Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/ephemeris/shed_tools_args.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 """This file contains the parser for shed_tools"""
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2
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3 import argparse
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4
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5 from .common_parser import get_common_args
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6
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7
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8 def parser():
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9 """construct the parser object"""
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10 common_arguments = get_common_args(log_file=True)
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11 shed_parser = argparse.ArgumentParser()
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12 subparsers = shed_parser.add_subparsers()
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13
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14 # A list of defaults is needed. Otherwise the shed-tools install parser will not return
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15 # update_tools in the name space and shed-tool update will not return all the install
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16 # variables.
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17 shed_parser.set_defaults(
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18 action="install",
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19 tool_list_file=None,
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20 tool_yaml=None,
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21 owner=None,
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22 name=None,
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23 tool_panel_section_id=None,
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24 tool_panel_section_label=None,
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25 revisions=None,
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26 tool_shed_url=None,
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27 skip_tool_dependencies=False,
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28 install_resolver_dependencies=False,
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29 force_latest_revision=False,
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30 test=False,
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31 test_user_api_key=None,
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32 test_user="ephemeris@galaxyproject.org",
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33 test_json="tool_test_output.json",
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34 test_existing=False,
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35 parallel_tests=1,
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36 )
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37
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38 # SUBPARSERS
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39 install_command_parser = subparsers.add_parser(
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40 "install",
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41 help="This installs tools in Galaxy from the Tool Shed."
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42 "Use shed-tools install --help for more information",
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43 parents=[common_arguments],
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44 )
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45 update_command_parser = subparsers.add_parser(
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46 "update",
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47 help="This updates all tools in Galaxy to the latest revision. "
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48 "Use shed-tools update --help for more information",
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49 parents=[common_arguments])
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50
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51 test_command_parser = subparsers.add_parser(
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52 "test",
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53 help="This tests the supplied list of tools in Galaxy. "
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54 "Use shed-tools test --help for more information",
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55 parents=[common_arguments])
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56
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57 # SUBPARSER DEFAULTS
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58 update_command_parser.set_defaults(
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59 action="update"
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60 )
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61
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62 test_command_parser.set_defaults(
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63 action="test"
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64 )
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65 install_command_parser.set_defaults(
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66 action="install"
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67 )
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68
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69 # COMMON OPTIONS
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70 for command_parser in [update_command_parser, install_command_parser, test_command_parser]:
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71 command_parser.add_argument(
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72 "-t", "--toolsfile",
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73 dest="tool_list_file",
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74 help="Tools file to use (see tool_list.yaml.sample)", )
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75 command_parser.add_argument(
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76 "-y", "--yaml_tool",
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77 dest="tool_yaml",
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78 help="Install tool represented by yaml string", )
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79 command_parser.add_argument(
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80 "--name",
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81 help="The name of the tool to install (only applicable "
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82 "if the tools file is not provided).")
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83 command_parser.add_argument(
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84 "--owner",
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85 help="The owner of the tool to install (only applicable "
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86 "if the tools file is not provided).")
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87 command_parser.add_argument(
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88 "--revisions",
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89 default=None,
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90 nargs='*',
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91 dest="revisions",
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92 help="The revisions of the tool repository that will be installed. "
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93 "All revisions must be specified after this flag by a space."
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94 "Example: --revisions 0a5c7992b1ac f048033da666"
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95 "(Only applicable if the tools file is not provided).")
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96 command_parser.add_argument(
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97 "--toolshed",
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98 dest="tool_shed_url",
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99 help="The Tool Shed URL where to install the tool from. "
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100 "This is applicable only if the tool info is "
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101 "provided as an option vs. in the tools file.")
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102
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103 # OPTIONS COMMON FOR UPDATE AND INSTALL
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104
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105 for command_parser in [update_command_parser, install_command_parser]:
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106 command_parser.add_argument(
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107 "--skip_install_tool_dependencies",
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108 action="store_false",
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109 dest="install_tool_dependencies",
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110 default=False, # Override True default for this function
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111 help=argparse.SUPPRESS) # Deprecated function. Leave for backwards compatibility.
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112 command_parser.add_argument(
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113 "--install_tool_dependencies",
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114 action="store_true",
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115 dest="install_tool_dependencies",
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116 help="Turn on installation of tool dependencies using classic toolshed packages. "
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117 "Can be overwritten on a per-tool basis in the tools file.")
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118 command_parser.add_argument(
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119 "--install_resolver_dependencies",
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120 action="store_true",
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121 dest="install_resolver_dependencies",
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122 default=True, # Override False default for this function
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123 help=argparse.SUPPRESS) # Deprecated function. Leave for backwards compatibility.
