproject/planemo/pull/688
1981 .. _Pull Request 689: https://github.com/galaxyproject/planemo/pull/689
1982 .. _Pull Request 690: https://github.com/galaxyproject/planemo/pull/690
1983 .. _Issue 494: https://github.com/galaxyproject/planemo/issues/494
1984 .. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665
1985 .. _Pull Request 675: https://github.com/galaxyproject/planemo/pull/675
1986 .. _Pull Request 680: https://github.com/galaxyproject/planemo/pull/680
1987 .. _Pull Request 682: https://github.com/galaxyproject/planemo/pull/682
1988 .. _Pull Request 683: https://github.com/galaxyproject/planemo/pull/683
1989 .. _Pull Request 662: https://github.com/galaxyproject/planemo/pull/662
1990 .. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665
1991 .. _Pull Request 664: https://github.com/galaxyproject/planemo/pull/664
1992 .. _84c4a73: https://github.com/galaxyproject/planemo/commit/84c4a73
1993 .. _32f41c9: https://github.com/galaxyproject/planemo/commit/32f41c9
1994 .. _3129216: https://github.com/galaxyproject/planemo/commit/3129216
1995 .. _b4ae44d: https://github.com/galaxyproject/planemo/commit/b4ae44d
1996 .. _3c95b7b: https://github.com/galaxyproject/planemo/commit/3c95b7b
1997 .. _06bcf19: https://github.com/galaxyproject/planemo/commit/06bcf19
1998 .. _525de8f: https://github.com/galaxyproject/planemo/commit/525de8f
1999 .. _9867e56: https://github.com/galaxyproject/planemo/commit/9867e56
2000 .. _ce0dc4e: https://github.com/galaxyproject/planemo/commit/ce0dc4e
2001 .. _4c0f100: https://github.com/galaxyproject/planemo/commit/4c0f100
2002 .. _04238d3: https://github.com/galaxyproject/planemo/commit/04238d3
2003 .. _ced5ce2: https://github.com/galaxyproject/planemo/commit/ced5ce2
2004 .. _9ab4a0d: https://github.com/galaxyproject/planemo/commit/9ab4a0d
2005 .. _Pull Request 640: https://github.com/galaxyproject/planemo/pull/640
2006 .. _0a1abfe: https://github.com/galaxyproject/planemo/commit/0a1abfe
2007 .. _Pull Request 649: https://github.com/galaxyproject/planemo/pull/649
2008 .. _Issue 620: https://github.com/galaxyproject/planemo/issues/620
2009 .. _Pull Request 643: https://github.com/galaxyproject/planemo/pull/643
2010 .. _Pull Request 642: https://github.com/galaxyproject/planemo/pull/642
2011 .. _Pull Request 641: https://github.com/galaxyproject/planemo/pull/641
2012 .. _Pull Request 639: https://github.com/galaxyproject/planemo/pull/639
2013 .. _Pull Request 635: https://github.com/galaxyproject/planemo/pull/635
2014 .. _Issue 633: https://github.com/galaxyproject/planemo/issues/633
2015 .. _Issue 260: https://github.com/galaxyproject/planemo/issues/260
2016 .. _Pull Request 638: https://github.com/galaxyproject/planemo/pull/638
2017 .. _6638caa: https://github.com/galaxyproject/planemo/commit/6638caa
2018 .. _8faf661: https://github.com/galaxyproject/planemo/commit/8faf661
2019 .. _e343b67: https://github.com/galaxyproject/planemo/commit/e343b67
2020 .. _Pull Request 634: https://github.com/galaxyproject/planemo/pull/634
2021 .. _84ebc1f: https://github.com/galaxyproject/planemo/commit/84ebc1f
2022 .. _03c9658: https://github.com/galaxyproject/planemo/commit/03c9658
2023 .. _08c067c: https://github.com/galaxyproject/planemo/commit/08c067c
2024 .. _fca4183: https://github.com/galaxyproject/planemo/commit/fca4183
2025 .. _Issue 564: https://github.com/galaxyproject/planemo/issues/564
2026 .. _Pull Request 628: https://github.com/galaxyproject/planemo/pull/628
2027 .. _Issue 515: https://github.com/galaxyproject/planemo/issues/515
2028 .. _Pull Request 629: https://github.com/galaxyproject/planemo/pull/629
2029 .. _Pull Request 614: https://github.com/galaxyproject/planemo/pull/614
2030 .. _32acd68: https://github.com/galaxyproject/planemo/commit/32acd68
2031 .. _4595953: https://github.com/galaxyproject/planemo/commit/4595953
2032 .. _Pull Request 612: https://github.com/galaxyproject/planemo/pull/612
2033 .. _Issue 388: https://github.com/galaxyproject/planemo/issues/388
2034 .. _Pull Request 610: https://github.com/galaxyproject/planemo/pull/610
2035 .. _Pull Request 609: https://github.com/galaxyproject/planemo/pull/609
2036 .. _Pull Request 608: https://github.com/galaxyproject/planemo/pull/608
2037 .. _Pull Request 605: https://github.com/galaxyproject/planemo/pull/605
2038 .. _Pull Request 606: https://github.com/galaxyproject/planemo/pull/606
2039 .. _Pull Request 602: https://github.com/galaxyproject/planemo/pull/602
2040 .. _Pull Request 570: https://github.com/galaxyproject/planemo/pull/570
2041 .. _9228416: https://github.com/galaxyproject/planemo/commit/9228416
2042 .. _50d3c4a: https://github.com/galaxyproject/planemo/commit/50d3c4a
