Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
Readme
.. figure:: https://raw.githubusercontent.com/jmchilton/planemo/master/docs/planemo_logo.png :alt: Planemo Logo :align: center :figwidth: 100% :target: https://github.com/galaxyproject/planemo
Command-line utilities to assist in developing Galaxy_ and Common Workflow Language_ artifacts -
including tools, workflows, and training materials.
.. image:: https://readthedocs.org/projects/planemo/badge/?version=latest :target: http://planemo.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status
.. image:: https://badge.fury.io/py/planemo.svg :target: https://pypi.python.org/pypi/planemo/ :alt: Planemo on the Python Package Index (PyPI)
.. image:: https://github.com/galaxyproject/planemo/workflows/Python%20CI/badge.svg :target: https://github.com/galaxyproject/planemo/actions?query=workflow%3A%22Python+CI%22
For a traditional Python installation of Planemo, first set up a virtualenv
for planemo (this example creates a new one in .venv) containing
Python 3.7 or newer and then install with pip. Planemo must be installed
with pip 7.0 or newer.
::
$ virtualenv .venv; . .venv/bin/activate
$ pip install "pip>=7" # Upgrade pip if needed.
$ pip install planemo
For information on updating Planemo, installing the latest development release,
or installing Planemo via Bioconda <https://github.com/bioconda/bioconda-recipes>__
installation <http://planemo.readthedocs.io/en/latest/installation.html>__
documentation.Planemo is also available as a virtual appliance <https://planemo.readthedocs.io/en/latest/appliance.html>_ bundled
with a preconfigured Galaxy server and set up for Galaxy_ and
Common Workflow Language_ tool development.
You can choose from open virtualization format (OVA_, .ova) or Docker_
appliances.
This quick start will assume you have a directory with one or more Galaxy
tool XML files. If no such directory is available, one can be quickly created for
demonstrating planemo as follows project_init --template=demo mytools; cd mytools.
Planemo can check tool XML files for common problems and best
practices using the lint command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>_
(also aliased as l).
::
$ planemo lint
Like many planemo commands - by default this will search the
current directory and use all tool files it finds. It can be explicitly
passed a path to tool files or a directory of tool files.
::
$ planemo l randomlines.xml
The lint command takes in additional options related to
reporting levels, exit code, etc. These options are described
in the docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>_
or (like with all commands) can be accessed by passing --help to it.
::
$ planemo l --help
Usage: planemo lint [OPTIONS] TOOL_PATH
Once tools are syntactically correct - it is time to test. The test
command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>__
can be used to test a tool or a directory of tools.
::
$ planemo test --galaxy_root=../galaxy randomlines.xml
If no --galaxy_root is defined, Planemo will download and configure
a disposable Galaxy instance for testing.
Planemo will create a HTML output report in the current directory named
tool_test_output.html (override with --test_output). See an
example <http://galaxyproject.github.io/planemo/tool_test_viewer.html?test_data_url=https://gist.githubusercontent.com/jmchilton/9d4351c9545d34209904/raw/9ed285d3cf98e435fc4a743320363275949ad63c/index>_
of such a report for Tophat.
Once tools have been linted and tested - the tools can be viewed in a
Galaxy interface using the serve (s) command <http://planemo.readthedocs.org/en/latest/commands.html#serve-command>__.
::
$ planemo serve
Like test, serve requires a Galaxy root and one can be
explicitly specified with --galaxy_root or installed dynamically
with --install_galaxy.
For more information on building Galaxy tools in general please check out
Building Galaxy Tools Using Planemo_.
For more information on developing Galaxy workflows with Planemo checkout
best practices for Galaxy Workflows_ and the description of Planemo's
test format_. For information on developing Galaxy training materials
checkout the contributing documentation <https://training.galaxyproject.org/training-material/topics/contributing/>__
on training.galaxyproject.org.
This quick start will assume you have a directory with one or more Common Workflow Language_ YAML files. If no such directory is available, one can be quickly created for
demonstrating planemo as follows planemo project_init --template=seqtk_complete_cwl mytools; cd mytools.
Planemo can check tools YAML files for common problems and best
practices using the lint command <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>_
(also aliased as l).
::
$ planemo lint
Like many planemo commands - by default this will search the
current directory and use all tool files it finds. It can be explicitly
passed a path to tool files or a directory of tool files.
::
$ planemo l seqtk_seq.cwl
The lint command takes in additional options related to
reporting levels, exit code, etc. These options are described
in the docs <http://planemo.readthedocs.org/en/latest/commands.html#lint-command>_
or (like with all commands) can be accessed by passing --help to it.
::
$ planemo l --help
Usage: planemo lint [OPTIONS] TOOL_PATH
Once tools are syntactically correct - it is time to test. The test
command <http://planemo.readthedocs.org/en/latest/commands.html#test-command>__
can be used to test a CWL tool, workflow, or a directories thereof.
::
$ planemo test --engine cwltool seqtk_seq.cwl
Planemo will create a HTML output report in the current directory named
tool_test_output.html. Check out the file seqtk_seq_tests.yml for
an example of Planemo test for a CWL tool. A test consists of any number of
jobs (with input descriptions) and corresponding output assertions.
Checkout the Commmon Workflow User Guide_ for more information on developing
CWL tools in general and Building Common Workflow Language Tools_ for more
information on using Planemo to develop CWL tools.
Planemo can help you publish tools to the Galaxy Tool Shed.
Check out Publishing to the Tool Shed_ for more information.
Planemo can help develop tools and Conda packages in unison.
Check out the Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-conda>__ or CWL <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda-cwl>__ version of the "Dependencies and Conda" tutorial
for more information.
Planemo can help develop tools that run in "Best Practice" containers for
scientific workflows. Check out the Galaxy <http://planemo.readthedocs.io/en/latest/writing_advanced.html#dependencies-and-containers>__ or CWL <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers-cwl>__ version of the "Dependencies and Containers" tutorial for more information.
.. _Galaxy: http://galaxyproject.org/
.. _GitHub: https://github.com/
.. _Conda: http://conda.pydata.org/
.. _Docker: https://www.docker.com/
.. _Vagrant: https://www.vagrantup.com/
.. _Travis CI: http://travis-ci.org/
.. _tools-devteam: https://github.com/galaxyproject/tools-devteam
.. _tools-iuc: https://github.com/galaxyproject/tools-iuc
.. _Building Galaxy Tools Using Planemo: http://planemo.readthedocs.io/en/latest/writing_standalone.html
.. _Publishing to the Tool Shed: http://planemo.readthedocs.org/en/latest/publishing.html
.. _Common Workflow Language: https://www.commonwl.org/
.. _Commmon Workflow User Guide: http://www.commonwl.org/user_guide/
.. _Building Common Workflow Language Tools: http://planemo.readthedocs.io/en/latest/writing_cwl_standalone.html
.. _OVA: https://en.wikipedia.org/wiki/Open_Virtualization_Format
.. _test format: https://planemo.readthedocs.io/en/latest/test_format.html
.. _best practices for Galaxy Workflows: https://planemo.readthedocs.io/en/latest/best_practices_workflows.html
.. to_doc
metadata.yaml files (thanks to @nsoranzo).
Pull Request 1439@bernt-matthias). Pull Request 1440@bernt-matthias). Pull Request 1437@nsoranzo).
Pull Request 1433--host parameter to allow listening on non-default hosts (thanks to
@selten). Pull Request 1430docker run (thanks to @bernt-matthias). Pull Request 1428@mvdbeek). Pull Request 1427@nsoranzo). Pull Request 1425package_name attribute on CondaTarget objects (thanks to
@nsoranzo). Pull Request 1424@nsoranzo). Pull Request 1422@nsoranzo). Pull Request 1419@nsoranzo). Pull Request 1416@bernt-matthias). Pull Request 1388@mvdbeek). Pull Request 1412@hexylena).
Pull Request 1410workflow_test_init (thanks to @mvdbeek). Pull Request 1408@mvdbeek). Pull Request 1407@nsoranzo). Pull Request 1406@mvdbeek).
Pull Request 1401@mvdbeek). Pull Request 1402@bernt-matthias). Pull Request 1398@mvdbeek). Pull Request 1400@mvdbeek).
Pull Request 1399@bernt-matthias). Pull Request 1396Astronomy, CLIP-seq and Materials science TS
categories (thanks to @bernt-matthias). Pull Request 1397@mvdbeek). Pull Request 1395@bernt-matthias). Pull Request 1394@hexylena).
Pull Request 1393@lldelisle). Pull Request 1391@mvdbeek). Pull Request 1389@Kulivox). Pull Request 1263@mvdbeek). Pull Request 1387@mvdbeek). Pull Request 1385@mstabrin). Pull Request 1384@bernt-matthias). Pull Request 1383@bernt-matthias). Pull Request 1382@paulzierep). Pull Request 1355planemo test (thanks to @bernt-matthias).
Pull Request 1378@nsoranzo). Pull Request 1379@mvdbeek). Pull Request 1377@nsoranzo). Pull Request 1375@nsoranzo). Pull Request 1374test_run_gxtool_randomlines test on Galaxy dev branch (thanks to
@nsoranzo). Pull Request 1373@bernt-matthias). Pull Request 1372@mvdbeek). Pull Request 1371@hexylena). Pull Request 1369--biocontainers option to shed_lint (thanks to @mvdbeek). Pull Request 1370@lldelisle). Pull Request 1364allow_none for finding repository (thanks to @mvdbeek). Pull Request 1358escape_non_unicode_symbols (thanks to @nsoranzo). Pull Request 1357@mvdbeek).
Pull Request 1265@lldelisle). Pull Request 1350@bernt-matthias). Pull Request 1275@bernt-matthias). Pull Request 1347@lldelisle). Pull Request 1348@wm75). Pull Request 1346@hexylena). Pull Request 1344planemo run tutorial
(thanks to @simonbray). Pull Request 1338@nsoranzo).
Pull Request 1337@SimonWaldherr).
Pull Request 1334@mvdbeek). Pull Request 1327@bernt-matthias). Pull Request 1332@simonbray). Pull Request 1330planemo shed_test (thanks to @mvdbeek). Pull Request 1329@mvdbeek). Pull Request 1326@nsoranzo). Pull Request 1322@bernt-matthias). Pull Request 1325@nsoranzo).
Pull Request 1320@lldelisle). Pull Request 1314@mvdbeek). Pull Request 1313for_paths when path is directory of tools (thanks to @mvdbeek).
Pull Request 1312@lldelisle). Pull Request 1310@mvdbeek). Pull Request 1308pytest.raises() instead of ad-hoc assert_raises_regexp() context
manager (thanks to @nsoranzo). Pull Request 1302@mvdbeek). Pull Request 1304@lldelisle). Pull Request 1305@lldelisle). Pull Request 1306@mvdbeek). Pull Request 1307@mvdbeek). Pull Request 1303@martenson). Pull Request 1247@simonbray). Pull Request 1249@bernt-matthias). Pull Request 1255@simonbray). Pull Request 1257@nsoranzo). Pull Request 1259@hexylena). Pull Request 1260@bernt-matthias). Pull Request 1262@bernt-matthias). Pull Request 1212@bernt-matthias).
Pull Request 1264@mvdbeek). Pull Request 1232@simonbray). Pull Request 1270None (thanks to @bernt-matthias). Pull Request 1274@gallardoalba). Pull Request 1278@gallardoalba).
Pull Request 1277@gallardoalba).
Pull Request 1279@gallardoalba).
Pull Request 1281planemo.autoupdate module (thanks to
@nsoranzo). Pull Request 1283@gallardoalba).
Pull Request 1280@gallardoalba).
Pull Request 1284planemo.glob and planemo.virtualenv (thanks
to @nsoranzo). Pull Request 1287conda_lint command (thanks to @nsoranzo). Pull Request 1288@adRn-s). Pull Request 1285@simonbray). Pull Request 1271planemo.runnable and planemo.workflow_lint
(thanks to @nsoranzo). Pull Request 1291--channels also affect mulled channels and update/extend howto use
bioconda artifacts (thanks to @bernt-matthias). Pull Request 1227@gallardoalba). Pull Request 1292@shiltemann). Pull Request 1293@mvdbeek). Pull Request 1276@mvdbeek). Pull Request 1295@mvdbeek). Pull Request 1294--tool_data_table options (thanks to
@mvdbeek). Pull Request 1296@mvdbeek). Pull Request 1298@mvdbeek). Pull Request 1299@mvdbeek). Pull Request 1297@profgiuseppe).
Pull Request 1244Pull Request 1242_Pull Request 1241_Pull Request 1239_@simonbray). Pull Request 1237Pull Request 1230_Pull Request 1228_best_practice_search() for changes in galaxy-tool-util Pull Request 1224_cleanup_job depend on --no_cleanup
(thanks to @bernt-matthias). Pull Request 1226@gallardoalba). Pull Request 1222@shiltemann). Pull Request 1217@simonbray). Pull Request 1213@simonbray). Pull Request 1214@simonbray). Pull Request 1215@simonbray). Pull Request 1209@stain). Pull Request 1206Pull Request 1207_@simonbray). Pull Request 1205@bernt-matthias). Pull Request 1198@simonbray). Pull Request 1140@simonbray). Pull Request 1200@simonbray). Pull Request 1201Pull Request 1196_@simonbray).
Pull Request 1188@simonbray).
Pull Request 1193@bernt-matthias).
Pull Request 1195--download_outputs flag (thanks to
@simonbray). Pull Request 1184Pull Request 1187_@simonbray). Pull Request 1151@simonbray). Pull Request 1153Pull Request 1179_Pull Request 1180_Pull Request 1182_Pull Request 1170_Pull Request 1171_Pull Request 1172_Pull Request 1173_Pull Request 1174_Pull Request 1177_Pull Request 1169_@bernt-matthias). Pull Request 1165@simonbray). Pull Request 1164--download_outputs flag for the run command
(thanks to @simonbray).
Pull Request 1157@simonbray).
Pull Request 1156run command
(thanks to @simonbray). Pull Request 1154Pull Request 1152_Pull Request 1146_Pull Request 1145_Pull Request 1144_Pull Request 1142_Pull Request 1095_Pull Request 1135, Pull Request 1133Pull Request 1134_
1133`_@simonbray).
Pull Request 1128ci_find_tools and ci_find_repos commands. Pull Request 1127_Pull Request 1126, Pull Request 1125,
Pull Request 1123_tabulate package for the list_invocations command.
Pull Request 1124_@simonbray).
Pull Request 1076planemo run to execute workflows (thanks to @simonbray).
Pull Request 1102workflow_upload command for publishing each workflow of a repository with many
workflows to their own standalone repository.
