Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/gxformat2-0.15.0.dist-info/METADATA @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 Metadata-Version: 2.1
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2 Name: gxformat2
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3 Version: 0.15.0
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4 Summary: Galaxy Workflow Format 2 Descriptions
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5 Home-page: https://github.com/galaxyproject/gxformat2
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6 Author: Galaxy Project and Community
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7 Author-email: jmchilton@gmail.com
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8 License: AFL
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9 Keywords: galaxy
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10 Platform: UNKNOWN
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11 Classifier: Development Status :: 5 - Production/Stable
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12 Classifier: Intended Audience :: Developers
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13 Classifier: Environment :: Console
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14 Classifier: License :: OSI Approved :: Academic Free License (AFL)
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15 Classifier: Operating System :: POSIX
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16 Classifier: Topic :: Software Development
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17 Classifier: Topic :: Software Development :: Code Generators
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18 Classifier: Topic :: Software Development :: Testing
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19 Classifier: Natural Language :: English
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20 Classifier: Programming Language :: Python :: 3
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21 Classifier: Programming Language :: Python :: 3.5
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22 Classifier: Programming Language :: Python :: 3.6
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23 Classifier: Programming Language :: Python :: 3.7
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24 Classifier: Programming Language :: Python :: 3.8
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25 Requires-Dist: six (>=1.9.0)
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26 Requires-Dist: bioblend
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27 Requires-Dist: pyyaml
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28
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29
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30 .. image:: https://readthedocs.org/projects/gxformat2/badge/?version=latest
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31 :target: https://gxformat2.readthedocs.io/en/latest/
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32
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33 .. image:: https://badge.fury.io/py/gxformat2.svg
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34 :target: https://pypi.python.org/pypi/gxformat2/
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35
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36 .. image:: https://github.com/galaxyproject/gxformat2/workflows/Python%20CI/badge.svg
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37 :target: https://github.com/galaxyproject/gxformat2/actions?query=workflow%3A%22Python+CI%22
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38
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39 .. image:: https://github.com/galaxyproject/gxformat2/workflows/Java%20CI/badge.svg
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40 :target: https://github.com/galaxyproject/gxformat2/actions?query=workflow%3A%22Java+CI%22
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41
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42 .. image:: https://img.shields.io/badge/latest%20schema-v19.09-blue
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43 :target: http://galaxyproject.github.io/gxformat2/v19_09.html
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44
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45 Format 2
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46 --------------
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47
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48 This package defines a high-level Galaxy_ workflow description termed "Format
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49 2". The current schema version is v19_09 and the schema can be found
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50 [here](http://galaxyproject.github.io/gxformat2/v19_09.html). This version of
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51 workflow format can be consumed by Galaxy versions 19.09, 20.01, 20.05 and the
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52 the forthcoming 20.09.
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53
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54 The Format 2 workflow description is still somewhat experimental and may
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55 yet change in small potentially backward incompatible ways until the format is
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56 exported by Galaxy by default.
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57
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58 The traditional Galaxy workflow description (files ending in .ga extension
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59 sometimes called native workflows in this project) was not designed to be
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60 concise and is neither readily human readable or human writable. Galaxy
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61 workflow Format 2 is being designed to addresses all three of these limitations.
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62 While also moving Galaxy's workflow description language toward standards such
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63 as the Common Workflow Language.
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64
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65 gxformat2
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66 --------------
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67
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68 This Python project can be installed from PyPI using ``pip``.
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69
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70 ::
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71
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72 $ pip install gxformat2
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73
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74 Checkout the project tests or how it used in projects such as Planemo and
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75 Galaxy to see how to use the gxformat2 library. Reference documentation for
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76 the `modules <https://gxformat2.readthedocs.io/en/latest/py-modindex.html>`__
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77 can be found as part of the project's documentation.
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78
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79 This project also includes various scripts for working with Galaxy workflows.
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80 Checkout their help for more information.
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81
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82 ::
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83
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84 $ gxwf-lint --help
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85 $ gxwf-viz --help
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86 $ gxwf-abstract-export --help
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87
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88 This library and associated scripts are licensed under the Academic Free License
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89 version 3.0.
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90
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91 .. _Galaxy: http://galaxyproject.org/
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92 .. _GitHub: https://github.com/
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93 .. _Travis CI: http://travis-ci.org/
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94
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95
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96
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97
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98 History
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99 -------
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100
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101 .. to_doc
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102
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103 ---------------------
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104 0.15.0 (2020-08-12)
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105 ---------------------
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106
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107 * Lint types of default values.
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108 * Fix bugs in schema related to differing type names between Galaxy and CWL.
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109 * Generate cwl v1.2 instead of cwl v1.2.0-dev5 release now that it has been released.
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110 * More testing of linting and CWL 1.2 export.
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111
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112 ---------------------
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113 0.14.0 (2020-08-11)
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114 ---------------------
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115
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116 * Bug fix where native export had explicit outputs declaration still in it (wouldn't break anything, but
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117 was deceptive).
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118 * Fixes for experimental CWL 1.2 abstract export.
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119 * Improve script structures and documentation.
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120 * Improve code structure - add more types, make more things immutable, mention mutability in docstrings.
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121
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122 ---------------------
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123 0.13.1 (2020-08-03)
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124 ---------------------
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125
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126 * Improve package structure - publish fixed sphinx docs, fix readme badges, add mypy typing support.
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127
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128 ---------------------
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129 0.13.0 (2020-07-30)
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130 ---------------------
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131
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132 * Add experimental export to CWL 1.2 using new abstract Operation classes.
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133
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134 ---------------------
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135 0.12.0 (2020-07-27)
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136 ---------------------
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137
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138 * Drop support for Python 2 - to support next bullet.