2043 .. _Issue 578: https://github.com/galaxyproject/planemo/issues/578
2044 .. _Pull Request 591: https://github.com/galaxyproject/planemo/pull/591
2045 .. _Pull Request 590: https://github.com/galaxyproject/planemo/pull/590
2046 .. _f0da66f: https://github.com/galaxyproject/planemo/commit/f0da66f
2047 .. _19b2ee9: https://github.com/galaxyproject/planemo/commit/19b2ee9
2048 .. _9da8387: https://github.com/galaxyproject/planemo/commit/9da8387
2049 .. _08cef54: https://github.com/galaxyproject/planemo/commit/08cef54
2050 .. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc
2051 .. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc
2052 .. _Issue 573: https://github.com/galaxyproject/planemo/issues/573
2053 .. _Pull Request 579: https://github.com/galaxyproject/planemo/pull/579
2054 .. _ccdd2d5: https://github.com/galaxyproject/planemo/commit/ccdd2d5
2055 .. _e925ba1: https://github.com/galaxyproject/planemo/commit/e925ba1
2056 .. _ea5324f: https://github.com/galaxyproject/planemo/commit/ea5324f
2057 .. _ca88b0c: https://github.com/galaxyproject/planemo/commit/ca88b0c
2058 .. _b6d8294: https://github.com/galaxyproject/planemo/commit/b6d8294
2059 .. _6a6f164: https://github.com/galaxyproject/planemo/commit/6a6f164
2060 .. _d6da3a8: https://github.com/galaxyproject/planemo/commit/d6da3a8
2061 .. _1ef05d2: https://github.com/galaxyproject/planemo/commit/1ef05d2
2062 .. _7cca2e4: https://github.com/galaxyproject/planemo/commit/7cca2e4
2063 .. _34538de: https://github.com/galaxyproject/planemo/commit/34538de
2064 .. _6f91719: https://github.com/galaxyproject/planemo/commit/6f91719
2065 .. _Pull Request 566: https://github.com/galaxyproject/planemo/pull/566
2066 .. _Pull Request 559: https://github.com/galaxyproject/planemo/pull/559
2067 .. _Pull Request 561: https://github.com/galaxyproject/planemo/pull/561
2068 .. _Pull Request 565: https://github.com/galaxyproject/planemo/pull/565
2069 .. _Pull Request 555: https://github.com/galaxyproject/planemo/pull/555
2070 .. _a8e797b: https://github.com/galaxyproject/planemo/commit/a8e797b
2071 .. _6c03de8: https://github.com/galaxyproject/planemo/commit/6c03de8
2072 .. _ef4b9f4: https://github.com/galaxyproject/planemo/commit/ef4b9f4
2073 .. _f7b6c7e: https://github.com/galaxyproject/planemo/commit/f7b6c7e
2074 .. _07d94bd: https://github.com/galaxyproject/planemo/commit/07d94bd
2075 .. _ca19910: https://github.com/galaxyproject/planemo/commit/ca19910
2076 .. _24008ab: https://github.com/galaxyproject/planemo/commit/24008ab
2077 .. _ce44e87: https://github.com/galaxyproject/planemo/commit/ce44e87
2078 .. _Pull Request 550: https://github.com/galaxyproject/planemo/pull/550
2079 .. _c2204b3: https://github.com/galaxyproject/planemo/commit/c2204b3
2080 .. _c262b6d: https://github.com/galaxyproject/planemo/commit/c262b6d
2081 .. _Pull Request 539: https://github.com/galaxyproject/planemo/pull/539
2082 .. _Pull Request 541: https://github.com/galaxyproject/planemo/pull/541
2083 .. _Pull Request 540: https://github.com/galaxyproject/planemo/pull/540
2084 .. _Pull Request 545: https://github.com/galaxyproject/planemo/pull/545
2085 .. _Pull Request 546: https://github.com/galaxyproject/planemo/pull/546
2086 .. _3ceaa40: https://github.com/galaxyproject/planemo/commit/3ceaa40
2087 .. _057f4f0: https://github.com/galaxyproject/planemo/commit/057f4f0
2088 .. _9fdf490: https://github.com/galaxyproject/planemo/commit/9fdf490
2089 .. _8c088c6: https://github.com/galaxyproject/planemo/commit/8c088c6
2090 .. _e2398fb: https://github.com/galaxyproject/planemo/commit/e2398fb
2091 .. _Pull Request 526: https://github.com/galaxyproject/planemo/pull/526
2092 .. _Pull Request 528: https://github.com/galaxyproject/planemo/pull/528
2093 .. _Pull Request 525: https://github.com/galaxyproject/planemo/pull/525
2094 .. _a811e65: https://github.com/galaxyproject/planemo/commit/a811e65
2095 .. _Pull Request 521: https://github.com/galaxyproject/planemo/pull/521
2096 .. _a066afb: https://github.com/galaxyproject/planemo/commit/a066afb
2097 .. _Pull Request 512: https://github.com/galaxyproject/planemo/pull/512
2098 .. _08bb354: https://github.com/galaxyproject/planemo/commit/08bb354
2099 .. _Pull Request 513: https://github.com/galaxyproject/planemo/pull/513
2100 .. _Pull Request 510: https://github.com/galaxyproject/planemo/pull/510
2101 .. _e890ab5: https://github.com/galaxyproject/planemo/commit/e890ab5
2102 .. _Pull Request 507: https://github.com/galaxyproject/planemo/pull/507
2103 .. _d53bcd6: https://github.com/galaxyproject/planemo/commit/d53bcd6
2104 .. _725b232: https://github.com/galaxyproject/planemo/commit/725b232