Pull Request 1091_@simonbray).
Pull Request 1083@bernt-matthias).
Pull Request 1108workflow_convert,
workflow_lint, workflow_job_init, and workflow_test_init
(thanks to @simonbray).
Pull Request 1101, Pull Request 1118, Pull Request 1121,
Pull Request 1116, Pull Request 1064Pull Request 1115_run_tests.sh invocation Pull Request 1099_@abretaud). Pull Request 1066@peterjc).
Pull Request 1068external_galaxy is used as the engine (thanks to
@simonbray).
Pull Request 1072@bedroesb).
Pull Request 1074@simonbray).
Pull Request 1079job_conf.xml template.
Pull Request 1086_Pull Request 1093_ci_find_repos command. Pull Request 1094_@martenson).
Pull Request 1096@martenson).
Pull Request 1110tutorial.md usage of citations (thanks to @blankenberg).
Pull Request 1114ZeroDivisionError when no tests are executed (thanks to @simonbray).
Pull Request 1120workflow_init_job.
Pull Request 1052_Pull Request 1058_Pull Request 1061, Pull Request 1062Pull Request 1060_Pull Request 1059_Pull Request 821_Pull Request 1026_@TMiguelT).
Pull Request 1038, Pull Request 1034_Pull Request 1028, Pull Request 1049, Pull Request 1051_
Pull Request 1044_run and test.
Pull Request 900, Pull Request 1029Pull Request 1043_@mblue9). Pull Request 1032Pull Request 994_Pull Request 993_--shed_install (thanks to @AndreasSko).
Pull Request 1001@bernt-matthias).
Pull Request 1021@bernt-matthias).
Pull Request 1022--group_tools option to ci_find_tools
(thanks to @bernt-matthias).
Pull Request 1008@shiltemann).
Pull Request 1013@shiltemann). Pull Request 1041Pull Request 1037_Pull Request 1031_@bernt-matthias).
Pull Request 1020gi._make_url() internal BioBlend method.@mr-c).
Pull Request 1015Pull Request 1023_Pull Request 1046_@blankenberg).
Pull Request 1025Pull Request 1024, Pull Request 1003,
Pull Request 1011, Pull Request 1006,
Pull Request 1040, Pull Request 1036,
Pull Request 1042_Pull Request 991_Pull Request 988_shell=True in subprocesses Pull Request 989_Pull Request 985_untar_to() subprocesses through the shell Pull Request 984_Pull Request 986_Pull Request 983_Pull Request 982_Pull Request 980_Pull Request 978_@bernt-matthias). Pull Request 979Pull Request 977_Pull Request 975_Pull Request 974_Pull Request 976_Pull Request 972_@hexylena). Pull Request 973Pull Request 971_@hexylena). Pull Request 970Pull Request 968_@nsoranzo). 1ab8530unicodify() on exceptions and subprocess outputs (thanks to
@nsoranzo) Pull Request 944None with empty string (thanks to @ic4f). Pull Request 950@bedroesb). Pull Request 958@nsoranzo).
Pull Request 959@martin-raden).
Pull Request 963@nsoranzo).
Pull Request 964Pull Request 966_@bebatut). Pull Request 926@shiltemann).
Pull Request 938@bebatut). Pull Request 943@nsoranzo).
Pull Request 940@nsoranzo).
Pull Request 937Pull Request 937_@selten). Pull Request 935@martenson). Pull Request 931@bernt-matthias). Pull Request 930@mvdbeek).
Pull Request 912@bebatut).
Pull Request 913@mvdbeek). Pull Request 917yaml.safe_load() instead of deprecated load() (thanks to @nsoranzo).
Pull Request 921tool_test_report.json to xunit (thanks to @mvdbeek).
Pull Request 918@mvdbeek).
Pull Request 924getchildren() (thanks to @nsoranzo).
Pull Request 925@mvdbeek).
Pull Request 908@bernt-matthias). Pull Request 909@mvdbeek). Pull Request 910@nsoranzo). 07dc6e0@blankenberg).
Pull Request 914@bgruening). Pull Request 915@nsoranzo). Pull Request 906planemo test --skip_venv (thanks to @nsoranzo).
Pull Request 907sudo: false from .travis.yml (thanks to @nsoranzo).
Pull Request 902planemo serve. Install Galaxy when the
directory specified with --galaxy_root does not exist or is empty. (thanks
to @nsoranzo). Pull Request 895, Issue 845_@martenson).
Pull Request 899, Issue 898_workflow_convert to convert a native .ga workflows to format 2 (yaml).
Pull Request 896_workflow_edit) to open workflow in a synchronized graphical editor.
Pull Request 894_@nsoranzo). Pull Request 876--conda_use_local option for planemo test (thanks to
@nsoranzo). Pull Request 876label set (thanks to
@bgruening). Pull Request 893__repr__ for TestCase to improve debugging Planemo
(thanks to @bgruening). Pull Request 892@martenson).
Pull Request 891@mvdbeek).
Pull Request 889W605 (thanks to @martenson). Pull Request 888@bebatut).
Pull Request 887@mvdbeek). Pull Request 874@bgruening).
Pull Request 867@hexylena). Pull Request 868ci_find_repos
(thanks to @nsoranzo). Pull Request 877Pull Request 871_gx_venv_None. Pull Request 870_@nsoranzo). Pull Request 864Pull Request 882_@bebatut).
Pull Request 861planemo test when TEMP env variable contain spaces (thanks to
@nsoranzo).
Pull Request 851@hexylena).
Pull Request 856@hexylena).
Pull Request 860@nsoranzo).
Pull Request 866@nsoranzo). bad810a_Pull Request 849_@bgruening).
Pull Request 847@katrinleinweber).
Pull Request 850Pull Request 843_test_shed_upload.py tests. 72d2ca7_@bgruening).
Pull Request 842--no_shed_install option, to prevent shed installs as part of workflow testing.
Pull Request 841_@hexylena). Pull Request 848Pull Request 837_Pull Request 833, Pull Request 836Pull Request 840_Pull Request 838_Pull Request 835_Pull Request 834_lint,
conda_install, conda_env, test, run, and mull.
Pull Request 828_Conda <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-conda>__
and Container <http://planemo.readthedocs.io/en/latest/writing_advanced_cwl.html#dependencies-and-containers>__
development with CWL tools that mirrors the existing tutorials for Galaxy tools - including new
CWL exercises, answers, and example project templates.
347c622_tool_init command to properly deal with
SoftwareRequirement s and generate more idiomatic CWL.
Pull Request 820, a5c72e3--engine toil) for testing and running CWL_ tools (requires
manually installing Toil_ with pip install toil in Planemo's environment).
Pull Request 831_documentation <http://planemo.readthedocs.io/en/latest/test_format.html>__
for the Galaxy Workflow and CWL_ test format files (includes information on configuring
various test engines).
Pull Request 832_Pull Request 830_conda_search command. Pull Request 826_Pull Request 822_Pull Request 829_Pull Request 827, Pull Request 818Pull Request 825_Pull Request 823_Pull Request 816_Pull Request 817_--engine.--engine for the
run, serve, and test commands.Pull Request 781_Pull Request 795_Pull Request 799_Pull Request 800_GALAXY_MEMORY_MB (thanks to @bernt-matthias).
Pull Request 801Pull Request 802_r channel with conda-forge (thanks to @bgruening).
Pull Request 805galaxy.xsd with latest Galaxy updates (thanks to @nsoranzo).
Pull Request 806requests.get() when validating http URLs (thanks to @nsoranzo).
Pull Request 809@bgruening). Pull Request 810Pull Request 790_Pull Request 787_Pull Request 792_Pull Request 803, dc443d6@nsoranzo).
Pull Request 768 and Pull Request 774_universal_newlines=True
(thanks to @peterjc).
Pull Request 764@mr-c).
Pull Request 756Pull Request 769_Pull Request 773_test
and run commands.
Pull Request 776_Pull Request 771_Pull Request 770_Pull Request 761_Pull Request 753_Pull Request 759_@nsoranzo).
Pull Request 747@nsoranzo). Pull Request 747@nsoranzo) .
Pull Request 743chmod doesn't support --recursive flag.
(thanks to @dfornika). Pull Request 739socket.error when linting URLs
(thanks to @nsoranzo). Pull Request 738Pull Request 745_galaxy-lib_ for various fixes
related to CWL_.--docker flag, for a few releases it would require
Galaxy use a container for every non-upload tool. This breaks various
conversion tools for instance and so was reverted.
Pull Request 733_@nsoranzo).
Pull Request 725--conda_auto_install help (thanks to @nsoranzo).
Pull Request 727Pull Request 729, Pull Request 732Pull Request 730_Pull Request 731_galaxy-lib_ for Conda fixes. (thanks @nsoranzo)
and updated CWL utilities. Pull Request 716, Pull Request 723@nsoranzo). Pull Request 715planemo command --help in main help
(thanks to @peterjc). Pull Request 709None requirement versions when registering containers
(thanks to @bgruening). Pull Request 704@mvdbeek). Pull Request 720Pull Request 701, 8a608e0planemo mull to use a default action of build-and-test since
build no longer cleans up itself. ecc1bc2_Pull Request 702_Pull Request 699_@manabuishii) 904d77acontainer_register to create pull requests against the newly finalized home of the
multi-package-containers registry repository.
9636682_use_global_config and use_env_var for options with unspecified defaults.
475104c_Pull Request 684_galaxy.xsd with latest upstream Galaxy updates (thanks to @nsoranzo).
Pull Request 687ci_find_repos command to not filter repos whose only modifications where
in subdirs (thanks to @nsoranzo).
Pull Request 688container_register for mulled version 2 and repository name changes.
Pull Request 689_container_register command.
Pull Request 690_shed_update not fail if there is nothing to update
(thanks to @nsoranzo). Issue 494, Pull Request 680_Pull Request 683_container_register for tool repositories.
Pull Request 675_hub binary installation for Mac OS X.
Pull Request 682_galaxy_root (thanks to @nsoranzo). Pull Request 662filter_paths() to not partial match paths when filtering shed repositories
(thanks to @nsoranzo). Pull Request 665.shed.yml files (thanks to @RJMW).
Pull Request 664/tmp as temp directory. b4ae44d_planemo run by reworking it to wait using urllib instead of sockets.
3129216_Pull Request 642, Pull Request 643planemo conda_search command for searching best practice channels
from the command line.
Pull Request 642_--conda_use_local
command.
Pull Request 643, Issue 620open (or just o) command to quickly open the last test results
(or any file if supplied). Pull Request 641_galaxy-lib_ update.
assert_command not detected as a valid test (fixes Issue 260_).lint --conda_requirements check that at least one actual requirement is found.
6638caa_conda_install to work with packages as well as just tools.
8faf661_--global option to conda_install to install requirements into global Conda setup
instead of using an environment.
8faf661_planemo lint --biocontainer that checks that a tool has an available BioContainer
registered.
0a1abfe_planemo mull command.
0a1abfe_planemo mull doesn't work out of the box on
Mac OS X.
0a1abfe_planemo.tools. 04238d3_MANIFEST.in entry that was migrated to galaxy-lib. ced5ce2_conda_env. Pull Request 640_Pull Request 639_--no_dependency_resolution option disabling conda dependency
resolver.
Pull Request 635, Issue 633Pull Request 638_@bgruening).
Pull Request 649Pull Request 634_shed_lint --urls introduced in 0.38.0.
84ebc1f_Pull Request 629, Issue 515shed_lint --tools for a suite lints the same tools multiple
times.
Issue 564, Pull Request 628galaxy-lib_ release. This means new installs start with
Miniconda 3 instead of Minicoda 2 and at a newer version. This fixes many
Conda_ related bugs.--conda_dependency_resolution, --conda_auto_install, and --conda_auto_init
are effectively enabled by default now. 4595953_@abretaud).
Pull Request 612bioconda_scripts (thanks to @nturaga)
Pull Request 614project_init.
Issue 388, Pull Request 610test command. Pull Request 609_@mr-c).
Pull Request 608@peterjc).
Pull Request 605@peterjc).
Pull Request 606@mvdbeek).
Pull Request 602@nturaga). Pull Request 570@bgruening). 50d3c4a@bgruening_).Issue 578_
(thanks to @peterjc). Pull Request 591conda-forge (thanks to @nsoranzo).
Pull Request 590mull command to build containers for tools based on Conda_
recipes matching requirement definitions. 08cef54_--mulled_containers flag on test, serve, and run
commands to run tools in "mulled" containers. Galaxy will first search
locally cache containers (such as ones built with mull), then search
the mulled namespace of quay.io, and finally build one on-demand if
needed using galaxy-lib and Involucro_ developed by @thriqon_.--conda_requirements flag on lint command to ensure requirements
can be resolved in best practice channels. 9da8387_conda_install command over multiple tool paths. 2e4e5fc_Makefile target.
19b2ee9_lint --urls false positives by being more restrictive with what is considered a URL
(fixed by @hexylena_ after detailed report from @peterjc).
Issue 573, Pull Request 579_planemo lint --no_xsd). 1ef05d2_conda_lint command to lint Conda_ recipes based
on anaconda-verify. 6a6f164clone and pull_request commands to ease PRs
(with documentation fixes from @martenson).
e925ba1, ea5324f_galaxy.xsd_ to allow version_command's to have an interpreter
attribute. 7cca2e4_@nsoranzo_ for Planemo's use of
git diff <https://git-scm.com/docs/git-diff>__.
6f91719_tool_init code from @nturaga's
Bioconductor work. ccdd2d5_Tool Factory_ code from tools-iuc. ca88b0cplanemo.xml.validation.setup.py. 34538deplanemo lint --xsd to use a fairly complete and newly official XSD
definition. Pull Request 566_@bgruening, @mvdbeek,
and @nsoranzo). Pull Request 559@ramezrawas). Pull Request 561@nsoranzo).
Pull Request 565ci_find_repos and ci_find_tools to ease
CI scripting.
Pull Request 555_--conda_dependency_resolution. f7b6c7e_--conda_dependency_resolution. f7b6c7e_update_planemo_recipe.bash. 6c03de8_tests/ directory and fix import order throughout
module. ef4b9f4_galaxy-lib_ release and change Conda_ semantics to match
recent updates to Galaxy. For the most robust Conda_ usage - use planemo 0.30+
with Galaxy 16.07 or master.
07d94bd_--conda_auto_init flag for conda_install. ca19910_PLANEMO_CONDA_PREFIX to set a default
for --conda_prefix.
24008ab_Pull Request 550_cp rather than symlink to $DOWNLOAD_CACHE in the
dependency_script command (thanks to @peterjc). c2204b3@peterjc).