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139 * Update schema parser for recent changes to schema salad.
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140
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141 ---------------------
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142 0.11.4 (2020-07-27)
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143 ---------------------
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144
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145 * Added abstraction for uniform access to workflow outputs across formats.
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146
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147 ---------------------
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148 0.11.3 (2020-07-23)
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149 ---------------------
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150
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151 * Bug fixes for exporting newer input concepts from native to Format 2.
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152 * Added abstraction for uniform access to workflow inputs across formats.
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153
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154 ---------------------
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155 0.11.2 (2020-07-22)
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156 ---------------------
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157
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158 * Rework cytoscape and helpers for reuse from Planemo.
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159 * Rev markdown validator for and from latest Galaxy changes.
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160
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161 ---------------------
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162 0.11.1 (2020-02-25)
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163 ---------------------
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164
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165 * Bug fix for gxwf-lint invocation from setup.py installed script.
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166
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167 ---------------------
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168 0.11.0 (2020-02-25)
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169 ---------------------
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170
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171 * Validate Galaxy Markdown in workflow reports as part of linting.
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172 * Improved null handling in native ga workflow linting.
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173 * Enhancements to workflow linting from Python. Lint for lack of documentation,
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174 tools using the test toolshed, and implement special linting for training
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175 material workflows to ensure a tag matches the workflow topic.
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176 * Add gxwf-viz script that produces a cytoscape visualization of a workflow.
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177
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178 ---------------------
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179 0.10.1 (2019-12-07)
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180 ---------------------
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181
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182 * Bug fix to handle outputs without labels in Format 2 - they
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183 don't validate per se but they are important for testing in the
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184 Galaxy framework.
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185
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186 ---------------------
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187 0.10.0 (2019-12-06)
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188 ---------------------
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189
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190 * Implement scheam, validation, linting (for Format 2 and .ga).
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191 * Handle new reports field in Galaxy 19.09 workflows.
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192 * Numerous fixes for conversiion to and from native workflows.
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193 * Numerous new test cases.
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194 * Implement Java project for valiating and linting both kinds of workflows.
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195
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196 ---------------------
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197 0.9.0 (2019-07-08)
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198 ---------------------
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199
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200 * Implement default values in gxformat2.
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201
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202 ---------------------
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203 0.8.4 (2019-06-24)
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204 ---------------------
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205
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206 * Fix output IDs of 0.
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207
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208 ---------------------
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209 0.8.3 (2019-05-23)
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210 ---------------------
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211
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212 * Implement set_columns PJA.
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213
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214 ---------------------
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215 0.8.2 (2019-03-16)
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216 ---------------------
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217
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218 * Allow another API return option for experimental tool creation API.
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219
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220 ---------------------
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221 0.8.1 (2019-03-11)
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222 ---------------------
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223
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224 * Implement change datatype PJA.
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225
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226 ---------------------
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227 0.8.0 (2018-11-01)
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228 ---------------------
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229
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230 * Implement experimental CWL-style step defaults (see Galaxy PR #6850).
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231
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232 ---------------------
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233 0.7.1 (2018-10-09)
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234 ---------------------
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235
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236 * Various small fixes for changes in 0.7.1.
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237
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238 ---------------------
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239 0.7.0 (2018-10-08)
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240 ---------------------
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241
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242 * Add some basic test cases.
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243 * Allow ID-map style listing of steps.
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244 * Ordered load (in addition to existing dump functionality) or ordering of steps in ID-map style variant works.
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245 * Allow CWL-style $graph defs that can define multiple workflows in a single file.
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246 * Initial work on de-duplicating subworkflow definitions on import.
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247 * Fix position handling while exporting workflow.
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248
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249 ---------------------
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250 0.6.1 (2018-10-01)
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251 ---------------------
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252
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253 * Fix export of non-data parameters and implicit workflow connections.
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254
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255 ---------------------
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256 0.6.0 (2018-10-01)
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257 ---------------------
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258
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259 * Various fixes, allow id map style workflow input definitions.
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260
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261 ---------------------
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262 0.5.0 (2018-10-01)
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263 ---------------------
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264
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265 * More fixes for PJA, add the ``doc`` keyword to format 2 workflows to match CWL workflows. Map to and from native Galaxy workflows as annotations.
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266
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267 ---------------------
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268 0.4.0 (2018-10-01)
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269 ---------------------
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270
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271 * Fixes for exporting PJA when exporting workflows from native .ga to format 2.
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272
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273 ---------------------
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274 0.3.2 (2018-10-01)
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275 ---------------------
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276
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277 * Fixes for exporting workflow outputs from native .ga to format 2, support for modern map style output definitions like CWL 1.0.
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278
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279 ---------------------
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280 0.3.1 (2018-10-01)
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281 ---------------------
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282
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283 * Fixes for exporting subworkflows from native .ga to format 2.
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284
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285 ---------------------
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286 0.3.0 (2018-09-30)
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287 ---------------------
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288
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289 * More cwl style inputs, initial work on conversion from native workflows, various small fixes and tweaks.
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290
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291 ---------------------
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292 0.2.0 (2018-02-21)
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293 ---------------------
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294
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295 * Bring in latest Galaxy updates - Python 3 fixes, safe YAML usage, and more PJA implemented.
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296
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297 ---------------------
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298 0.1.1 (2016-08-15)
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299 ---------------------
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300
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301 * Fix one Python 3 incompatibility.
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302
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303 ---------------------
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304 0.1.0 (2016-05-02)
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305 ---------------------
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306
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307 * Initial version - code from Galaxy's test framework with changes
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308 based on planemo testing.
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309
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310