2105 .. _Pull Request 498: https://github.com/galaxyproject/planemo/pull/498
2106 .. _01584c5: https://github.com/galaxyproject/planemo/commit/01584c5
2107 .. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9
2108 .. _0298510: https://github.com/galaxyproject/planemo/commit/0298510
2109 .. _02a08a0: https://github.com/galaxyproject/planemo/commit/02a08a0
2110 .. _05cc9f4: https://github.com/galaxyproject/planemo/commit/05cc9f485ee87bc344e3f43bb1cfd025a16a6247
2111 .. _069e7ba: https://github.com/galaxyproject/planemo/commit/069e7ba
2112 .. _08de8de: https://github.com/galaxyproject/planemo/commit/08de8de
2113 .. _0bd4ff0: https://github.com/galaxyproject/planemo/commit/0bd4ff0
2114 .. _0e4f70a: https://github.com/galaxyproject/planemo/commit/0e4f70a
2115 .. _0f8cb10: https://github.com/galaxyproject/planemo/commit/0f8cb10
2116 .. _13a5ae7: https://github.com/galaxyproject/planemo/commit/13a5ae7
2117 .. _15804be: https://github.com/galaxyproject/planemo/commit/15804be
2118 .. _15d33c7: https://github.com/galaxyproject/planemo/commit/15d33c7
2119 .. _182fe57: https://github.com/galaxyproject/planemo/commit/182fe57
2120 .. _1927168: https://github.com/galaxyproject/planemo/commit/1927168
2121 .. _1982076: https://github.com/galaxyproject/planemo/commit/1982076
2122 .. _19900a6: https://github.com/galaxyproject/planemo/commit/19900a6
2123 .. _1a157d4: https://github.com/galaxyproject/planemo/commit/1a157d4
2124 .. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493
2125 .. _1c6cfbb: https://github.com/galaxyproject/planemo/commit/1c6cfbb
2126 .. _1c7ee5b: https://github.com/galaxyproject/planemo/commit/1c7ee5b
2127 .. _1cd0e2d: https://github.com/galaxyproject/planemo/commit/1cd0e2d
2128 .. _1e3668a: https://github.com/galaxyproject/planemo/commit/1e3668a
2129 .. _2052db0: https://github.com/galaxyproject/planemo/commit/2052db0
2130 .. _20a8680: https://github.com/galaxyproject/planemo/commit/20a86807cb7ea87db2dbc0197ae08a40df3ab2bc
2131 .. _21bb463: https://github.com/galaxyproject/planemo/commit/21bb463ad6c321bcb669603049a5e89a69766ad9
2132 .. _25ef0d5: https://github.com/galaxyproject/planemo/commit/25ef0d5
2133 .. _26e378e: https://github.com/galaxyproject/planemo/commit/26e378e
2134 .. _26e3cdb: https://github.com/galaxyproject/planemo/commit/26e3cdb
2135 .. _2a7c792: https://github.com/galaxyproject/planemo/commit/2a7c792
2136 .. _2ae2b49: https://github.com/galaxyproject/planemo/commit/2ae2b49
2137 .. _2e41e0a: https://github.com/galaxyproject/planemo/commit/2e41e0a
2138 .. _2f66fc3: https://github.com/galaxyproject/planemo/commit/2f66fc3
2139 .. _30a9c3f: https://github.com/galaxyproject/planemo/commit/30a9c3f
2140 .. _32c6e7f: https://github.com/galaxyproject/planemo/commit/32c6e7f78bb8f04d27615cfd8948b0b89f27b4e6
2141 .. _33294d2: https://github.com/galaxyproject/planemo/commit/33294d2
2142 .. _334f2d4: https://github.com/galaxyproject/planemo/commit/334f2d4
2143 .. _343902d: https://github.com/galaxyproject/planemo/commit/343902d
2144 .. _3499ca0: https://github.com/galaxyproject/planemo/commit/3499ca0a15affcaf8ac9efc55880da40b0626679
2145 .. _358a42c: https://github.com/galaxyproject/planemo/commit/358a42c
2146 .. _36ac6d8: https://github.com/galaxyproject/planemo/commit/36ac6d8
2147 .. _36f7cb1: https://github.com/galaxyproject/planemo/commit/36f7cb114f77731f90860d513a930e10ce5c1ba5
2148 .. _37dcc07: https://github.com/galaxyproject/planemo/commit/37dcc07
2149 .. _39fedd2: https://github.com/galaxyproject/planemo/commit/39fedd2
2150 .. _3f4ab44: https://github.com/galaxyproject/planemo/commit/3f4ab44
2151 .. _40a1f57: https://github.com/galaxyproject/planemo/commit/40a1f57
2152 .. _411a8da: https://github.com/galaxyproject/planemo/commit/411a8da21c92ba37c7ad95bfce9928d9b8fd998e
2153 .. _44de95c: https://github.com/galaxyproject/planemo/commit/44de95c0d7087a5822941959f9a062f6382e329b
2154 .. _45135ff: https://github.com/galaxyproject/planemo/commit/45135ff
2155 .. _4823c5e: https://github.com/galaxyproject/planemo/commit/4823c5e
2156 .. _49c5c1e: https://github.com/galaxyproject/planemo/commit/49c5c1e
2157 .. _4c71299: https://github.com/galaxyproject/planemo/commit/4c71299
2158 .. _4cd571c: https://github.com/galaxyproject/planemo/commit/4cd571c
2159 .. _4d29bf1: https://github.com/galaxyproject/planemo/commit/4d29bf1
2160 .. _4d6f7d9: https://github.com/galaxyproject/planemo/commit/4d6f7d9
2161 .. _4e1377c: https://github.com/galaxyproject/planemo/commit/4e1377c
2162 .. _4f61025: https://github.com/galaxyproject/planemo/commit/4f61025
2163 .. _508dce7: https://github.com/galaxyproject/planemo/commit/508dce7