Pull Request 539dependency_script command
(thanks to @peterjc). Pull Request 541, Pull Request 545_@nsoranzo).
Pull Request 540@nsoranzo). Pull Request 546@nsoranzo). 9fdf490@nsoranzo). 3ceaa40@nsoranzo).
057f4f0shed_lint in script run by travis_init (thanks to @peterjc).
Pull Request 528travis_init command (thanks to @peterjc).
Pull Request 512@peterjc).
Pull Request 521@peterjc).
Pull Request 510planemo test --no_cache_galaxy under TravisCI (thanks to @peterjc).
Pull Request 513@martenson).
Pull Request 498, 725b232_expect_num_outputs to planemo FAQ. a066afb_Pull Request 526_@nsoranzo). 8c088c6make lint-readme (RST link errors) (thanks to @peterjc).
Pull Request 525@bgruening, @gregvonkuster, and @nsoranzo).
e890ab5, 08bb354_, e2398fb_@pstew).
Pull Request 507Pull Request 491_docker_galaxy engine type. eb039c0_, Issue 15_Pull Request 488_@mvdbeek.
Pull Request 484Engine and Runnable abstractions - Planemo now has
beta support for testing Galaxy workflows and CWL_ tools with Galaxy and
any CWL_ artifact with cwltool_.
Pull Request 454, 7be1bf5job_conf.xml handling, fixes bugs caused by
galaxy_root having existing and incompatible job_conf.xml files
and makes it possible to specify defaults with fixed server name. c4dfd55_profile_create, profile_delete, and
profile_list) and profile improvements (automatic postgres database
creation support). Pull Request 480, a87899bPull Request 479_Issue 475_.serve and test.
5d08b67_serve command - make test-data
available as an FTP folder, (on 16.07) automatically log
in an admin user, and many more options (such as those
required for "profiles" and a --daemon mode).test output.
Pull Request 472, f3c6917lint) and
building (tool_init) CWL_ tools. a4e6958_, b0b867e_,
4cd571c_config_directory
path (thanks to @mvdbeek). efc5f30--no_cache_galaxy option (thanks to Gildas Le
Corguillé). d8f2038_cwltool dependency version - upstream changes broke
compatibility. 65b999d_@remimarenco). 069e7ba@martenson).
fea51fc, 13a5ae7_GALAXY_SLOTS and running planemo
on a cluster. 45135ff_, e0acf91_~/.planemo.yml including --job_config_file
and Conda_ configuration options. e769118_, 26e378e_tool_init commans options typos (thanks to
Nitesh Turaga). 826d371_planemo.galaxy package. 8e96864_@blankenberg). b1c8f1d--galaxy_sqlite_database option to
--galaxy_database_seed and fix it so it actually works.
f7554d1_--extra_tools option to serve command. 02a08a0_docs/), Python import order, and docstrings.
a13a120_, 6e1e726_, 95d5cba_.shed.yml owner against credentials during shed
creation", test was incorrect and preventing uploads.
Pull Request 425, Issue 246Pull Request 429_shed_test. ce8e1be_galaxy-lib_ dependency to 16.4.1 to fix wget usage in
newer versions of wget. d76b489_shed_update.
Pull Request 428, Issue 416Pull Request 426, Issue 420.shed.yml owner against credentials during shed creation.
Pull Request 425, Issue 246shed_create. 358a42c_Pull Request 403_galaxy-lib_ for more linting.--skip_venv to support running Galaxy 16.01 inside of
conda environments. 9f3957d_galaxy-lib_ on PyPI_ instead of previous hacks....
Pull Request 394_.svn directories.
Issue 391_@bgruening. 63e456c@einon.
Pull Request 390@hexylena. Pull Request 394repo_id change, @hexylena. Pull Request 398test command. 94097c7_virtualenv not on PATH, have Planemo create one for Galaxy.
5b97f2e_@martenson.
0f8cb10, 01584c5_, b757791_six version requirement. 1c7ee5b_Issue 184_Issue 362_shed_diff --shed_target local thanks
to Gwendoline Andres and Gildas Le Corguillé at ABiMS Roscoff.
Pull Request 375_shed_diff printing to stdout if -o isn't specified.
f3394e7_shed_diff improvements to XML diffing and XUnit reporting.
af7448c_, 83e227a_shed_diff results if --verbose flagged.
9427b47_test_report command for rebuilding reports from structured JSON.
99ee51a_@bgruening. 2a7c792Issue 373_--cwl_engine argument to cwl_run command. dd94ddc_Issue 361_cwl_run command that runs a
CWL tool and job file through Galaxy. 49c5c1e_--cwl flag to serve to experimentally serve CWL tools
in Galaxy.
Pull Request 339_cwl_script command to convert
a CWL job to a bash script. 508dce7_@hexylena).
Pull Request 343shed_diff and shed_update
XUnit reports. Pull Request 344_@hexylena.
Pull Request 350Pull Request 345_Epigenetics as Tool Shed category. Pull Request 351_@natefoo).
Pull Request 356--cite_url to tool_init. fdb1b51_tool_init bug fix. f854138_setup.py_ for cwltool and bioblend_ changes. 1a157d4_docker_shell usability (thanks to @kellrott).
Pull Request 334@kellrott).
Pull Request 333@hexylena).
Pull Request 335, Issue 313_Issue 329_shed_update (thanks to @martenson).
Pull Request 322@hexylena).
Pull Request 330Pull Request 316_.txt and .md test outputs
(thanks to @hexylena). Pull Request 327@martenson). 949a36dmktemp Python standard library function
(thanks to @hexylena). Pull Request 330dependency_script to convert Tool Shed dependencies
into shell scripts - thanks to @peterjc.
Pull Request 310, f798c7e_, Issue 303_~/.planemo.yml.
Pull Request 314_@hexylena.
Pull Request 304shed_diff command - thanks to
@hexylena. Pull Request 305shed_build command for building repository tarballs -
thanks to @kellrott. Pull Request 297lint commands - thanks to @mvdbeek.
Pull Request 292serve command - thanks to @lparsons.
Pull Request 312Tool Factory_ - thanks
to @peterjc. dad2d9dMakefile - thanks to
@lparsons. Pull Request 311@mr-c. Pull Request 309Pull Request 307_-host - thanks in
part to @chambm. Pull Request 301-host and --port in
~/.planemo.yml. Pull Request 301_~/.planemo.yml sample comments - thanks to @martenson.
Pull Request 287@bgruening. Pull Request 285diff command - thanks to @martenson. Pull Request 284-t as shorthand for --shed_target (thanks to Peter Cock).
Pull Request 278_tool_init command to use from_work_dir only if file in command
(thanks to bug report and initial fix outline by Gildas Le Corguillé).
Pull Request 277_Pull Request 256, Pull Request 253, Pull Request 254,
Pull Request 255, Pull Request 251, Issue 272shed_init producing non-standard type hints. Issue 243,
f0610d7argument but not a
name. Issue 245, aad1eed--galaxy_install will still force a fetch).
Pull Request 235_Docuementation <http://planemo.readthedocs.org/en/latest/appliance.html>__
has been updated to reflect new and vastly improved Docker and Vagrant
virtual appliances are now available, as well as a new VirtualBox OVA
variant.detect_errors
and output collections). Issue 233, 334f2d4shed_test help text. Issue 223_Pull Request 230_Issue 231_Issue 240_shed_test and shed_serve for test and local tool sheds.
f3cafaa_--failed flag for the test command to rerun
previously faied tests. Pull Request 210_shed_update to upload contents and update repository
metadata. Pull Request 216_shed_test and shed_serve commands to test and view
published artifacts in the Tool Shed. Pull Request 213, Issue 176Issue 150_Pull Request 200_--ensure_metadata option to shed_lint to ensure .shed.yml
files contain many repository. Pull Request 215_make targets including ones
for setting up git pre-commit hooks. cc8abb6_, Issue 209_Pull Request 203, Pull Request 206shed_diff not in the repository root directory
(thanks to Peter Cock). Pull Request 207, Issue 205shed_diff with directories not yet in Tool Shed.
Pull Request 208_--shed_target
values. Issue 217_Issue 211_planemo lint to use current directory if
explicit paths are not supplied. 1e3668a_.shed.yml
files - thanks to Peter Cock. Issue 180, Pull Request 185,
Pull Request 196_.shed.yml- thanks to Peter Cock. Pull Request 186_lint now warns if tool ids contain whitespace. Pull Request 190_Pull Request 187_cp command - thanks to Peter Cock. 6bcf699_Issue 188_shed_diff folder naming. Issue 192_tool_init command. Issue 189_shed_lint to check for valid actions in tool_dependencies.xml
files. 8117e03_shed_lint to check for required files based on repository type.
Issue 156_shed_upload. Issue 179_Issue 181_lint to verify data inputs specify a format attribute.
8117e03_@peterjc. fe7ad46@petrkadlec_ from puradesign.cz <http://puradesign.cz/en>__ and @carlfeberhard_ from the Galaxy Project.
Issue 108_shed_diff command - it now produces a meaningful
exit codes and doesn't report differences if these correspond to attributes
that will be automatically populated by the Tool Shed. Issue 167_shed_diff code to implement a new --check_diff
option for shed_upload - to check for meaningful differences before
updating repositories. Issue 168_shed_upload if the .shed.yml is
located in a git repository. Issue 170_shed_ operations to operate on git URLs directly. Issue 169_.shed.yml
repository resolution - bug reported by @peterjc. Issue 158--fail_fast command-line option. * Issue 114, Pull Request 173shed_init command. 1cd0e2d_-r/--recursive option to shed_download and shed_diff
commands and allow these commands to work with .shed.yml files defining
multipe repositories. 40a1f57_--port option to the serve and tool_factory commands.
15804be_setup.py_ during the 0.9.0 development cycle
@peterjc. Pull Request 171@bgruening. Pull Request 175@takadonet). Issue 161@peterjc. Pull Request 164, Issue 159_@peterjc. Pull Request 155, b86fe1f_shed_lint was not respecting the -r/--recursive flag.
9ff0d2d_config_init command thanks to @bgruening. Pull Request 151lint warning about parallelism tag reported by
@peterjc. 9bf1eabshed_lint command that verifies various aspects of tool
shed repositories - including XSD_ validation of repository_dependencies.xml
and tool_dependencies.xml files, best practices for README files, and the
contents of .shed.yml files. This requires the lxml_ library to be available
to Planemo or the application xmllint_ to be on its PATH. Pull Request 130_
Issue 89_ Issue 91_ 912df02_ d26929e_ 36ac6d8_lint
is executed with the new --xsd flag. This validation occurs against the
unofficial Galaxy Tool XSD project <https://github.com/JeanFred/Galaxy-XSD>__
maintained by @JeanFred. This requires the lxml library to be
available to Planemo or the application xmllint_ to be on its PATH.
Pull Request 130_ 912df02_lint command using the new
--skip option. 26e3cdb_.shed.yml to map a directory to many,
custom Tool Shed repositories during shed operaitons such shed_upload
including automatically mapping tools to their own directories and automatically
building suites repositories. Pull Request 143_shed_upload more intelligent when building tar files so that package
and suite repositories may have README files in source control and they will
just be filtered out during upload. 53edd99_shed_init command that will help bootstrap .shed.yml
files in the specified directory. cc1a447_shed_init to automatically build a repository_rependencies.xml
file corresponding to a Galaxy workflow (.ga file). Issue 118_ 988de1d_lint to be passed multiple
files. 343902d_ Issue 139_-r/--recursive option to shed_create and lint commands. 63cd431_
01f2af9_shed_diff command. 965511d_Issue 138_test help thanks to first time contributor @pvanheus.
Pull Request 129 1982076_help element when linting tools. Issue 124_lint warnings when configfiles are defined in a tool. 1a85493_.shed.yml files. b7d9e96_test command for newer versions of nose_. 33294d2_normalize should not
be used to update the contents of tool files at this time. 08de8de_command attributes when linting tools (anything but
interpreter). 4f61025_publishing <http://planemo.readthedocs.org/en/latest/publishing.html>__),
and testing related improvements (test coverage has risen from 65% to over
80% during this release cycle).shed_create command to create Tool Shed repositories from
.shed.yml files (thanks to E. Rasche). Pull Request 101_shed_upload
with the new --force_repository_creation flag (thanks to E. Rasche).
Pull Request 102_.shed.yml when creating tar files
for shed_upload (thanks to Björn Grüning). Pull Request 99_shed_upload (thanks to Dave Bouvier). Pull Request 104_Contributor Code of Conduct <https://planemo.readthedocs.org/en/latest/conduct.html>__.