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124 command_parser.add_argument(
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125 "--skip_install_resolver_dependencies",
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126 action="store_false",
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127 dest="install_resolver_dependencies",
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128 help="Skip installing tool dependencies through resolver (e.g. conda). "
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129 "Will be ignored on galaxy releases older than 16.07. "
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130 "Can be overwritten on a per-tool basis in the tools file")
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131 command_parser.add_argument(
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132 "--skip_install_repository_dependencies",
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133 action="store_false",
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134 dest="install_repository_dependencies",
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135 help="Skip installing the repository dependencies."
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136 )
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137 command_parser.add_argument(
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138 "--test",
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139 action="store_true",
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140 dest="test",
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141 help="Run tool tests on install tools, requires Galaxy 18.05 or newer."
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142 )
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143 command_parser.add_argument(
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144 "--test_existing",
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145 action="store_true",
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146 help="If testing tools during install, also run tool tests on repositories already installed "
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147 "(i.e. skipped repositories)."
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148 )
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149 command_parser.add_argument(
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150 "--test_json",
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151 dest="test_json",
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152 default="tool_test_output.json",
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153 help="If testing tools, record tool test output to specified file. "
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154 "This file can be turned into reports with ``planemo test_reports <output.json>``."
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155 )
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156 command_parser.add_argument(
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157 "--test_user_api_key",
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158 dest="test_user",
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159 help="If testing tools, a user is needed to execute the tests. "
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160 "This can be different the --api_key which is assumed to be an admin key. "
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161 "If --api_key is a valid user (e.g. it is not a master API key) this does "
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162 "not need to be specified and --api_key will be reused."
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163 )
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164 command_parser.add_argument(
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165 "--test_user",
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166 dest="test_user",
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167 help="If testing tools, a user is needed to execute the tests. "
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168 "If --api_key is a master api key (i.e. not tied to a real user) and "
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169 "--test_user_api_key isn't specified, this user email will be used. This "
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170 "user will be created if needed."
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171 )
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172 command_parser.add_argument(
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173 "--parallel_tests",
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174 dest="parallel_tests",
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175 default=1,
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176 type=int,
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177 help="Specify the maximum number of tests that will be run in parallel."
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178 )
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179
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180 # OPTIONS UNIQUE TO INSTALL
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181
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182 install_command_parser.add_argument(
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183 "--section",
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184 dest="tool_panel_section_id",
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185 help="Galaxy tool panel section ID where the tool will "
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186 "be installed (the section must exist in Galaxy; "
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187 "only applicable if the tools file is not provided).")
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188 install_command_parser.add_argument(
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189 "--section_label",
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190 default=None,
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191 dest="tool_panel_section_label",
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192 help="Galaxy tool panel section label where tool will be installed "
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193 "(if the section does not exist, it will be created; "
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194 "only applicable if the tools file is not provided).")
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195
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196 install_command_parser.add_argument(
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197 "--latest",
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198 action="store_true",
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199 dest="force_latest_revision",
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200 help="Will override the revisions in the tools file and always install the latest revision.")
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201
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202 # OPTIONS UNIQUE TO TEST
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203 # Same test_json as above but language modified for test instead of install/update.
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204 test_command_parser.add_argument(
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205 "--test_json",
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206 default="tool_test_output.json",
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207 dest="test_json",
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208 help="Record tool test output to specified file. "
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209 "This file can be turned into reports with ``planemo test_reports <output.json>``."
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210 )
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211
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212 test_command_parser.add_argument(
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213 "--test_user_api_key",
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214 dest="test_user_api_key",
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215 help="A user is needed to execute the tests. "
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216 "This can be different the --api_key which is assumed to be an admin key. "
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217 "If --api_key is a valid user (e.g. it is not a master API key) this does "
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218 "not need to be specified and --api_key will be reused."
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219 )
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220 test_command_parser.add_argument(
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221 "--test_user",
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222 dest="test_user",
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223 help="A user is needed to execute the tests. "
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224 "If --api_key is a master api key (i.e. not tied to a real user) and "
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225 "--test_user_api_key isn't specified, this user email will be used. This "
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226 "user will be created if needed."
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227 )
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228 test_command_parser.add_argument(
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229 "--parallel_tests",
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230 dest="parallel_tests",
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231 default=1,
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232 type=int,
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233 help="Specify the maximum number of tests that will be run in parallel."
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234 )
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235
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236 return shed_parser