2164 .. _53a6766: https://github.com/galaxyproject/planemo/commit/53a6766cdebdddc976189f6dc6a264bb4105c4bf
2165 .. _53edd99: https://github.com/galaxyproject/planemo/commit/53edd99
2166 .. _552059f: https://github.com/galaxyproject/planemo/commit/552059f
2167 .. _572e754: https://github.com/galaxyproject/planemo/commit/572e754
2168 .. _5b97f2e: https://github.com/galaxyproject/planemo/commit/5b97f2e
2169 .. _5d08b67: https://github.com/galaxyproject/planemo/commit/5d08b67
2170 .. _5d7db92: https://github.com/galaxyproject/planemo/commit/5d7db92
2171 .. _5e0b6d1: https://github.com/galaxyproject/planemo/commit/5e0b6d1
2172 .. _63cd431: https://github.com/galaxyproject/planemo/commit/63cd431
2173 .. _63e456c: https://github.com/galaxyproject/planemo/commit/63e456c
2174 .. _6409449: https://github.com/galaxyproject/planemo/commit/6409449
2175 .. _6514ff5: https://github.com/galaxyproject/planemo/commit/6514ff5
2176 .. _65b999d: https://github.com/galaxyproject/planemo/commit/65b999d21bacc133a80ecf5f61e0728afec66ccc
2177 .. _6b4e7a6: https://github.com/galaxyproject/planemo/commit/6b4e7a6
2178 .. _6bcf699: https://github.com/galaxyproject/planemo/commit/6bcf699
2179 .. _6d0f502: https://github.com/galaxyproject/planemo/commit/6d0f502
2180 .. _6d81a94: https://github.com/galaxyproject/planemo/commit/6d81a94
2181 .. _6e1e726: https://github.com/galaxyproject/planemo/commit/6e1e726
2182 .. _7572e99: https://github.com/galaxyproject/planemo/commit/7572e99
2183 .. _764ce01: https://github.com/galaxyproject/planemo/commit/764ce01
2184 .. _775bf49: https://github.com/galaxyproject/planemo/commit/775bf49
2185 .. _776773c: https://github.com/galaxyproject/planemo/commit/776773c
2186 .. _78f8274: https://github.com/galaxyproject/planemo/commit/78f82747996e4a28f96c85ad72efe5e54c8c74bd
2187 .. _7be1bf5: https://github.com/galaxyproject/planemo/commit/7be1bf5
2188 .. _7c69bf6: https://github.com/galaxyproject/planemo/commit/7c69bf6
2189 .. _7d07782: https://github.com/galaxyproject/planemo/commit/7d077828559c9c9c352ac814f9e3b86b1b3a2a9f
2190 .. _8117e03: https://github.com/galaxyproject/planemo/commit/8117e03
2191 .. _8207026: https://github.com/galaxyproject/planemo/commit/8207026
2192 .. _826d371: https://github.com/galaxyproject/planemo/commit/826d371
2193 .. _82e8b1f: https://github.com/galaxyproject/planemo/commit/82e8b1f17eae526aeb341cb4fffb8d09d73bb419
2194 .. _834bfb2: https://github.com/galaxyproject/planemo/commit/834bfb2929d367892a3abe9c0b88d5a0277d7905
2195 .. _83e227a: https://github.com/galaxyproject/planemo/commit/83e227a
2196 .. _85b9614: https://github.com/galaxyproject/planemo/commit/85b961465f46351507f80ddc3758349535060502
2197 .. _89674cb: https://github.com/galaxyproject/planemo/commit/89674cb
2198 .. _8b31850: https://github.com/galaxyproject/planemo/commit/8b31850
2199 .. _8e96864: https://github.com/galaxyproject/planemo/commit/8e96864
2200 .. _8eda729: https://github.com/galaxyproject/planemo/commit/8eda729
2201 .. _912df02: https://github.com/galaxyproject/planemo/commit/912df02
2202 .. _916f610: https://github.com/galaxyproject/planemo/commit/916f610
2203 .. _93b7bda: https://github.com/galaxyproject/planemo/commit/93b7bda
2204 .. _94097c7: https://github.com/galaxyproject/planemo/commit/94097c7
2205 .. _9427b47: https://github.com/galaxyproject/planemo/commit/9427b47
2206 .. _94645ed: https://github.com/galaxyproject/planemo/commit/94645ed
2207 .. _949a36d: https://github.com/galaxyproject/planemo/commit/949a36d
2208 .. _95d5cba: https://github.com/galaxyproject/planemo/commit/95d5cba
2209 .. _965511d: https://github.com/galaxyproject/planemo/commit/965511d
2210 .. _988de1d: https://github.com/galaxyproject/planemo/commit/988de1d
2211 .. _98fdc8c: https://github.com/galaxyproject/planemo/commit/98fdc8c
2212 .. _99ee51a: https://github.com/galaxyproject/planemo/commit/99ee51a
2213 .. _9bf1eab: https://github.com/galaxyproject/planemo/commit/9bf1eab
2214 .. _9e746b4: https://github.com/galaxyproject/planemo/commit/9e746b455e3b15219878cddcdeda722979639401
2215 .. _9f3957d: https://github.com/galaxyproject/planemo/commit/9f3957d
2216 .. _9ff0d2d: https://github.com/galaxyproject/planemo/commit/9ff0d2d
2217 .. _CWL: http://www.commonwl.org/
2218 .. _Issue 108: https://github.com/galaxyproject/planemo/issues/108
2219 .. _Issue 114: https://github.com/galaxyproject/planemo/issues/114
2220 .. _Issue 118: https://github.com/galaxyproject/planemo/issues/118
2221 .. _Issue 124: https://github.com/galaxyproject/planemo/issues/#124
2222 .. _Issue 138: https://github.com/galaxyproject/planemo/issues/#138
2223 .. _Issue 139: https://github.com/galaxyproject/planemo/issues/139