Pull Request 113_tool_test_output.json from Tool Shed tar file created with
shed_upload (thanks to Dave Bouvier). Pull Request 111_0.5.3. Fixed Issue 88_.--install_galaxy by default (disable with
--no_cache_galaxy). d755fe7_tool_init to quote file names (thanks to Peter Cock). Pull Request 98_..shed.yml (thanks to Björn Grüning). Pull Request 99_--macros flag to tool_init command to generate a macro file as part of tool generation. ec6e30f_stdio tags in tool XML files. 8207026_--version option. Issue 78_--no_cleanup option for test and serve commands to
persist temp files. 2e41e0a_Issue 80_setup.py_ for installing non-Python data from PyPI_ (required newer
for tool_factory command and reStructuredText linting). Thanks to
Damion Dooley for the bug report. Issue 83_tool_init command for bootstrapping creation of new
tools (with tutorial <http://planemo.readthedocs.org/en/latest/writing.html>.) 78f8274normalize command for reorganizing tool XML and macro
debugging. e8c1d45_tool_factory command to spin up Galaxy pre-configured the
Tool Factory. 9e746b4command blocks. b8d90ab_help blocks, including verifying valid
reStructuredText. 411a8da_serve command not killing Galaxy properly when complete. 53a6766_serve command display tools at the top level instead of in shallow sections. badc25f_setup.py more functionality works out
of the box. 85b9614_Issue 70_-r) to the shed_upload command to recursively upload
subdirectories (thanks to E. Rasche). Pull Request 68_Pull Request 63_Issue 61, dff4f33test-data now it is
test_data). 834bfb2_tool_data_table_conf.xml.sample file if
tool_data_table_conf.xml.test is unavailable. Should allow some
new tools to be tested without modifying Galaxy's global
tool_data_table_conf.xml file. ac4f828_Pull Request 56_~/.planemo.yml and disabling
JSON output. 21bb463_project_init for BSD tar (thanks to Nitesh Turaga for the bug
report.) a4110a8_Pull Request 51_Pull Request 6_shed_diff) between local repositories and
the Tool Shed (based on scripts by Peter Cock). Pull Request 33_test-data target. Pull Request 1_share_test command for embedding test result links in pull
requests. Pull Request 40_Pull Request 29_Pull Request 22,
Pull Request 23.. github_links .. _Pull Request 1439: https://github.com/galaxyproject/planemo/pull/1439 .. _Pull Request 1440: https://github.com/galaxyproject/planemo/pull/1440 .. _Pull Request 1437: https://github.com/galaxyproject/planemo/pull/1437 .. _Pull Request 1433: https://github.com/galaxyproject/planemo/pull/1433 .. _Pull Request 1430: https://github.com/galaxyproject/planemo/pull/1430 .. _Pull Request 1428: https://github.com/galaxyproject/planemo/pull/1428 .. _Pull Request 1427: https://github.com/galaxyproject/planemo/pull/1427 .. _Pull Request 1425: https://github.com/galaxyproject/planemo/pull/1425 .. _Pull Request 1424: https://github.com/galaxyproject/planemo/pull/1424 .. _Pull Request 1422: https://github.com/galaxyproject/planemo/pull/1422 .. _Pull Request 1419: https://github.com/galaxyproject/planemo/pull/1419 .. _Pull Request 1416: https://github.com/galaxyproject/planemo/pull/1416 .. _Pull Request 1388: https://github.com/galaxyproject/planemo/pull/1388 .. _Pull Request 1412: https://github.com/galaxyproject/planemo/pull/1412 .. _Pull Request 1410: https://github.com/galaxyproject/planemo/pull/1410 .. _Pull Request 1408: https://github.com/galaxyproject/planemo/pull/1408 .. _Pull Request 1407: https://github.com/galaxyproject/planemo/pull/1407 .. _Pull Request 1406: https://github.com/galaxyproject/planemo/pull/1406 .. _Pull Request 1401: https://github.com/galaxyproject/planemo/pull/1401 .. _Pull Request 1402: https://github.com/galaxyproject/planemo/pull/1402 .. _Pull Request 1398: https://github.com/galaxyproject/planemo/pull/1398 .. _Pull Request 1400: https://github.com/galaxyproject/planemo/pull/1400 .. _Pull Request 1399: https://github.com/galaxyproject/planemo/pull/1399 .. _Pull Request 1396: https://github.com/galaxyproject/planemo/pull/1396 .. _Pull Request 1397: https://github.com/galaxyproject/planemo/pull/1397 .. _Pull Request 1395: https://github.com/galaxyproject/planemo/pull/1395 .. _Pull Request 1394: https://github.com/galaxyproject/planemo/pull/1394 .. _Pull Request 1393: https://github.com/galaxyproject/planemo/pull/1393 .. _Pull Request 1391: https://github.com/galaxyproject/planemo/pull/1391 .. _Pull Request 1389: https://github.com/galaxyproject/planemo/pull/1389 .. _Pull Request 1263: https://github.com/galaxyproject/planemo/pull/1263 .. _Pull Request 1387: https://github.com/galaxyproject/planemo/pull/1387 .. _Pull Request 1385: https://github.com/galaxyproject/planemo/pull/1385 .. _Pull Request 1384: https://github.com/galaxyproject/planemo/pull/1384 .. _Pull Request 1383: https://github.com/galaxyproject/planemo/pull/1383 .. _Pull Request 1382: https://github.com/galaxyproject/planemo/pull/1382 .. _Pull Request 1355: https://github.com/galaxyproject/planemo/pull/1355 .. _Pull Request 1378: https://github.com/galaxyproject/planemo/pull/1378 .. _Pull Request 1379: https://github.com/galaxyproject/planemo/pull/1379 .. _Pull Request 1377: https://github.com/galaxyproject/planemo/pull/1377 .. _Pull Request 1375: https://github.com/galaxyproject/planemo/pull/1375 .. _Pull Request 1374: https://github.com/galaxyproject/planemo/pull/1374 .. _Pull Request 1373: https://github.com/galaxyproject/planemo/pull/1373 .. _Pull Request 1372: https://github.com/galaxyproject/planemo/pull/1372 .. _Pull Request 1371: https://github.com/galaxyproject/planemo/pull/1371 .. _Pull Request 1369: https://github.com/galaxyproject/planemo/pull/1369 .. _Pull Request 1370: https://github.com/galaxyproject/planemo/pull/1370 .. _Pull Request 1364: https://github.com/galaxyproject/planemo/pull/1364 .. _Pull Request 1358: https://github.com/galaxyproject/planemo/pull/1358 .. _Pull Request 1357: https://github.com/galaxyproject/planemo/pull/1357 .. _Pull Request 1265: https://github.com/galaxyproject/planemo/pull/1265 .. _Pull Request 1350: https://github.com/galaxyproject/planemo/pull/1350 .. _Pull Request 1275: https://github.com/galaxyproject/planemo/pull/1275 .. _Pull Request 1347: https://github.com/galaxyproject/planemo/pull/1347 .. _Pull Request 1348: https://github.com/galaxyproject/planemo/pull/1348 .. _Pull Request 1346: https://github.com/galaxyproject/planemo/pull/1346 .. _Pull Request 1344: https://github.com/galaxyproject/planemo/pull/1344 .. _Pull Request 1338: https://github.com/galaxyproject/planemo/pull/1338 .. _Pull Request 1337: https://github.com/galaxyproject/planemo/pull/1337 .. _Pull Request 1334: https://github.com/galaxyproject/planemo/pull/1334 .. _Pull Request 1327: https://github.com/galaxyproject/planemo/pull/1327 .. _Pull Request 1332: https://github.com/galaxyproject/planemo/pull/1332 .. _Pull Request 1330: https://github.com/galaxyproject/planemo/pull/1330 .. _Pull Request 1329: https://github.com/galaxyproject/planemo/pull/1329 .. _Pull Request 1326: https://github.com/galaxyproject/planemo/pull/1326 .. _Pull Request 1322: https://github.com/galaxyproject/planemo/pull/1322 .. _Pull Request 1325: https://github.com/galaxyproject/planemo/pull/1325 .. _Pull Request 1320: https://github.com/galaxyproject/planemo/pull/1320 .. _Pull Request 1314: https://github.com/galaxyproject/planemo/pull/1314 .. _Pull Request 1313: https://github.com/galaxyproject/planemo/pull/1313 .. _Pull Request 1312: https://github.com/galaxyproject/planemo/pull/1312 .. _Pull Request 1310: https://github.com/galaxyproject/planemo/pull/1310 .. _Pull Request 1308: https://github.com/galaxyproject/planemo/pull/1308 .. _Pull Request 1302: https://github.com/galaxyproject/planemo/pull/1302 .. _Pull Request 1303: https://github.com/galaxyproject/planemo/pull/1303 .. _Pull Request 1304: https://github.com/galaxyproject/planemo/pull/1304 .. _Pull Request 1305: https://github.com/galaxyproject/planemo/pull/1305 .. _Pull Request 1306: https://github.com/galaxyproject/planemo/pull/1306 .. _Pull Request 1307: https://github.com/galaxyproject/planemo/pull/1307 .. _Pull Request 1247: https://github.com/galaxyproject/planemo/pull/1247 .. _Pull Request 1249: https://github.com/galaxyproject/planemo/pull/1249 .. _Pull Request 1255: https://github.com/galaxyproject/planemo/pull/1255 .. _Pull Request 1257: https://github.com/galaxyproject/planemo/pull/1257 .. _Pull Request 1259: https://github.com/galaxyproject/planemo/pull/1259 .. _Pull Request 1260: https://github.com/galaxyproject/planemo/pull/1260 .. _Pull Request 1262: https://github.com/galaxyproject/planemo/pull/1262 .. _Pull Request 1212: https://github.com/galaxyproject/planemo/pull/1212 .. _Pull Request 1264: https://github.com/galaxyproject/planemo/pull/1264 .. _Pull Request 1232: https://github.com/galaxyproject/planemo/pull/1232 .. _Pull Request 1270: https://github.com/galaxyproject/planemo/pull/1270 .. _Pull Request 1274: https://github.com/galaxyproject/planemo/pull/1274 .. _Pull Request 1278: https://github.com/galaxyproject/planemo/pull/1278 .. _Pull Request 1277: https://github.com/galaxyproject/planemo/pull/1277 .. _Pull Request 1279: https://github.com/galaxyproject/planemo/pull/1279 .. _Pull Request 1281: https://github.com/galaxyproject/planemo/pull/1281 .. _Pull Request 1283: https://github.com/galaxyproject/planemo/pull/1283 .. _Pull Request 1280: https://github.com/galaxyproject/planemo/pull/1280 .. _Pull Request 1284: https://github.com/galaxyproject/planemo/pull/1284 .. _Pull Request 1287: https://github.com/galaxyproject/planemo/pull/1287 .. _Pull Request 1288: https://github.com/galaxyproject/planemo/pull/1288 .. _Pull Request 1285: https://github.com/galaxyproject/planemo/pull/1285 .. _Pull Request 1271: https://github.com/galaxyproject/planemo/pull/1271 .. _Pull Request 1291: https://github.com/galaxyproject/planemo/pull/1291 .. _Pull Request 1227: https://github.com/galaxyproject/planemo/pull/1227 .. _Pull Request 1292: https://github.com/galaxyproject/planemo/pull/1292 .. _Pull Request 1293: https://github.com/galaxyproject/planemo/pull/1293 .. _Pull Request 1276: https://github.com/galaxyproject/planemo/pull/1276 .. _Pull Request 1295: https://github.com/galaxyproject/planemo/pull/1295 .. _Pull Request 1294: https://github.com/galaxyproject/planemo/pull/1294 .. _Pull Request 1296: https://github.com/galaxyproject/planemo/pull/1296 .. _Pull Request 1298: https://github.com/galaxyproject/planemo/pull/1298 .. _Pull Request 1299: https://github.com/galaxyproject/planemo/pull/1299 .. _Pull Request 1297: https://github.com/galaxyproject/planemo/pull/1297 .. _Pull Request 1244: https://github.com/galaxyproject/planemo/pull/1244 .. _Pull Request 1242: https://github.com/galaxyproject/planemo/pull/1242 .. _Pull Request 1241: https://github.com/galaxyproject/planemo/pull/1241 .. _Pull Request 1239: https://github.com/galaxyproject/planemo/pull/1239 .. _Pull Request 1237: https://github.com/galaxyproject/planemo/pull/1237 .. _Pull Request 1230: https://github.com/galaxyproject/planemo/pull/1230 .. _Pull Request 1228: https://github.com/galaxyproject/planemo/pull/1228 .. _Pull Request 1224: https://github.com/galaxyproject/planemo/pull/1224 .. _Pull Request 1226: https://github.com/galaxyproject/planemo/pull/1226 .. _Pull Request 1222: https://github.com/galaxyproject/planemo/pull/1222 .. _Pull Request 1217: https://github.com/galaxyproject/planemo/pull/1217 .. _Pull Request 1213: https://github.com/galaxyproject/planemo/pull/1213 .. _Pull Request 1214: https://github.com/galaxyproject/planemo/pull/1214 .. _Pull Request 1215: https://github.com/galaxyproject/planemo/pull/1215 .. _Pull Request 1209: https://github.com/galaxyproject/planemo/pull/1209 .. _Pull Request 1206: https://github.com/galaxyproject/planemo/pull/1206 .. _Pull Request 1207: https://github.com/galaxyproject/planemo/pull/1207 .. _Pull Request 1205: https://github.com/galaxyproject/planemo/pull/1205 .. _Pull Request 1198: https://github.com/galaxyproject/planemo/pull/1198 .. _Pull Request 1140: https://github.com/galaxyproject/planemo/pull/1140 .. _Pull Request 1200: https://github.com/galaxyproject/planemo/pull/1200 .. _Pull Request 1201: https://github.com/galaxyproject/planemo/pull/1201 .. _Pull Request 1188: https://github.com/galaxyproject/planemo/pull/1188 .. _Pull Request 1193: https://github.com/galaxyproject/planemo/pull/1193 .. _Pull Request 1195: https://github.com/galaxyproject/planemo/pull/1195 .. _Pull Request 1196: https://github.com/galaxyproject/planemo/pull/1196 .. _Pull Request 1184: https://github.com/galaxyproject/planemo/pull/1184 .. _Pull Request 1187: https://github.com/galaxyproject/planemo/pull/1187 .. _Pull Request 1151: https://github.com/galaxyproject/planemo/pull/1151 .. _Pull Request 1153: https://github.com/galaxyproject/planemo/pull/1153 .. _Pull Request 1179: https://github.com/galaxyproject/planemo/pull/1179 .. _Pull Request 1180: https://github.com/galaxyproject/planemo/pull/1180 .. _Pull Request 1182: https://github.com/galaxyproject/planemo/pull/1182 .. _Pull