2224 .. _Issue 150: https://github.com/galaxyproject/planemo/issues/150
2225 .. _Issue 156: https://github.com/galaxyproject/planemo/issues/156
2226 .. _Issue 158: https://github.com/galaxyproject/planemo/issues/158
2227 .. _Issue 159: https://github.com/galaxyproject/planemo/issues/159
2228 .. _Issue 15: https://github.com/galaxyproject/planemo/issues/15
2229 .. _Issue 161: https://github.com/galaxyproject/planemo/issues/161
2230 .. _Issue 167: https://github.com/galaxyproject/planemo/issues/167
2231 .. _Issue 168: https://github.com/galaxyproject/planemo/issues/168
2232 .. _Issue 169: https://github.com/galaxyproject/planemo/issues/169
2233 .. _Issue 170: https://github.com/galaxyproject/planemo/issues/170
2234 .. _Issue 176: https://github.com/galaxyproject/planemo/issues/176
2235 .. _Issue 179: https://github.com/galaxyproject/planemo/issues/179
2236 .. _Issue 180: https://github.com/galaxyproject/planemo/issues/180
2237 .. _Issue 181: https://github.com/galaxyproject/planemo/issues/181
2238 .. _Issue 184: https://github.com/galaxyproject/planemo/issues/184
2239 .. _Issue 186: https://github.com/galaxyproject/planemo/issues/186
2240 .. _Issue 188: https://github.com/galaxyproject/planemo/issues/188
2241 .. _Issue 189: https://github.com/galaxyproject/planemo/issues/189
2242 .. _Issue 192: https://github.com/galaxyproject/planemo/issues/192
2243 .. _Issue 205: https://github.com/galaxyproject/planemo/issues/205
2244 .. _Issue 206: https://github.com/galaxyproject/planemo/issues/206
2245 .. _Issue 209: https://github.com/galaxyproject/planemo/issues/209
2246 .. _Issue 211: https://github.com/galaxyproject/planemo/issues/211
2247 .. _Issue 217: https://github.com/galaxyproject/planemo/issues/217
2248 .. _Issue 223: https://github.com/galaxyproject/planemo/issues/223
2249 .. _Issue 231: https://github.com/galaxyproject/planemo/issues/231
2250 .. _Issue 233: https://github.com/galaxyproject/planemo/issues/233
2251 .. _Issue 240: https://github.com/galaxyproject/planemo/issues/240
2252 .. _Issue 243: https://github.com/galaxyproject/planemo/issues/243
2253 .. _Issue 245: https://github.com/galaxyproject/planemo/issues/245
2254 .. _Issue 246: https://github.com/galaxyproject/planemo/issues/246
2255 .. _Issue 272: https://github.com/galaxyproject/planemo/issues/272
2256 .. _Issue 303: https://github.com/galaxyproject/planemo/issues/303
2257 .. _Issue 313: https://github.com/galaxyproject/planemo/issues/313
2258 .. _Issue 329: https://github.com/galaxyproject/planemo/issues/329
2259 .. _Issue 333: https://github.com/galaxyproject/planemo/issues/333
2260 .. _Issue 361: https://github.com/galaxyproject/planemo/issues/361
2261 .. _Issue 362: https://github.com/galaxyproject/planemo/issues/362
2262 .. _Issue 373: https://github.com/galaxyproject/planemo/issues/373
2263 .. _Issue 391: https://github.com/galaxyproject/planemo/issues/391
2264 .. _Issue 416: https://github.com/galaxyproject/planemo/issues/416
2265 .. _Issue 420: https://github.com/galaxyproject/planemo/issues/420
2266 .. _Issue 475: https://github.com/galaxyproject/planemo/issues/475
2267 .. _Issue 61: https://github.com/galaxyproject/planemo/issues/61
2268 .. _Issue 70: https://github.com/galaxyproject/planemo/issues/70
2269 .. _Issue 78: https://github.com/galaxyproject/planemo/issues/78
2270 .. _Issue 80: https://github.com/galaxyproject/planemo/issues/80
2271 .. _Issue 83: https://github.com/galaxyproject/planemo/issues/83
2272 .. _Issue 88: https://github.com/galaxyproject/planemo/issues/88
2273 .. _Issue 89: https://github.com/galaxyproject/planemo/issues/#89
2274 .. _Issue 91: https://github.com/galaxyproject/planemo/issues/#91
2275 .. _Pull Request 101: https://github.com/galaxyproject/planemo/pull/101
2276 .. _Pull Request 102: https://github.com/galaxyproject/planemo/pull/102
2277 .. _Pull Request 104: https://github.com/galaxyproject/planemo/pull/104
2278 .. _Pull Request 111: https://github.com/galaxyproject/planemo/pull/111
2279 .. _Pull Request 113: https://github.com/galaxyproject/planemo/pull/113
2280 .. _Pull Request 129: https://github.com/galaxyproject/planemo/pull/129
2281 .. _Pull Request 130: https://github.com/galaxyproject/planemo/pull/130
2282 .. _Pull Request 143: https://github.com/galaxyproject/planemo/pull/143
2283 .. _Pull Request 151: https://github.com/galaxyproject/planemo/pull/151
2284 .. _Pull Request 155: https://github.com/galaxyproject/planemo/pull/155
2285 .. _Pull Request 164: https://github.com/galaxyproject/planemo/pull/164
2286 .. _Pull Request 171: https://github.com/galaxyproject/planemo/pull/171
2287 .. _Pull Request 173: https://github.com/galaxyproject/planemo/pull/173
2288 .. _Pull Request 175: https://github.com/galaxyproject/planemo/pull/175
2289 .. _Pull Request 185: https://github.com/galaxyproject/planemo/pull/185
2290 .. _Pull Request 186: https://github.com/galaxyproject/planemo/pull/186
2291 .. _Pull Request 187: https://github.com/galaxyproject/planemo/pull/187
2292 .. _Pull Request 190: https://github.com/galaxyproject/planemo/pull/190
2293 .. _Pull Request 196: https://github.com/galaxyproject/planemo/pull/196
2294 .. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1
2295 .. _Pull Request 200: https://github.com/galaxyproject/planemo/pull/200
2296 .. _Pull Request 203: https://github.com/galaxyproject/planemo/pull/203
2297 .. _Pull Request 206: https://github.com/galaxyproject/planemo/pull/206
2298 .. _Pull Request 207: https://github.com/galaxyproject/planemo/pull/207
2299 .. _Pull Request 208: https://github.com/galaxyproject/planemo/pull/208
2300 .. _Pull Request 210: https://github.com/galaxyproject/planemo/pull/210
2301 .. _Pull Request 213: https://github.com/galaxyproject/planemo/pull/213
2302 .. _Pull Request 215: https://github.com/galaxyproject/planemo/pull/215
2303 .. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216
2304 .. _Pull Request 22: https://github.com/galaxyproject/planemo/pull/22
2305 .. _Pull Request 230: https://github.com/galaxyproject/planemo/pull/230
2306 .. _Pull Request 235: https://github.com/galaxyproject/planemo/pull/235
2307 .. _Pull Request 23: https://github.com/galaxyproject/planemo/pull/23
2308 .. _Pull Request 251: https://github.com/galaxyproject/planemo/pull/251
2309 .. _Pull Request 253: https://github.com/galaxyproject/planemo/pull/253
2310 .. _Pull Request 254: https://github.com/galaxyproject/planemo/pull/254
2311 .. _Pull Request 255: https://github.com/galaxyproject/planemo/pull/255
2312 .. _Pull Request 256: https://github.com/galaxyproject/planemo/pull/256
2313 .. _Pull Request 277: https://github.com/galaxyproject/planemo/pull/277
2314 .. _Pull Request 278: https://github.com/galaxyproject/planemo/pull/278
2315 .. _Pull Request 284: https://github.com/galaxyproject/planemo/pull/284
2316 .. _Pull Request 285: https://github.com/galaxyproject/planemo/pull/285
2317 .. _Pull Request 287: https://github.com/galaxyproject/planemo/pull/287
2318 .. _Pull Request 292: https://github.com/galaxyproject/planemo/pull/292
2319 .. _Pull Request 297: https://github.com/galaxyproject/planemo/pull/297
2320 .. _Pull Request 29: https://github.com/galaxyproject/planemo/pull/29
2321 .. _Pull Request 301: https://github.com/galaxyproject/planemo/pull/301
2322 .. _Pull Request 304: https://github.com/galaxyproject/planemo/pull/304
2323 .. _Pull Request 305: https://github.com/galaxyproject/planemo/pull/305
2324 .. _Pull Request 307: https://github.com/galaxyproject/planemo/pull/307
2325 .. _Pull Request 309: https://github.com/galaxyproject/planemo/pull/309
2326 .. _Pull Request 310: https://github.com/galaxyproject/planemo/pull/310
2327 .. _Pull Request 311: https://github.com/galaxyproject/planemo/pull/311
2328 .. _Pull Request 312: https://github.com/galaxyproject/planemo/pull/312
2329 .. _Pull Request 314: https://github.com/galaxyproject/planemo/pull/314
2330 .. _Pull Request 316: https://github.com/galaxyproject/planemo/pull/316
2331 .. _Pull Request 322: https://github.com/galaxyproject/planemo/pull/322
2332 .. _Pull Request 327: https://github.com/galaxyproject/planemo/pull/327
2333 .. _Pull Request 330: https://github.com/galaxyproject/planemo/pull/330
2334 .. _Pull Request 333: https://github.com/galaxyproject/planemo/pull/333
2335 .. _Pull Request 334: https://github.com/galaxyproject/planemo/pull/334
2336 .. _Pull Request 335: https://github.com/galaxyproject/planemo/pull/335
2337 .. _Pull Request 339: https://github.com/galaxyproject/planemo/pull/339
2338 .. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33
2339 .. _Pull Request 343: https://github.com/galaxyproject/planemo/pull/343
2340 .. _Pull Request 344: https://github.com/galaxyproject/planemo/pull/344
2341 .. _Pull Request 345: https://github.com/galaxyproject/planemo/pull/345
2342 .. _Pull Request 350: https://github.com/galaxyproject/planemo/pull/350
2343 .. _Pull Request 351: https://github.com/galaxyproject/planemo/pull/351
2344 .. _Pull Request 356: https://github.com/galaxyproject/planemo/pull/356
2345 .. _Pull Request 375: https://github.com/galaxyproject/planemo/pull/375
2346 .. _Pull Request 390: https://github.com/galaxyproject/planemo/pull/390
2347 .. _Pull Request 394: https://github.com/galaxyproject/planemo/pull/394