Request 1170: https://github.com/galaxyproject/planemo/pull/1170 .. _Pull Request 1171: https://github.com/galaxyproject/planemo/pull/1171 .. _Pull Request 1172: https://github.com/galaxyproject/planemo/pull/1172 .. _Pull Request 1173: https://github.com/galaxyproject/planemo/pull/1173 .. _Pull Request 1174: https://github.com/galaxyproject/planemo/pull/1174 .. _Pull Request 1177: https://github.com/galaxyproject/planemo/pull/1177 .. _Pull Request 1169: https://github.com/galaxyproject/planemo/pull/1169 .. _Pull Request 1165: https://github.com/galaxyproject/planemo/pull/1165 .. _Pull Request 1164: https://github.com/galaxyproject/planemo/pull/1164 .. _Pull Request 1157: https://github.com/galaxyproject/planemo/pull/1157 .. _Pull Request 1156: https://github.com/galaxyproject/planemo/pull/1156 .. _Pull Request 1154: https://github.com/galaxyproject/planemo/pull/1154 .. _Pull Request 1152: https://github.com/galaxyproject/planemo/pull/1152 .. _Pull Request 1146: https://github.com/galaxyproject/planemo/pull/1146 .. _Pull Request 1145: https://github.com/galaxyproject/planemo/pull/1145 .. _Pull Request 1144: https://github.com/galaxyproject/planemo/pull/1144 .. _Pull Request 1142: https://github.com/galaxyproject/planemo/pull/1142 .. _Pull Request 1095: https://github.com/galaxyproject/planemo/pull/1095 .. _Pull Request 1135: https://github.com/galaxyproject/planemo/pull/1135 .. _Pull Request 1134: https://github.com/galaxyproject/planemo/pull/1134 .. _Pull Request 1133: https://github.com/galaxyproject/planemo/pull/1133 .. _Pull Request 1128: https://github.com/galaxyproject/planemo/pull/1128 .. _Pull Request 1127: https://github.com/galaxyproject/planemo/pull/1127 .. _Pull Request 1126: https://github.com/galaxyproject/planemo/pull/1126 .. _Pull Request 1125: https://github.com/galaxyproject/planemo/pull/1125 .. _Pull Request 1124: https://github.com/galaxyproject/planemo/pull/1124 .. _Pull Request 1123: https://github.com/galaxyproject/planemo/pull/1123 .. _Pull Request 1064: https://github.com/galaxyproject/planemo/pull/1064 .. _Pull Request 1066: https://github.com/galaxyproject/planemo/pull/1066 .. _Pull Request 1068: https://github.com/galaxyproject/planemo/pull/1068 .. _Pull Request 1072: https://github.com/galaxyproject/planemo/pull/1072 .. _Pull Request 1074: https://github.com/galaxyproject/planemo/pull/1074 .. _Pull Request 1076: https://github.com/galaxyproject/planemo/pull/1076 .. _Pull Request 1079: https://github.com/galaxyproject/planemo/pull/1079 .. _Pull Request 1083: https://github.com/galaxyproject/planemo/pull/1083 .. _Pull Request 1086: https://github.com/galaxyproject/planemo/pull/1086 .. _Pull Request 1091: https://github.com/galaxyproject/planemo/pull/1091 .. _Pull Request 1093: https://github.com/galaxyproject/planemo/pull/1093 .. _Pull Request 1094: https://github.com/galaxyproject/planemo/pull/1094 .. _Pull Request 1096: https://github.com/galaxyproject/planemo/pull/1096 .. _Pull Request 1099: https://github.com/galaxyproject/planemo/pull/1099 .. _Pull Request 1101: https://github.com/galaxyproject/planemo/pull/1101 .. _Pull Request 1102: https://github.com/galaxyproject/planemo/pull/1102 .. _Pull Request 1108: https://github.com/galaxyproject/planemo/pull/1108 .. _Pull Request 1110: https://github.com/galaxyproject/planemo/pull/1110 .. _Pull Request 1114: https://github.com/galaxyproject/planemo/pull/1114 .. _Pull Request 1115: https://github.com/galaxyproject/planemo/pull/1115 .. _Pull Request 1116: https://github.com/galaxyproject/planemo/pull/1116 .. _Pull Request 1118: https://github.com/galaxyproject/planemo/pull/1118 .. _Pull Request 1120: https://github.com/galaxyproject/planemo/pull/1120 .. _Pull Request 1121: https://github.com/galaxyproject/planemo/pull/1121 .. _Pull Request 821: https://github.com/galaxyproject/planemo/pull/821 .. _Pull Request 1052: https://github.com/galaxyproject/planemo/pull/1052 .. _Pull Request 1061: https://github.com/galaxyproject/planemo/pull/1061 .. _Pull Request 1062: https://github.com/galaxyproject/planemo/pull/1062 .. _Pull Request 1060: https://github.com/galaxyproject/planemo/pull/1060 .. _Pull Request 1059: https://github.com/galaxyproject/planemo/pull/1059 .. _Pull Request 1058: https://github.com/galaxyproject/planemo/pull/1058 .. _Pull Request 1051: https://github.com/galaxyproject/planemo/pull/1051 .. _Pull Request 1049: https://github.com/galaxyproject/planemo/pull/1049 .. _Pull Request 1046: https://github.com/galaxyproject/planemo/pull/1046 .. _Pull Request 1044: https://github.com/galaxyproject/planemo/pull/1044 .. _Pull Request 1043: https://github.com/galaxyproject/planemo/pull/1043 .. _Pull Request 1042: https://github.com/galaxyproject/planemo/pull/1042 .. _Pull Request 1041: https://github.com/galaxyproject/planemo/pull/1041 .. _Pull Request 1040: https://github.com/galaxyproject/planemo/pull/1040 .. _Pull Request 1038: https://github.com/galaxyproject/planemo/pull/1038 .. _Pull Request 1037: https://github.com/galaxyproject/planemo/pull/1037 .. _Pull Request 1036: https://github.com/galaxyproject/planemo/pull/1036 .. _Pull Request 1034: https://github.com/galaxyproject/planemo/pull/1034 .. _Pull Request 1032: https://github.com/galaxyproject/planemo/pull/1032 .. _Pull Request 1029: https://github.com/galaxyproject/planemo/pull/1029 .. _Pull Request 1028: https://github.com/galaxyproject/planemo/pull/1028 .. _Pull Request 1031: https://github.com/galaxyproject/planemo/pull/1031 .. _Pull Request 1026: https://github.com/galaxyproject/planemo/pull/1026 .. _Pull Request 994: https://github.com/galaxyproject/planemo/pull/994 .. _Pull Request 993: https://github.com/galaxyproject/planemo/pull/993 .. _Pull Request 1001: https://github.com/galaxyproject/planemo/pull/1001 .. _Pull Request 1003: https://github.com/galaxyproject/planemo/pull/1003 .. _Pull Request 900: https://github.com/galaxyproject/planemo/pull/900 .. _Pull Request 1008: https://github.com/galaxyproject/planemo/pull/1008 .. _Pull Request 1006: https://github.com/galaxyproject/planemo/pull/1006 .. _Pull Request 1011: https://github.com/galaxyproject/planemo/pull/1011 .. _Pull Request 1017: https://github.com/galaxyproject/planemo/pull/1017 .. _Pull Request 1015: https://github.com/galaxyproject/planemo/pull/1015 .. _Pull Request 1013: https://github.com/galaxyproject/planemo/pull/1013 .. _Pull Request 1020: https://github.com/galaxyproject/planemo/pull/1020 .. _Pull Request 1021: https://github.com/galaxyproject/planemo/pull/1021 .. _Pull Request 1022: https://github.com/galaxyproject/planemo/pull/1022 .. _Pull Request 1023: https://github.com/galaxyproject/planemo/pull/1023 .. _Pull Request 1025: https://github.com/galaxyproject/planemo/pull/1025 .. _Pull Request 1024: https://github.com/galaxyproject/planemo/pull/1024 .. _Pull Request 991: https://github.com/galaxyproject/planemo/pull/991 .. _Pull Request 988: https://github.com/galaxyproject/planemo/pull/988 .. _Pull Request 989: https://github.com/galaxyproject/planemo/pull/989 .. _Pull Request 985: https://github.com/galaxyproject/planemo/pull/985 .. _Pull Request 984: https://github.com/galaxyproject/planemo/pull/984 .. _Pull Request 986: https://github.com/galaxyproject/planemo/pull/986 .. _Pull Request 983: https://github.com/galaxyproject/planemo/pull/983 .. _Pull Request 982: https://github.com/galaxyproject/planemo/pull/982 .. _Pull Request 980: https://github.com/galaxyproject/planemo/pull/980 .. _Pull Request 978: https://github.com/galaxyproject/planemo/pull/978 .. _Pull Request 979: https://github.com/galaxyproject/planemo/pull/979 .. _Pull Request 977: https://github.com/galaxyproject/planemo/pull/977 .. _Pull Request 975: https://github.com/galaxyproject/planemo/pull/975 .. _Pull Request 974: https://github.com/galaxyproject/planemo/pull/974 .. _Pull Request 976: https://github.com/galaxyproject/planemo/pull/976 .. _Pull Request 972: https://github.com/galaxyproject/planemo/pull/972 .. _Pull Request 973: https://github.com/galaxyproject/planemo/pull/973 .. _Pull Request 971: https://github.com/galaxyproject/planemo/pull/971 .. _Pull Request 970: https://github.com/galaxyproject/planemo/pull/970 .. _Pull Request 968: https://github.com/galaxyproject/planemo/pull/968 .. _1ab8530: https://github.com/galaxyproject/planemo/commit/1ab8530 .. _Pull Request 966: https://github.com/galaxyproject/planemo/pull/966 .. _Pull Request 964: https://github.com/galaxyproject/planemo/pull/964 .. _Pull Request 963: https://github.com/galaxyproject/planemo/pull/963 .. _Pull Request 959: https://github.com/galaxyproject/planemo/pull/959 .. _Pull Request 958: https://github.com/galaxyproject/planemo/pull/958 .. _Pull Request 950: https://github.com/galaxyproject/planemo/pull/950 .. _Pull Request 944: https://github.com/galaxyproject/planemo/pull/944 .. _Pull Request 926: https://github.com/galaxyproject/planemo/pull/926 .. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937 .. _Pull Request 938: https://github.com/galaxyproject/planemo/pull/938 .. _Pull Request 943: https://github.com/galaxyproject/planemo/pull/943 .. _Pull Request 940: https://github.com/galaxyproject/planemo/pull/940 .. _Pull Request 937: https://github.com/galaxyproject/planemo/pull/937 .. _Pull Request 935: https://github.com/galaxyproject/planemo/pull/935 .. _Pull Request 931: https://github.com/galaxyproject/planemo/pull/931 .. _Pull Request 930: https://github.com/galaxyproject/planemo/pull/930 .. _Pull Request 913: https://github.com/galaxyproject/planemo/pull/913 .. _Pull Request 917: https://github.com/galaxyproject/planemo/pull/917 .. _Pull Request 921: https://github.com/galaxyproject/planemo/pull/921 .. _Pull Request 918: https://github.com/galaxyproject/planemo/pull/918 .. _Pull Request 924: https://github.com/galaxyproject/planemo/pull/924 .. _Pull Request 925: https://github.com/galaxyproject/planemo/pull/925 .. _Pull Request 912: https://github.com/galaxyproject/planemo/pull/912 .. _Pull Request 915: https://github.com/galaxyproject/planemo/pull/915 .. _Pull Request 914: https://github.com/galaxyproject/planemo/pull/914 .. _07dc6e0: https://github.com/galaxyproject/planemo/commit/07dc6e0 .. _Pull Request 910: https://github.com/galaxyproject/planemo/pull/910 .. _Pull Request 909: https://github.com/galaxyproject/planemo/pull/909 .. _Pull Request 908: https://github.com/galaxyproject/planemo/pull/908 .. _Pull Request 907: https://github.com/galaxyproject/planemo/pull/907 .. _Pull Request 906: https://github.com/galaxyproject/planemo/pull/906 .. _Pull Request 902: https://github.com/galaxyproject/planemo/pull/902 .. _Pull Request 895: https://github.com/galaxyproject/planemo/pull/895 .. _Issue 845: https://github.com/galaxyproject/planemo/issues/845 .. _Issue 898: https://github.com/galaxyproject/planemo/issues/898 .. _Pull Request 899: https://github.com/galaxyproject/planemo/pull/899 .. _Pull Request 896: https://github.com/galaxyproject/planemo/pull/896 .. _Pull Request 894: https://github.com/galaxyproject/planemo/pull/894 .. _Pull Request 876: https://github.com/galaxyproject/planemo/pull/876 .. _Pull Request 893: https://github.com/galaxyproject/planemo/pull/893 .. _Pull Request 892: https://github.com/galaxyproject/planemo/pull/892 .. _Pull Request 891: https://github.com/galaxyproject/planemo/pull/891 .. _Pull Request 889: https://github.com/galaxyproject/planemo/pull/889 .. _Pull Request 888: https://github.com/galaxyproject/planemo/pull/888 .. _Pull Request 887: https://github.com/galaxyproject/planemo/pull/887 .. _Pull Request 882: https://github.com/galaxyproject/planemo/pull/882 .. _Pull Request 877: https://github.com/galaxyproject/planemo/pull/877 .. _Pull Request 874: https://github.com/galaxyproject/planemo/pull/874 .. _Pull Request 871: https://github.com/galaxyproject/planemo/pull/871 .. _Pull Request 870: https://github.com/galaxyproject/planemo/pull/870 .. _Pull Request 864: https://github.com/galaxyproject/planemo/pull/864 .. _Pull Request 867: https://github.com/galaxyproject/planemo/pull/867 .. _Pull Request 868: https://github.com/galaxyproject/planemo/pull/868 .. _bad810a: https://github.com/galaxyproject/planemo/commit/bad810a .. _Pull Request 851: https://github.com/galaxyproject/planemo/pull/851 .. _Pull Request 856: https://github.com/galaxyproject/planemo/pull/856 .. _Pull Request 860: https://github.com/galaxyproject/planemo/pull/860 .. _Pull Request 866: https://github.com/galaxyproject/planemo/pull/866 .. _Pull Request 861: https://github.com/galaxyproject/planemo/pull/861 .. _324c776: https://github.com/galaxyproject/planemo/commit/324c776 .. _72d2ca7: https://github.com/galaxyproject/planemo/commit/72d2ca7 .. _b12b117: https://github.com/galaxyproject/planemo/commit/b12b117 .. _016b923: https://github.com/galaxyproject/planemo/commit/016b923 .. _2002b49: https://github.com/galaxyproject/planemo/commit/2002b49 .. _Pull Request 843: https://github.com/galaxyproject/planemo/pull/843 .. _Pull Request 842: https://github.com/galaxyproject/planemo/pull/842 .. _Pull