2348 .. _Pull Request 398: https://github.com/galaxyproject/planemo/pull/398
2349 .. _Pull Request 403: https://github.com/galaxyproject/planemo/pull/403
2350 .. _Pull Request 40: https://github.com/galaxyproject/planemo/pull/40
2351 .. _Pull Request 425: https://github.com/galaxyproject/planemo/pull/425
2352 .. _Pull Request 426: https://github.com/galaxyproject/planemo/pull/426
2353 .. _Pull Request 428: https://github.com/galaxyproject/planemo/pull/428
2354 .. _Pull Request 429: https://github.com/galaxyproject/planemo/pull/429
2355 .. _Pull Request 454: https://github.com/galaxyproject/planemo/pull/454
2356 .. _Pull Request 472: https://github.com/galaxyproject/planemo/pull/472
2357 .. _Pull Request 479: https://github.com/galaxyproject/planemo/pull/479
2358 .. _Pull Request 480: https://github.com/galaxyproject/planemo/pull/480
2359 .. _Pull Request 484: https://github.com/galaxyproject/planemo/pull/484
2360 .. _Pull Request 488: https://github.com/galaxyproject/planemo/pull/488
2361 .. _Pull Request 491: https://github.com/galaxyproject/planemo/pull/491
2362 .. _Pull Request 51: https://github.com/galaxyproject/planemo/pull/51
2363 .. _Pull Request 56: https://github.com/galaxyproject/planemo/pull/56
2364 .. _Pull Request 63: https://github.com/galaxyproject/planemo/pull/63
2365 .. _Pull Request 68: https://github.com/galaxyproject/planemo/pull/68
2366 .. _Pull Request 6: https://github.com/galaxyproject/planemo/pull/6
2367 .. _Pull Request 98: https://github.com/galaxyproject/planemo/pull/98
2368 .. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99
2369 .. _XSD: http://www.w3schools.com/schema/
2370 .. _a13a120: https://github.com/galaxyproject/planemo/commit/a13a120
2371 .. _a2c13e4: https://github.com/galaxyproject/planemo/commit/a2c13e46259e3be35de1ecaae858ba818bb94734
2372 .. _a2ee135: https://github.com/galaxyproject/planemo/commit/a2ee135
2373 .. _a4110a8: https://github.com/galaxyproject/planemo/commit/a4110a85a770988e5cd3c31ccc9475717897d59c
2374 .. _a4e6958: https://github.com/galaxyproject/planemo/commit/a4e6958
2375 .. _a58a3b8: https://github.com/galaxyproject/planemo/commit/a58a3b8
2376 .. _a87899b: https://github.com/galaxyproject/planemo/commit/a87899b
2377 .. _aad1eed: https://github.com/galaxyproject/planemo/commit/aad1eed
2378 .. _ac4f828: https://github.com/galaxyproject/planemo/commit/ac4f82898f7006799142503a33c3978428660ce7
2379 .. _ad3b2f0: https://github.com/galaxyproject/planemo/commit/ad3b2f0
2380 .. _af39061: https://github.com/galaxyproject/planemo/commit/af390612004dab636d8696839bb723d39f97c85d
2381 .. _af7448c: https://github.com/galaxyproject/planemo/commit/af7448c
2382 .. _b0b867e: https://github.com/galaxyproject/planemo/commit/b0b867e
2383 .. _b1c8f1d: https://github.com/galaxyproject/planemo/commit/b1c8f1d
2384 .. _b53006d: https://github.com/galaxyproject/planemo/commit/b53006d
2385 .. _b757791: https://github.com/galaxyproject/planemo/commit/b757791
2386 .. _b7d9e96: https://github.com/galaxyproject/planemo/commit/b7d9e96
2387 .. _b86fe1f: https://github.com/galaxyproject/planemo/commit/b86fe1f
2388 .. _b8d90ab: https://github.com/galaxyproject/planemo/commit/b8d90abab8bf53ae2e7cca4317223c01af9ab68c
2389 .. _b9232e5: https://github.com/galaxyproject/planemo/commit/b9232e55e713abbd1d9ce8b0b34cbec6c701dc17
2390 .. _badc25f: https://github.com/galaxyproject/planemo/commit/badc25fca495b61457ffb2e027f3fe9cf17c798f
2391 .. _bioblend: https://github.com/galaxyproject/bioblend/
2392 .. _c1713d2: https://github.com/galaxyproject/planemo/commit/c1713d2
2393 .. _c23569f: https://github.com/galaxyproject/planemo/commit/c23569f
2394 .. _c444855: https://github.com/galaxyproject/planemo/commit/c444855
2395 .. _c4dfd55: https://github.com/galaxyproject/planemo/commit/c4dfd55
2396 .. _c8640b6: https://github.com/galaxyproject/planemo/commit/c8640b6
2397 .. _cb5b906: https://github.com/galaxyproject/planemo/commit/cb5b906
2398 .. _cc1a447: https://github.com/galaxyproject/planemo/commit/cc1a447
2399 .. _cc8abb6: https://github.com/galaxyproject/planemo/commit/cc8abb6
2400 .. _ce8e1be: https://github.com/galaxyproject/planemo/commit/ce8e1be
2401 .. _cwltool: https://github.com/common-workflow-language/cwltool/.. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e
2402 .. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e
2403 .. _d755fe7: https://github.com/galaxyproject/planemo/commit/d755fe7
2404 .. _d76b489: https://github.com/galaxyproject/planemo/commit/d76b489
2405 .. _d8f2038: https://github.com/galaxyproject/planemo/commit/d8f2038
2406 .. _dad2d9d: https://github.com/galaxyproject/planemo/commit/dad2d9d
2407 .. _dd94ddc: https://github.com/galaxyproject/planemo/commit/dd94ddc
2408 .. _dff4f33: https://github.com/galaxyproject/planemo/commit/dff4f33c750a8dbe651c38e149a26dd42e706a82
2409 .. _e0577e7: https://github.com/galaxyproject/planemo/commit/e0577e7
2410 .. _e0acf91: https://github.com/galaxyproject/planemo/commit/e0acf91
2411 .. _e38c436: https://github.com/galaxyproject/planemo/commit/e38c436
2412 .. _e769118: https://github.com/galaxyproject/planemo/commit/e769118
2413 .. _e8c1d45: https://github.com/galaxyproject/planemo/commit/e8c1d45f0c9a11bcf69ec2967836c3b8f432dd97
2414 .. _eb039c0: https://github.com/galaxyproject/planemo/commit/eb039c0
2415 .. _ec6e30f: https://github.com/galaxyproject/planemo/commit/ec6e30f
2416 .. _efc5f30: https://github.com/galaxyproject/planemo/commit/efc5f30
2417 .. _f0610d7: https://github.com/galaxyproject/planemo/commit/f0610d7
2418 .. _f3394e7: https://github.com/galaxyproject/planemo/commit/f3394e7
2419 .. _f3c6917: https://github.com/galaxyproject/planemo/commit/f3c6917
2420 .. _f3cafaa: https://github.com/galaxyproject/planemo/commit/f3cafaa
2421 .. _f7554d1: https://github.com/galaxyproject/planemo/commit/f7554d1
2422 .. _f798c7e: https://github.com/galaxyproject/planemo/commit/f798c7e
2423 .. _f854138: https://github.com/galaxyproject/planemo/commit/f854138
2424 .. _f99f6c1: https://github.com/galaxyproject/planemo/commit/f99f6c1
2425 .. _fba3874: https://github.com/galaxyproject/planemo/commit/fba3874
2426 .. _fdb1b51: https://github.com/galaxyproject/planemo/commit/fdb1b51
2427 .. _fdce74c: https://github.com/galaxyproject/planemo/commit/fdce74c
2428 .. _fe7ad46: https://github.com/galaxyproject/planemo/commit/fe7ad46
2429 .. _fea51fc: https://github.com/galaxyproject/planemo/commit/fea51fc
2430 .. _lxml: http://lxml.de/
2431 .. _nose: https://nose.readthedocs.org/en/latest/
2432 .. _xmllint: http://xmlsoft.org/xmllint.html
2433 .. _Conda: http://conda.pydata.org/
2434 .. _Tool Factory: http://bioinformatics.oxfordjournals.org/content/early/2012/09/27/bioinformatics.bts573.full.pdf
2435 .. _git: https://git-scm.com/
2436 .. _anaconda-verify: https://github.com/ContinuumIO/anaconda-verify
2437 .. _galaxy.xsd: https://github.com/galaxyproject/planemo/blob/master/planemo/xml/xsd/tool/galaxy.xsd
2438 .. _setup.py: https://github.com/galaxyproject/planemo/blob/master/setup.py
2439 .. _Bioconductor: https://www.bioconductor.org/
2440 .. _tools-iuc: https://github.com/galaxyproject/tools-iuc
2441 .. _PyPI: https://pypi.python.org/pypi
2442 .. _Involucro: https://github.com/involucro/involucro
2443 .. _Bioconda: https://bioconda.github.io/
2444 .. _pip: https://pip.pypa.io/en/stable/
2445 .. _BioContainers: http://biocontainers.pro/
2446 .. _Toil: https://github.com/BD2KGenomics/toil
2447 .. _quay.io: https://quay.io/
2448 .. _galaxy-lib: https://github.com/galaxyproject/galaxy-lib
2449 .. _@abretaud: https://github.com/abretaud
2450 .. _@hexylena: https://github.com/hexylena
2451 .. _@peterjc: https://github.com/peterjc
2452 .. _@mr-c: https://github.com/mr-c
2453 .. _@martenson: https://github.com/martenson
2454 .. _@nsoranzo: https://github.com/nsoranzo
2455 .. _@nturaga: https://github.com/nturaga
2456 .. _@bgruening: https://github.com/bgruening
2457 .. _@carlfeberhard: https://github.com/carlfeberhard
2458 .. _@lparsons: https://github.com/lparsons
2459 .. _@kellrott: https://github.com/kellrott
2460 .. _@mvdbeek: https://github.com/mvdbeek
2461 .. _@natefoo: https://github.com/natefoo
2462 .. _@pstew: https://github.com/pstew
2463 .. _@ramezrawas: https://github.com/ramezrawas
2464 .. _@chambm: https://github.com/chambm
2465 .. _@takadonet: https://github.com/takadonet
2466 .. _@petrkadlec: https://github.com/petrkadlec
2467 .. _@pvanheus: https://github.com/pvanheus
2468 .. _@einon: https://github.com/einon
2469 .. _@blankenberg: https://github.com/blankenberg
2470 .. _@JeanFred: https://github.com/JeanFred
2471 .. _@gregvonkuster: https://github.com/gregvonkuster
2472 .. _@remimarenco: https://github.com/remimarenco
2473 .. _@thriqon: https://github.com/thriqon
2474 .. _@RJMW: https://github.com/RJMW
2475 .. _@manabuishii: https://github.com/manabuishii
2476 .. _@dfornika: https://github.com/dfornika
2477 .. _@bernt-matthias: https://github.com/bernt-matthias
2478 .. _@katrinleinweber: https://github.com/katrinleinweber
2479 .. _@bebatut: https://github.com/bebatut
2480 .. _@selten: https://github.com/selten
2481 .. _@shiltemann: https://github.com/shiltemann
2482 .. _@bedroesb: https://github.com/bedroesb
2483 .. _@ic4f: https://github.com/ic4f
2484 .. _@martin-raden: https://github.com/martin-raden
2485
2486