Request 841: https://github.com/galaxyproject/planemo/pull/841 .. _Pull Request 847: https://github.com/galaxyproject/planemo/pull/847 .. _Pull Request 848: https://github.com/galaxyproject/planemo/pull/848 .. _Pull Request 849: https://github.com/galaxyproject/planemo/pull/849 .. _Pull Request 850: https://github.com/galaxyproject/planemo/pull/850 .. _Pull Request 836: https://github.com/galaxyproject/planemo/pull/836 .. _Pull Request 833: https://github.com/galaxyproject/planemo/pull/833 .. _Pull Request 837: https://github.com/galaxyproject/planemo/pull/837 .. _Pull Request 840: https://github.com/galaxyproject/planemo/pull/840 .. _Pull Request 838: https://github.com/galaxyproject/planemo/pull/838 .. _Pull Request 834: https://github.com/galaxyproject/planemo/pull/834 .. _Pull Request 835: https://github.com/galaxyproject/planemo/pull/835 .. _347c622: https://github.com/galaxyproject/planemo/commit/347c622 .. _Pull Request 832: https://github.com/galaxyproject/planemo/pull/832 .. _Pull Request 831: https://github.com/galaxyproject/planemo/pull/831 .. _Pull Request 830: https://github.com/galaxyproject/planemo/pull/830 .. _Pull Request 829: https://github.com/galaxyproject/planemo/pull/829 .. _Pull Request 828: https://github.com/galaxyproject/planemo/pull/828 .. _Pull Request 826: https://github.com/galaxyproject/planemo/pull/826 .. _Pull Request 827: https://github.com/galaxyproject/planemo/pull/827 .. _Pull Request 825: https://github.com/galaxyproject/planemo/pull/825 .. _Pull Request 820: https://github.com/galaxyproject/planemo/pull/820 .. _Pull Request 823: https://github.com/galaxyproject/planemo/pull/823 .. _Pull Request 822: https://github.com/galaxyproject/planemo/pull/822 .. _a5c72e3: https://github.com/galaxyproject/planemo/commit/a5c72e3 .. _Pull Request 818: https://github.com/galaxyproject/planemo/pull/818 .. _Pull Request 816: https://github.com/galaxyproject/planemo/pull/816 .. _Pull Request 817: https://github.com/galaxyproject/planemo/pull/817 .. _Pull Request 795: https://github.com/galaxyproject/planemo/pull/795 .. _Pull Request 799: https://github.com/galaxyproject/planemo/pull/799 .. _Pull Request 800: https://github.com/galaxyproject/planemo/pull/800 .. _Pull Request 781: https://github.com/galaxyproject/planemo/pull/781 .. _Pull Request 801: https://github.com/galaxyproject/planemo/pull/801 .. _Pull Request 802: https://github.com/galaxyproject/planemo/pull/802 .. _Pull Request 803: https://github.com/galaxyproject/planemo/pull/803 .. _Pull Request 805: https://github.com/galaxyproject/planemo/pull/805 .. _Pull Request 806: https://github.com/galaxyproject/planemo/pull/806 .. _Pull Request 809: https://github.com/galaxyproject/planemo/pull/809 .. _Pull Request 810: https://github.com/galaxyproject/planemo/pull/810 .. _Pull Request 787: https://github.com/galaxyproject/planemo/pull/787 .. _Pull Request 792: https://github.com/galaxyproject/planemo/pull/792 .. _dc443d6: https://github.com/galaxyproject/planemo/commit/dc443d6 .. _8cfe9e9: https://github.com/galaxyproject/planemo/commit/8cfe9e9 .. _41f7df1: https://github.com/galaxyproject/planemo/commit/41f7df1 .. _Pull Request 790: https://github.com/galaxyproject/planemo/pull/790 .. _Pull Request 776: https://github.com/galaxyproject/planemo/pull/776 .. _Pull Request 774: https://github.com/galaxyproject/planemo/pull/774 .. _Pull Request 773: https://github.com/galaxyproject/planemo/pull/773 .. _Pull Request 771: https://github.com/galaxyproject/planemo/pull/771 .. _Pull Request 770: https://github.com/galaxyproject/planemo/pull/770 .. _Pull Request 769: https://github.com/galaxyproject/planemo/pull/769 .. _Pull Request 768: https://github.com/galaxyproject/planemo/pull/768 .. _Pull Request 764: https://github.com/galaxyproject/planemo/pull/764 .. _Pull Request 761: https://github.com/galaxyproject/planemo/pull/761 .. _Pull Request 759: https://github.com/galaxyproject/planemo/pull/759 .. _Pull Request 756: https://github.com/galaxyproject/planemo/pull/756 .. _Pull Request 753: https://github.com/galaxyproject/planemo/pull/753 .. _Pull Request 747: https://github.com/galaxyproject/planemo/pull/747 .. _Pull Request 745: https://github.com/galaxyproject/planemo/pull/745 .. _Pull Request 743: https://github.com/galaxyproject/planemo/pull/743 .. _Pull Request 739: https://github.com/galaxyproject/planemo/pull/739 .. _Pull Request 738: https://github.com/galaxyproject/planemo/pull/738 .. _Pull Request 725: https://github.com/galaxyproject/planemo/pull/725 .. _Pull Request 727: https://github.com/galaxyproject/planemo/pull/727 .. _Pull Request 729: https://github.com/galaxyproject/planemo/pull/729 .. _Pull Request 730: https://github.com/galaxyproject/planemo/pull/730 .. _Pull Request 731: https://github.com/galaxyproject/planemo/pull/731 .. _Pull Request 733: https://github.com/galaxyproject/planemo/pull/733 .. _Pull Request 732: https://github.com/galaxyproject/planemo/pull/732 .. _Pull Request 704: https://github.com/galaxyproject/planemo/pull/704 .. _Pull Request 709: https://github.com/galaxyproject/planemo/pull/709 .. _Pull Request 715: https://github.com/galaxyproject/planemo/pull/715 .. _Pull Request 716: https://github.com/galaxyproject/planemo/pull/716 .. _Pull Request 720: https://github.com/galaxyproject/planemo/pull/720 .. _Pull Request 723: https://github.com/galaxyproject/planemo/pull/723 .. _8a608e0: https://github.com/galaxyproject/planemo/commit/8a608e0 .. _ecc1bc2: https://github.com/galaxyproject/planemo/commit/ecc1bc2 .. _Pull Request 702: https://github.com/galaxyproject/planemo/pull/702 .. _Pull Request 701: https://github.com/galaxyproject/planemo/pull/701 .. _Pull Request 699: https://github.com/galaxyproject/planemo/pull/699 .. _91b6fa0: https://github.com/galaxyproject/planemo/commit/91b6fa0 .. _904d77a: https://github.com/galaxyproject/planemo/commit/904d77a .. _9636682: https://github.com/galaxyproject/planemo/commit/9636682 .. _475104c: https://github.com/galaxyproject/planemo/commit/475104c .. _Pull Request 684: https://github.com/galaxyproject/planemo/pull/684 .. _Pull Request 687: https://github.com/galaxyproject/planemo/pull/687 .. _Pull Request 688: https://github.com/galaxyproject/planemo/pull/688 .. _Pull Request 689: https://github.com/galaxyproject/planemo/pull/689 .. _Pull Request 690: https://github.com/galaxyproject/planemo/pull/690 .. _Issue 494: https://github.com/galaxyproject/planemo/issues/494 .. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665 .. _Pull Request 675: https://github.com/galaxyproject/planemo/pull/675 .. _Pull Request 680: https://github.com/galaxyproject/planemo/pull/680 .. _Pull Request 682: https://github.com/galaxyproject/planemo/pull/682 .. _Pull Request 683: https://github.com/galaxyproject/planemo/pull/683 .. _Pull Request 662: https://github.com/galaxyproject/planemo/pull/662 .. _Pull Request 665: https://github.com/galaxyproject/planemo/pull/665 .. _Pull Request 664: https://github.com/galaxyproject/planemo/pull/664 .. _84c4a73: https://github.com/galaxyproject/planemo/commit/84c4a73 .. _32f41c9: https://github.com/galaxyproject/planemo/commit/32f41c9 .. _3129216: https://github.com/galaxyproject/planemo/commit/3129216 .. _b4ae44d: https://github.com/galaxyproject/planemo/commit/b4ae44d .. _3c95b7b: https://github.com/galaxyproject/planemo/commit/3c95b7b .. _06bcf19: https://github.com/galaxyproject/planemo/commit/06bcf19 .. _525de8f: https://github.com/galaxyproject/planemo/commit/525de8f .. _9867e56: https://github.com/galaxyproject/planemo/commit/9867e56 .. _ce0dc4e: https://github.com/galaxyproject/planemo/commit/ce0dc4e .. _4c0f100: https://github.com/galaxyproject/planemo/commit/4c0f100 .. _04238d3: https://github.com/galaxyproject/planemo/commit/04238d3 .. _ced5ce2: https://github.com/galaxyproject/planemo/commit/ced5ce2 .. _9ab4a0d: https://github.com/galaxyproject/planemo/commit/9ab4a0d .. _Pull Request 640: https://github.com/galaxyproject/planemo/pull/640 .. _0a1abfe: https://github.com/galaxyproject/planemo/commit/0a1abfe .. _Pull Request 649: https://github.com/galaxyproject/planemo/pull/649 .. _Issue 620: https://github.com/galaxyproject/planemo/issues/620 .. _Pull Request 643: https://github.com/galaxyproject/planemo/pull/643 .. _Pull Request 642: https://github.com/galaxyproject/planemo/pull/642 .. _Pull Request 641: https://github.com/galaxyproject/planemo/pull/641 .. _Pull Request 639: https://github.com/galaxyproject/planemo/pull/639 .. _Pull Request 635: https://github.com/galaxyproject/planemo/pull/635 .. _Issue 633: https://github.com/galaxyproject/planemo/issues/633 .. _Issue 260: https://github.com/galaxyproject/planemo/issues/260 .. _Pull Request 638: https://github.com/galaxyproject/planemo/pull/638 .. _6638caa: https://github.com/galaxyproject/planemo/commit/6638caa .. _8faf661: https://github.com/galaxyproject/planemo/commit/8faf661 .. _e343b67: https://github.com/galaxyproject/planemo/commit/e343b67 .. _Pull Request 634: https://github.com/galaxyproject/planemo/pull/634 .. _84ebc1f: https://github.com/galaxyproject/planemo/commit/84ebc1f .. _03c9658: https://github.com/galaxyproject/planemo/commit/03c9658 .. _08c067c: https://github.com/galaxyproject/planemo/commit/08c067c .. _fca4183: https://github.com/galaxyproject/planemo/commit/fca4183 .. _Issue 564: https://github.com/galaxyproject/planemo/issues/564 .. _Pull Request 628: https://github.com/galaxyproject/planemo/pull/628 .. _Issue 515: https://github.com/galaxyproject/planemo/issues/515 .. _Pull Request 629: https://github.com/galaxyproject/planemo/pull/629 .. _Pull Request 614: https://github.com/galaxyproject/planemo/pull/614 .. _32acd68: https://github.com/galaxyproject/planemo/commit/32acd68 .. _4595953: https://github.com/galaxyproject/planemo/commit/4595953 .. _Pull Request 612: https://github.com/galaxyproject/planemo/pull/612 .. _Issue 388: https://github.com/galaxyproject/planemo/issues/388 .. _Pull Request 610: https://github.com/galaxyproject/planemo/pull/610 .. _Pull Request 609: https://github.com/galaxyproject/planemo/pull/609 .. _Pull Request 608: https://github.com/galaxyproject/planemo/pull/608 .. _Pull Request 605: https://github.com/galaxyproject/planemo/pull/605 .. _Pull Request 606: https://github.com/galaxyproject/planemo/pull/606 .. _Pull Request 602: https://github.com/galaxyproject/planemo/pull/602 .. _Pull Request 570: https://github.com/galaxyproject/planemo/pull/570 .. _9228416: https://github.com/galaxyproject/planemo/commit/9228416 .. _50d3c4a: https://github.com/galaxyproject/planemo/commit/50d3c4a .. _Issue 578: https://github.com/galaxyproject/planemo/issues/578 .. _Pull Request 591: https://github.com/galaxyproject/planemo/pull/591 .. _Pull Request 590: https://github.com/galaxyproject/planemo/pull/590 .. _f0da66f: https://github.com/galaxyproject/planemo/commit/f0da66f .. _19b2ee9: https://github.com/galaxyproject/planemo/commit/19b2ee9 .. _9da8387: https://github.com/galaxyproject/planemo/commit/9da8387 .. _08cef54: https://github.com/galaxyproject/planemo/commit/08cef54 .. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc .. _2e4e5fc: https://github.com/galaxyproject/planemo/commit/2e4e5fc .. _Issue 573: https://github.com/galaxyproject/planemo/issues/573 .. _Pull Request 579: https://github.com/galaxyproject/planemo/pull/579 .. _ccdd2d5: https://github.com/galaxyproject/planemo/commit/ccdd2d5 .. _e925ba1: https://github.com/galaxyproject/planemo/commit/e925ba1 .. _ea5324f: https://github.com/galaxyproject/planemo/commit/ea5324f .. _ca88b0c: https://github.com/galaxyproject/planemo/commit/ca88b0c .. _b6d8294: https://github.com/galaxyproject/planemo/commit/b6d8294 .. _6a6f164: https://github.com/galaxyproject/planemo/commit/6a6f164 .. _d6da3a8: https://github.com/galaxyproject/planemo/commit/d6da3a8 .. _1ef05d2: https://github.com/galaxyproject/planemo/commit/1ef05d2 .. _7cca2e4: https://github.com/galaxyproject/planemo/commit/7cca2e4 .. _34538de: https://github.com/galaxyproject/planemo/commit/34538de .. _6f91719: https://github.com/galaxyproject/planemo/commit/6f91719 .. _Pull Request 566: https://github.com/galaxyproject/planemo/pull/566 .. _Pull Request 559: https://github.com/galaxyproject/planemo/pull/559 .. _Pull Request 561: https://github.com/galaxyproject/planemo/pull/561 .. _Pull Request 565: https://github.com/galaxyproject/planemo/pull/565 .. _Pull Request 555: https://github.com/galaxyproject/planemo/pull/555 .. _a8e797b: https://github.com/galaxyproject/planemo/commit/a8e797b .. _6c03de8: https://github.com/galaxyproject/planemo/commit/6c03de8 .. _ef4b9f4: https://github.com/galaxyproject/planemo/commit/ef4b9f4 .. _f7b6c7e: https://github.com/galaxyproject/planemo/commit/f7b6c7e .. _07d94bd: https://github.com/galaxyproject/planemo/commit/07d94bd .. _ca19910: https://github.com/galaxyproject/planemo/commit/ca19910 .. _24008ab: https://github.com/galaxyproject/planemo/commit/24008ab .. _ce44e87: https://github.com/galaxyproject/planemo/commit/ce44e87 .. _Pull Request 550: https://github.com/galaxyproject/planemo/pull/550 .. _c2204b3: https://github.com/galaxyproject/planemo/commit/c2204b3 .. _c262b6d: https://github.com/galaxyproject/planemo/commit/c262b6d .. _Pull Request 539: https://github.com/galaxyproject/planemo/pull/539 .. _Pull Request 541: https://github.com/galaxyproject/planemo/pull/541 .. _Pull Request 540: https://github.com/galaxyproject/planemo/pull/540 .. _Pull Request 545: https://github.com/galaxyproject/planemo/pull/545 .. _Pull Request 546: https://github.com/galaxyproject/planemo/pull/546 .. _3ceaa40: https://github.com/galaxyproject/planemo/commit/3ceaa40 .. _057f4f0: https://github.com/galaxyproject/planemo/commit/057f4f0 .. _9fdf490: https://github.com/galaxyproject/planemo/commit/9fdf490 .. _8c088c6: https://github.com/galaxyproject/planemo/commit/8c088c6 .. _e2398fb: https://github.com/galaxyproject/planemo/commit/e2398fb .. _Pull Request 526: https://github.com/galaxyproject/planemo/pull/526 .. _Pull Request 528: https://github.com/galaxyproject/planemo/pull/528 .. _Pull Request 525: https://github.com/galaxyproject/planemo/pull/525 .. _a811e65: https://github.com/galaxyproject/planemo/commit/a811e65 .. _Pull Request 521: https://github.com/galaxyproject/planemo/pull/521 .. _a066afb: https://github.com/galaxyproject/planemo/commit/a066afb .. _Pull Request 512: https://github.com/galaxyproject/planemo/pull/512 .. _08bb354: https://github.com/galaxyproject/planemo/commit/08bb354 .. _Pull Request 513: https://github.com/galaxyproject/planemo/pull/513 .. _Pull Request 510: https://github.com/galaxyproject/planemo/pull/510 .. _e890ab5: https://github.com/galaxyproject/planemo/commit/e890ab5 .. _Pull Request 507: https://github.com/galaxyproject/planemo/pull/507 .. _d53bcd6: https://github.com/galaxyproject/planemo/commit/d53bcd6 .. _725b232: https://github.com/galaxyproject/planemo/commit/725b232 .. _Pull Request 498: https://github.com/galaxyproject/planemo/pull/498 .. _01584c5: https://github.com/galaxyproject/planemo/commit/01584c5 .. _01f2af9: https://github.com/galaxyproject/planemo/commit/01f2af9 .. _0298510: https://github.com/galaxyproject/planemo/commit/0298510 .. _02a08a0: https://github.com/galaxyproject/planemo/commit/02a08a0 .. _05cc9f4: https://github.com/galaxyproject/planemo/commit/05cc9f485ee87bc344e3f43bb1cfd025a16a6247 .. _069e7ba: https://github.com/galaxyproject/planemo/commit/069e7ba .. _08de8de: https://github.com/galaxyproject/planemo/commit/08de8de .. _0bd4ff0: https://github.com/galaxyproject/planemo/commit/0bd4ff0 .. _0e4f70a: https://github.com/galaxyproject/planemo/commit/0e4f70a .. _0f8cb10: https://github.com/galaxyproject/planemo/commit/0f8cb10 .. _13a5ae7: https://github.com/galaxyproject/planemo/commit/13a5ae7 .. _15804be: https://github.com/galaxyproject/planemo/commit/15804be .. _15d33c7: https://github.com/galaxyproject/planemo/commit/15d33c7 .. _182fe57: https://github.com/galaxyproject/planemo/commit/182fe57 .. _1927168: https://github.com/galaxyproject/planemo/commit/1927168 .. _1982076: https://github.com/galaxyproject/planemo/commit/1982076 .. _19900a6: https://github.com/galaxyproject/planemo/commit/19900a6 .. _1a157d4: https://github.com/galaxyproject/planemo/commit/1a157d4 .. _1a85493: https://github.com/galaxyproject/planemo/commit/1a85493 .. _1c6cfbb: https://github.com/galaxyproject/planemo/commit/1c6cfbb .. _1c7ee5b: https://github.com/galaxyproject/planemo/commit/1c7ee5b .. _1cd0e2d: https://github.com/galaxyproject/planemo/commit/1cd0e2d .. _1e3668a: https://github.com/galaxyproject/planemo/commit/1e3668a .. _2052db0: https://github.com/galaxyproject/planemo/commit/2052db0 .. _20a8680: https://github.com/galaxyproject/planemo/commit/20a86807cb7ea87db2dbc0197ae08a40df3ab2bc .. _21bb463: https://github.com/galaxyproject/planemo/commit/21bb463ad6c321bcb669603049a5e89a69766ad9 .. _25ef0d5: https://github.com/galaxyproject/planemo/commit/25ef0d5 .. _26e378e: https://github.com/galaxyproject/planemo/commit/26e378e .. _26e3cdb: https://github.com/galaxyproject/planemo/commit/26e3cdb .. _2a7c792: https://github.com/galaxyproject/planemo/commit/2a7c792 .. _2ae2b49: https://github.com/galaxyproject/planemo/commit/2ae2b49 .. _2e41e0a: https://github.com/galaxyproject/planemo/commit/2e41e0a .. _2f66fc3: https://github.com/galaxyproject/planemo/commit/2f66fc3 .. _30a9c3f: https://github.com/galaxyproject/planemo/commit/30a9c3f .. _32c6e7f: https://github.com/galaxyproject/planemo/commit/32c6e7f78bb8f04d27615cfd8948b0b89f27b4e6 .. _33294d2: https://github.com/galaxyproject/planemo/commit/33294d2 .. _334f2d4: https://github.com/galaxyproject/planemo/commit/334f2d4 .. _343902d: https://github.com/galaxyproject/planemo/commit/343902d .. _3499ca0: https://github.com/galaxyproject/planemo/commit/3499ca0a15affcaf8ac9efc55880da40b0626679 .. _358a42c: https://github.com/galaxyproject/planemo/commit/358a42c .. _36ac6d8: https://github.com/galaxyproject/planemo/commit/36ac6d8 .. _36f7cb1: https://github.com/galaxyproject/planemo/commit/36f7cb114f77731f90860d513a930e10ce5c1ba5 .. _37dcc07: https://github.com/galaxyproject/planemo/commit/37dcc07 .. _39fedd2: https://github.com/galaxyproject/planemo/commit/39fedd2 .. _3f4ab44: https://github.com/galaxyproject/planemo/commit/3f4ab44 .. _40a1f57: https://github.com/galaxyproject/planemo/commit/40a1f57 .. _411a8da: https://github.com/galaxyproject/planemo/commit/411a8da21c92ba37c7ad95bfce9928d9b8fd998e .. _44de95c: https://github.com/galaxyproject/planemo/commit/44de95c0d7087a5822941959f9a062f6382e329b .. _45135ff: https://github.com/galaxyproject/planemo/commit/45135ff .. _4823c5e: https://github.com/galaxyproject/planemo/commit/4823c5e .. _49c5c1e: https://github.com/galaxyproject/planemo/commit/49c5c1e .. _4c71299: https://github.com/galaxyproject/planemo/commit/4c71299 .. _4cd571c: https://github.com/galaxyproject/planemo/commit/4cd571c .. _4d29bf1: https://github.com/galaxyproject/planemo/commit/4d29bf1 .. _4d6f7d9: https://github.com/galaxyproject/planemo/commit/4d6f7d9 .. _4e1377c: https://github.com/galaxyproject/planemo/commit/4e1377c .. _4f61025: https://github.com/galaxyproject/planemo/commit/4f61025 .. _508dce7: https://github.com/galaxyproject/planemo/commit/508dce7 .. _53a6766: https://github.com/galaxyproject/planemo/commit/53a6766cdebdddc976189f6dc6a264bb4105c4bf .. _53edd99: https://github.com/galaxyproject/planemo/commit/53edd99 .. _552059f: https://github.com/galaxyproject/planemo/commit/552059f .. _572e754: https://github.com/galaxyproject/planemo/commit/572e754 .. _5b97f2e: https://github.com/galaxyproject/planemo/commit/5b97f2e .. _5d08b67: https://github.com/galaxyproject/planemo/commit/5d08b67 .. _5d7db92: https://github.com/galaxyproject/planemo/commit/5d7db92 .. _5e0b6d1: https://github.com/galaxyproject/planemo/commit/5e0b6d1 .. _63cd431: https://github.com/galaxyproject/planemo/commit/63cd431 .. _63e456c: https://github.com/galaxyproject/planemo/commit/63e456c .. _6409449: https://github.com/galaxyproject/planemo/commit/6409449 .. _6514ff5: 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https://github.com/galaxyproject/planemo/commit/8eda729 .. _912df02: https://github.com/galaxyproject/planemo/commit/912df02 .. _916f610: https://github.com/galaxyproject/planemo/commit/916f610 .. _93b7bda: https://github.com/galaxyproject/planemo/commit/93b7bda .. _94097c7: https://github.com/galaxyproject/planemo/commit/94097c7 .. _9427b47: https://github.com/galaxyproject/planemo/commit/9427b47 .. _94645ed: https://github.com/galaxyproject/planemo/commit/94645ed .. _949a36d: https://github.com/galaxyproject/planemo/commit/949a36d .. _95d5cba: https://github.com/galaxyproject/planemo/commit/95d5cba .. _965511d: https://github.com/galaxyproject/planemo/commit/965511d .. _988de1d: https://github.com/galaxyproject/planemo/commit/988de1d .. _98fdc8c: https://github.com/galaxyproject/planemo/commit/98fdc8c .. _99ee51a: https://github.com/galaxyproject/planemo/commit/99ee51a .. _9bf1eab: https://github.com/galaxyproject/planemo/commit/9bf1eab .. _9e746b4: 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_Issue 161: https://github.com/galaxyproject/planemo/issues/161 .. _Issue 167: https://github.com/galaxyproject/planemo/issues/167 .. _Issue 168: https://github.com/galaxyproject/planemo/issues/168 .. _Issue 169: https://github.com/galaxyproject/planemo/issues/169 .. _Issue 170: https://github.com/galaxyproject/planemo/issues/170 .. _Issue 176: https://github.com/galaxyproject/planemo/issues/176 .. _Issue 179: https://github.com/galaxyproject/planemo/issues/179 .. _Issue 180: https://github.com/galaxyproject/planemo/issues/180 .. _Issue 181: https://github.com/galaxyproject/planemo/issues/181 .. _Issue 184: https://github.com/galaxyproject/planemo/issues/184 .. _Issue 186: https://github.com/galaxyproject/planemo/issues/186 .. _Issue 188: https://github.com/galaxyproject/planemo/issues/188 .. _Issue 189: https://github.com/galaxyproject/planemo/issues/189 .. _Issue 192: https://github.com/galaxyproject/planemo/issues/192 .. _Issue 205: https://github.com/galaxyproject/planemo/issues/205 .. _Issue 206: https://github.com/galaxyproject/planemo/issues/206 .. _Issue 209: https://github.com/galaxyproject/planemo/issues/209 .. _Issue 211: https://github.com/galaxyproject/planemo/issues/211 .. _Issue 217: https://github.com/galaxyproject/planemo/issues/217 .. _Issue 223: https://github.com/galaxyproject/planemo/issues/223 .. _Issue 231: https://github.com/galaxyproject/planemo/issues/231 .. _Issue 233: https://github.com/galaxyproject/planemo/issues/233 .. _Issue 240: https://github.com/galaxyproject/planemo/issues/240 .. _Issue 243: https://github.com/galaxyproject/planemo/issues/243 .. _Issue 245: https://github.com/galaxyproject/planemo/issues/245 .. _Issue 246: https://github.com/galaxyproject/planemo/issues/246 .. _Issue 272: https://github.com/galaxyproject/planemo/issues/272 .. _Issue 303: https://github.com/galaxyproject/planemo/issues/303 .. _Issue 313: https://github.com/galaxyproject/planemo/issues/313 .. _Issue 329: https://github.com/galaxyproject/planemo/issues/329 .. _Issue 333: https://github.com/galaxyproject/planemo/issues/333 .. _Issue 361: https://github.com/galaxyproject/planemo/issues/361 .. _Issue 362: https://github.com/galaxyproject/planemo/issues/362 .. _Issue 373: https://github.com/galaxyproject/planemo/issues/373 .. _Issue 391: https://github.com/galaxyproject/planemo/issues/391 .. _Issue 416: https://github.com/galaxyproject/planemo/issues/416 .. _Issue 420: https://github.com/galaxyproject/planemo/issues/420 .. _Issue 475: https://github.com/galaxyproject/planemo/issues/475 .. _Issue 61: https://github.com/galaxyproject/planemo/issues/61 .. _Issue 70: https://github.com/galaxyproject/planemo/issues/70 .. _Issue 78: https://github.com/galaxyproject/planemo/issues/78 .. _Issue 80: https://github.com/galaxyproject/planemo/issues/80 .. _Issue 83: https://github.com/galaxyproject/planemo/issues/83 .. _Issue 88: https://github.com/galaxyproject/planemo/issues/88 .. _Issue 89: https://github.com/galaxyproject/planemo/issues/#89 .. _Issue 91: https://github.com/galaxyproject/planemo/issues/#91 .. _Pull Request 101: https://github.com/galaxyproject/planemo/pull/101 .. _Pull Request 102: https://github.com/galaxyproject/planemo/pull/102 .. _Pull Request 104: https://github.com/galaxyproject/planemo/pull/104 .. _Pull Request 111: https://github.com/galaxyproject/planemo/pull/111 .. _Pull Request 113: https://github.com/galaxyproject/planemo/pull/113 .. _Pull Request 129: https://github.com/galaxyproject/planemo/pull/129 .. _Pull Request 130: https://github.com/galaxyproject/planemo/pull/130 .. _Pull Request 143: https://github.com/galaxyproject/planemo/pull/143 .. _Pull Request 151: https://github.com/galaxyproject/planemo/pull/151 .. _Pull Request 155: https://github.com/galaxyproject/planemo/pull/155 .. _Pull Request 164: https://github.com/galaxyproject/planemo/pull/164 .. _Pull Request 171: https://github.com/galaxyproject/planemo/pull/171 .. _Pull Request 173: https://github.com/galaxyproject/planemo/pull/173 .. _Pull Request 175: https://github.com/galaxyproject/planemo/pull/175 .. _Pull Request 185: https://github.com/galaxyproject/planemo/pull/185 .. _Pull Request 186: https://github.com/galaxyproject/planemo/pull/186 .. _Pull Request 187: https://github.com/galaxyproject/planemo/pull/187 .. _Pull Request 190: https://github.com/galaxyproject/planemo/pull/190 .. _Pull Request 196: https://github.com/galaxyproject/planemo/pull/196 .. _Pull Request 1: https://github.com/galaxyproject/planemo/pull/1 .. _Pull Request 200: https://github.com/galaxyproject/planemo/pull/200 .. _Pull Request 203: https://github.com/galaxyproject/planemo/pull/203 .. _Pull Request 206: https://github.com/galaxyproject/planemo/pull/206 .. _Pull Request 207: https://github.com/galaxyproject/planemo/pull/207 .. _Pull Request 208: https://github.com/galaxyproject/planemo/pull/208 .. _Pull Request 210: https://github.com/galaxyproject/planemo/pull/210 .. _Pull Request 213: https://github.com/galaxyproject/planemo/pull/213 .. _Pull Request 215: https://github.com/galaxyproject/planemo/pull/215 .. _Pull Request 216: https://github.com/galaxyproject/planemo/pull/216 .. _Pull Request 22: https://github.com/galaxyproject/planemo/pull/22 .. _Pull Request 230: https://github.com/galaxyproject/planemo/pull/230 .. _Pull Request 235: https://github.com/galaxyproject/planemo/pull/235 .. _Pull Request 23: https://github.com/galaxyproject/planemo/pull/23 .. _Pull Request 251: https://github.com/galaxyproject/planemo/pull/251 .. _Pull Request 253: https://github.com/galaxyproject/planemo/pull/253 .. _Pull Request 254: https://github.com/galaxyproject/planemo/pull/254 .. _Pull Request 255: https://github.com/galaxyproject/planemo/pull/255 .. _Pull Request 256: https://github.com/galaxyproject/planemo/pull/256 .. _Pull Request 277: https://github.com/galaxyproject/planemo/pull/277 .. _Pull Request 278: https://github.com/galaxyproject/planemo/pull/278 .. _Pull Request 284: https://github.com/galaxyproject/planemo/pull/284 .. _Pull Request 285: https://github.com/galaxyproject/planemo/pull/285 .. _Pull Request 287: https://github.com/galaxyproject/planemo/pull/287 .. _Pull Request 292: https://github.com/galaxyproject/planemo/pull/292 .. _Pull Request 297: https://github.com/galaxyproject/planemo/pull/297 .. _Pull Request 29: https://github.com/galaxyproject/planemo/pull/29 .. _Pull Request 301: https://github.com/galaxyproject/planemo/pull/301 .. _Pull Request 304: https://github.com/galaxyproject/planemo/pull/304 .. _Pull Request 305: https://github.com/galaxyproject/planemo/pull/305 .. _Pull Request 307: https://github.com/galaxyproject/planemo/pull/307 .. _Pull Request 309: https://github.com/galaxyproject/planemo/pull/309 .. _Pull Request 310: https://github.com/galaxyproject/planemo/pull/310 .. _Pull Request 311: https://github.com/galaxyproject/planemo/pull/311 .. _Pull Request 312: https://github.com/galaxyproject/planemo/pull/312 .. _Pull Request 314: https://github.com/galaxyproject/planemo/pull/314 .. _Pull Request 316: https://github.com/galaxyproject/planemo/pull/316 .. _Pull Request 322: https://github.com/galaxyproject/planemo/pull/322 .. _Pull Request 327: https://github.com/galaxyproject/planemo/pull/327 .. _Pull Request 330: https://github.com/galaxyproject/planemo/pull/330 .. _Pull Request 333: https://github.com/galaxyproject/planemo/pull/333 .. _Pull Request 334: https://github.com/galaxyproject/planemo/pull/334 .. _Pull Request 335: https://github.com/galaxyproject/planemo/pull/335 .. _Pull Request 339: https://github.com/galaxyproject/planemo/pull/339 .. _Pull Request 33: https://github.com/galaxyproject/planemo/pull/33 .. _Pull Request 343: https://github.com/galaxyproject/planemo/pull/343 .. _Pull Request 344: https://github.com/galaxyproject/planemo/pull/344 .. _Pull Request 345: https://github.com/galaxyproject/planemo/pull/345 .. _Pull Request 350: https://github.com/galaxyproject/planemo/pull/350 .. _Pull Request 351: https://github.com/galaxyproject/planemo/pull/351 .. _Pull Request 356: https://github.com/galaxyproject/planemo/pull/356 .. _Pull Request 375: https://github.com/galaxyproject/planemo/pull/375 .. _Pull Request 390: https://github.com/galaxyproject/planemo/pull/390 .. _Pull Request 394: https://github.com/galaxyproject/planemo/pull/394 .. _Pull Request 398: https://github.com/galaxyproject/planemo/pull/398 .. _Pull Request 403: https://github.com/galaxyproject/planemo/pull/403 .. _Pull Request 40: https://github.com/galaxyproject/planemo/pull/40 .. _Pull Request 425: https://github.com/galaxyproject/planemo/pull/425 .. _Pull Request 426: https://github.com/galaxyproject/planemo/pull/426 .. _Pull Request 428: https://github.com/galaxyproject/planemo/pull/428 .. _Pull Request 429: https://github.com/galaxyproject/planemo/pull/429 .. _Pull Request 454: https://github.com/galaxyproject/planemo/pull/454 .. _Pull Request 472: https://github.com/galaxyproject/planemo/pull/472 .. _Pull Request 479: https://github.com/galaxyproject/planemo/pull/479 .. _Pull Request 480: https://github.com/galaxyproject/planemo/pull/480 .. _Pull Request 484: https://github.com/galaxyproject/planemo/pull/484 .. _Pull Request 488: https://github.com/galaxyproject/planemo/pull/488 .. _Pull Request 491: https://github.com/galaxyproject/planemo/pull/491 .. _Pull Request 51: https://github.com/galaxyproject/planemo/pull/51 .. _Pull Request 56: https://github.com/galaxyproject/planemo/pull/56 .. _Pull Request 63: https://github.com/galaxyproject/planemo/pull/63 .. _Pull Request 68: https://github.com/galaxyproject/planemo/pull/68 .. _Pull Request 6: https://github.com/galaxyproject/planemo/pull/6 .. _Pull Request 98: https://github.com/galaxyproject/planemo/pull/98 .. _Pull Request 99: https://github.com/galaxyproject/planemo/pull/99 .. _XSD: http://www.w3schools.com/schema/ .. _a13a120: https://github.com/galaxyproject/planemo/commit/a13a120 .. _a2c13e4: https://github.com/galaxyproject/planemo/commit/a2c13e46259e3be35de1ecaae858ba818bb94734 .. _a2ee135: https://github.com/galaxyproject/planemo/commit/a2ee135 .. _a4110a8: https://github.com/galaxyproject/planemo/commit/a4110a85a770988e5cd3c31ccc9475717897d59c .. _a4e6958: https://github.com/galaxyproject/planemo/commit/a4e6958 .. _a58a3b8: https://github.com/galaxyproject/planemo/commit/a58a3b8 .. _a87899b: https://github.com/galaxyproject/planemo/commit/a87899b .. _aad1eed: https://github.com/galaxyproject/planemo/commit/aad1eed .. _ac4f828: https://github.com/galaxyproject/planemo/commit/ac4f82898f7006799142503a33c3978428660ce7 .. _ad3b2f0: https://github.com/galaxyproject/planemo/commit/ad3b2f0 .. _af39061: https://github.com/galaxyproject/planemo/commit/af390612004dab636d8696839bb723d39f97c85d .. _af7448c: https://github.com/galaxyproject/planemo/commit/af7448c .. _b0b867e: https://github.com/galaxyproject/planemo/commit/b0b867e .. _b1c8f1d: https://github.com/galaxyproject/planemo/commit/b1c8f1d .. _b53006d: https://github.com/galaxyproject/planemo/commit/b53006d .. _b757791: https://github.com/galaxyproject/planemo/commit/b757791 .. _b7d9e96: https://github.com/galaxyproject/planemo/commit/b7d9e96 .. _b86fe1f: https://github.com/galaxyproject/planemo/commit/b86fe1f .. _b8d90ab: https://github.com/galaxyproject/planemo/commit/b8d90abab8bf53ae2e7cca4317223c01af9ab68c .. _b9232e5: https://github.com/galaxyproject/planemo/commit/b9232e55e713abbd1d9ce8b0b34cbec6c701dc17 .. _badc25f: https://github.com/galaxyproject/planemo/commit/badc25fca495b61457ffb2e027f3fe9cf17c798f .. _bioblend: https://github.com/galaxyproject/bioblend/ .. _c1713d2: https://github.com/galaxyproject/planemo/commit/c1713d2 .. _c23569f: https://github.com/galaxyproject/planemo/commit/c23569f .. _c444855: https://github.com/galaxyproject/planemo/commit/c444855 .. _c4dfd55: https://github.com/galaxyproject/planemo/commit/c4dfd55 .. _c8640b6: https://github.com/galaxyproject/planemo/commit/c8640b6 .. _cb5b906: https://github.com/galaxyproject/planemo/commit/cb5b906 .. _cc1a447: https://github.com/galaxyproject/planemo/commit/cc1a447 .. _cc8abb6: https://github.com/galaxyproject/planemo/commit/cc8abb6 .. _ce8e1be: https://github.com/galaxyproject/planemo/commit/ce8e1be .. _cwltool: https://github.com/common-workflow-language/cwltool/.. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e .. _d26929e: https://github.com/galaxyproject/planemo/commit/d26929e .. _d755fe7: https://github.com/galaxyproject/planemo/commit/d755fe7 .. _d76b489: https://github.com/galaxyproject/planemo/commit/d76b489 .. _d8f2038: https://github.com/galaxyproject/planemo/commit/d8f2038 .. _dad2d9d: https://github.com/galaxyproject/planemo/commit/dad2d9d .. _dd94ddc: https://github.com/galaxyproject/planemo/commit/dd94ddc .. _dff4f33: https://github.com/galaxyproject/planemo/commit/dff4f33c750a8dbe651c38e149a26dd42e706a82 .. _e0577e7: https://github.com/galaxyproject/planemo/commit/e0577e7 .. _e0acf91: https://github.com/galaxyproject/planemo/commit/e0acf91 .. _e38c436: https://github.com/galaxyproject/planemo/commit/e38c436 .. _e769118: https://github.com/galaxyproject/planemo/commit/e769118 .. _e8c1d45: https://github.com/galaxyproject/planemo/commit/e8c1d45f0c9a11bcf69ec2967836c3b8f432dd97 .. _eb039c0: https://github.com/galaxyproject/planemo/commit/eb039c0 .. _ec6e30f: https://github.com/galaxyproject/planemo/commit/ec6e30f .. _efc5f30: https://github.com/galaxyproject/planemo/commit/efc5f30 .. _f0610d7: https://github.com/galaxyproject/planemo/commit/f0610d7 .. _f3394e7: https://github.com/galaxyproject/planemo/commit/f3394e7 .. _f3c6917: https://github.com/galaxyproject/planemo/commit/f3c6917 .. _f3cafaa: https://github.com/galaxyproject/planemo/commit/f3cafaa .. _f7554d1: https://github.com/galaxyproject/planemo/commit/f7554d1 .. _f798c7e: https://github.com/galaxyproject/planemo/commit/f798c7e .. _f854138: https://github.com/galaxyproject/planemo/commit/f854138 .. _f99f6c1: https://github.com/galaxyproject/planemo/commit/f99f6c1 .. _fba3874: https://github.com/galaxyproject/planemo/commit/fba3874 .. _fdb1b51: https://github.com/galaxyproject/planemo/commit/fdb1b51 .. _fdce74c: https://github.com/galaxyproject/planemo/commit/fdce74c .. _fe7ad46: https://github.com/galaxyproject/planemo/commit/fe7ad46 .. _fea51fc: https://github.com/galaxyproject/planemo/commit/fea51fc .. _lxml: http://lxml.de/ .. _nose: https://nose.readthedocs.org/en/latest/ .. _xmllint: http://xmlsoft.org/xmllint.html .. _Conda: http://conda.pydata.org/ .. _Tool Factory: http://bioinformatics.oxfordjournals.org/content/early/2012/09/27/bioinformatics.bts573.full.pdf .. _git: https://git-scm.com/ .. _anaconda-verify: https://github.com/ContinuumIO/anaconda-verify .. _galaxy.xsd: https://github.com/galaxyproject/planemo/blob/master/planemo/xml/xsd/tool/galaxy.xsd .. _setup.py: https://github.com/galaxyproject/planemo/blob/master/setup.py .. _Bioconductor: https://www.bioconductor.org/ .. _tools-iuc: https://github.com/galaxyproject/tools-iuc .. _PyPI: https://pypi.python.org/pypi .. _Involucro: https://github.com/involucro/involucro .. _Bioconda: https://bioconda.github.io/ .. _pip: https://pip.pypa.io/en/stable/ .. _BioContainers: http://biocontainers.pro/ .. _Toil: https://github.com/BD2KGenomics/toil .. _quay.io: https://quay.io/ .. _galaxy-lib: https://github.com/galaxyproject/galaxy-lib .. _gxwf: https://github.com/simonbray/gxwf .. _Cheetah: https://cheetahtemplate.org/users_guide/intro.html .. _Allure: http://allure.qatools.ru/ .. _@abretaud: https://github.com/abretaud .. _@hexylena: https://github.com/hexylena .. _@peterjc: https://github.com/peterjc .. _@mr-c: https://github.com/mr-c .. _@martenson: https://github.com/martenson .. _@nsoranzo: https://github.com/nsoranzo .. _@nturaga: https://github.com/nturaga .. _@bgruening: https://github.com/bgruening .. _@carlfeberhard: https://github.com/carlfeberhard .. _@lparsons: https://github.com/lparsons .. _@kellrott: https://github.com/kellrott .. _@mvdbeek: https://github.com/mvdbeek .. _@natefoo: https://github.com/natefoo .. _@pstew: https://github.com/pstew .. _@ramezrawas: https://github.com/ramezrawas .. _@chambm: https://github.com/chambm .. _@takadonet: https://github.com/takadonet .. _@petrkadlec: https://github.com/petrkadlec .. _@pvanheus: https://github.com/pvanheus .. _@einon: https://github.com/einon .. _@blankenberg: https://github.com/blankenberg .. _@JeanFred: https://github.com/JeanFred .. _@gregvonkuster: https://github.com/gregvonkuster .. _@remimarenco: https://github.com/remimarenco .. _@thriqon: https://github.com/thriqon .. _@RJMW: https://github.com/RJMW .. _@manabuishii: https://github.com/manabuishii .. _@dfornika: https://github.com/dfornika .. _@bernt-matthias: https://github.com/bernt-matthias .. _@katrinleinweber: https://github.com/katrinleinweber .. _@bebatut: https://github.com/bebatut .. _@selten: https://github.com/selten .. _@shiltemann: https://github.com/shiltemann .. _@bedroesb: https://github.com/bedroesb .. _@ic4f: https://github.com/ic4f .. _@martin-raden: https://github.com/martin-raden .. _@andreassko: https://github.com/andreassko .. _@mblue9: https://github.com/mblue9 .. _@TMiguelT: https://github.com/TMiguelT .. _@bedroesb: https://github.com/bedroesb .. _@simonbray: https://github.com/simonbray .. _@gallardoalba: https://github.com/gallardoalba .. _@stain: https://github.com/stain .. _@profgiuseppe: https://github.com/profgiuseppe .. _@adRn-s: https://github.com/adRn-s .. _@lldelisle: https://github.com/lldelisle .. _@wm75: https://github.com/wm75 .. _@SimonWaldherr: https://github.com/SimonWaldherr .. _@mstabrin: https://github.com/mstabrin .. _@paulzierep: https://github.com/paulzierep .. _@Kulivox: https://github.com/Kulivox
FAQs
Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).
We found that planemo demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 5 open source maintainers collaborating on the project.
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