Mercurial > repos > shellac > guppy_basecaller
comparison env/lib/python3.7/site-packages/ephemeris/shed_tools_args.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
| author | shellac |
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| date | Sat, 02 May 2020 07:14:21 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:26e78fe6e8c4 |
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| 1 """This file contains the parser for shed_tools""" | |
| 2 | |
| 3 import argparse | |
| 4 | |
| 5 from .common_parser import get_common_args | |
| 6 | |
| 7 | |
| 8 def parser(): | |
| 9 """construct the parser object""" | |
| 10 common_arguments = get_common_args(log_file=True) | |
| 11 shed_parser = argparse.ArgumentParser() | |
| 12 subparsers = shed_parser.add_subparsers() | |
| 13 | |
| 14 # A list of defaults is needed. Otherwise the shed-tools install parser will not return | |
| 15 # update_tools in the name space and shed-tool update will not return all the install | |
| 16 # variables. | |
| 17 shed_parser.set_defaults( | |
| 18 action="install", | |
| 19 tool_list_file=None, | |
| 20 tool_yaml=None, | |
| 21 owner=None, | |
| 22 name=None, | |
| 23 tool_panel_section_id=None, | |
| 24 tool_panel_section_label=None, | |
| 25 revisions=None, | |
| 26 tool_shed_url=None, | |
| 27 skip_tool_dependencies=False, | |
| 28 install_resolver_dependencies=False, | |
| 29 force_latest_revision=False, | |
| 30 test=False, | |
| 31 test_user_api_key=None, | |
| 32 test_user="ephemeris@galaxyproject.org", | |
| 33 test_json="tool_test_output.json", | |
| 34 test_existing=False, | |
| 35 parallel_tests=1, | |
| 36 ) | |
| 37 | |
| 38 # SUBPARSERS | |
| 39 install_command_parser = subparsers.add_parser( | |
| 40 "install", | |
| 41 help="This installs tools in Galaxy from the Tool Shed." | |
| 42 "Use shed-tools install --help for more information", | |
| 43 parents=[common_arguments], | |
| 44 ) | |
| 45 update_command_parser = subparsers.add_parser( | |
| 46 "update", | |
| 47 help="This updates all tools in Galaxy to the latest revision. " | |
| 48 "Use shed-tools update --help for more information", | |
| 49 parents=[common_arguments]) | |
| 50 | |
| 51 test_command_parser = subparsers.add_parser( | |
| 52 "test", | |
| 53 help="This tests the supplied list of tools in Galaxy. " | |
| 54 "Use shed-tools test --help for more information", | |
| 55 parents=[common_arguments]) | |
| 56 | |
| 57 # SUBPARSER DEFAULTS | |
| 58 update_command_parser.set_defaults( | |
| 59 action="update" | |
| 60 ) | |
| 61 | |
| 62 test_command_parser.set_defaults( | |
| 63 action="test" | |
| 64 ) | |
| 65 install_command_parser.set_defaults( | |
| 66 action="install" | |
| 67 ) | |
| 68 | |
| 69 # COMMON OPTIONS | |
| 70 for command_parser in [update_command_parser, install_command_parser, test_command_parser]: | |
| 71 command_parser.add_argument( | |
| 72 "-t", "--toolsfile", | |
| 73 dest="tool_list_file", | |
| 74 help="Tools file to use (see tool_list.yaml.sample)", ) | |
| 75 command_parser.add_argument( | |
| 76 "-y", "--yaml_tool", | |
| 77 dest="tool_yaml", | |
| 78 help="Install tool represented by yaml string", ) | |
| 79 command_parser.add_argument( | |
| 80 "--name", | |
| 81 help="The name of the tool to install (only applicable " | |
| 82 "if the tools file is not provided).") | |
| 83 command_parser.add_argument( | |
| 84 "--owner", | |
| 85 help="The owner of the tool to install (only applicable " | |
| 86 "if the tools file is not provided).") | |
| 87 command_parser.add_argument( | |
| 88 "--revisions", | |
| 89 default=None, | |
| 90 nargs='*', | |
| 91 dest="revisions", | |
| 92 help="The revisions of the tool repository that will be installed. " | |
| 93 "All revisions must be specified after this flag by a space." | |
| 94 "Example: --revisions 0a5c7992b1ac f048033da666" | |
| 95 "(Only applicable if the tools file is not provided).") | |
| 96 command_parser.add_argument( | |
| 97 "--toolshed", | |
| 98 dest="tool_shed_url", | |
| 99 help="The Tool Shed URL where to install the tool from. " | |
| 100 "This is applicable only if the tool info is " | |
| 101 "provided as an option vs. in the tools file.") | |
| 102 | |
| 103 # OPTIONS COMMON FOR UPDATE AND INSTALL | |
| 104 | |
| 105 for command_parser in [update_command_parser, install_command_parser]: | |
| 106 command_parser.add_argument( | |
| 107 "--skip_install_tool_dependencies", | |
| 108 action="store_false", | |
| 109 dest="install_tool_dependencies", | |
| 110 default=False, # Override True default for this function | |
| 111 help=argparse.SUPPRESS) # Deprecated function. Leave for backwards compatibility. | |
| 112 command_parser.add_argument( | |
| 113 "--install_tool_dependencies", | |
| 114 action="store_true", | |
| 115 dest="install_tool_dependencies", | |
| 116 help="Turn on installation of tool dependencies using classic toolshed packages. " | |
| 117 "Can be overwritten on a per-tool basis in the tools file.") | |
| 118 command_parser.add_argument( | |
| 119 "--install_resolver_dependencies", | |
| 120 action="store_true", | |
| 121 dest="install_resolver_dependencies", | |
| 122 default=True, # Override False default for this function | |
| 123 help=argparse.SUPPRESS) # Deprecated function. Leave for backwards compatibility. | |
| 124 command_parser.add_argument( | |
| 125 "--skip_install_resolver_dependencies", | |
| 126 action="store_false", | |
| 127 dest="install_resolver_dependencies", | |
| 128 help="Skip installing tool dependencies through resolver (e.g. conda). " | |
| 129 "Will be ignored on galaxy releases older than 16.07. " | |
| 130 "Can be overwritten on a per-tool basis in the tools file") | |
| 131 command_parser.add_argument( | |
| 132 "--skip_install_repository_dependencies", | |
| 133 action="store_false", | |
| 134 dest="install_repository_dependencies", | |
| 135 help="Skip installing the repository dependencies." | |
| 136 ) | |
| 137 command_parser.add_argument( | |
| 138 "--test", | |
| 139 action="store_true", | |
| 140 dest="test", | |
| 141 help="Run tool tests on install tools, requires Galaxy 18.05 or newer." | |
| 142 ) | |
| 143 command_parser.add_argument( | |
| 144 "--test_existing", | |
| 145 action="store_true", | |
| 146 help="If testing tools during install, also run tool tests on repositories already installed " | |
| 147 "(i.e. skipped repositories)." | |
| 148 ) | |
| 149 command_parser.add_argument( | |
| 150 "--test_json", | |
| 151 dest="test_json", | |
| 152 default="tool_test_output.json", | |
| 153 help="If testing tools, record tool test output to specified file. " | |
| 154 "This file can be turned into reports with ``planemo test_reports <output.json>``." | |
| 155 ) | |
| 156 command_parser.add_argument( | |
| 157 "--test_user_api_key", | |
| 158 dest="test_user", | |
| 159 help="If testing tools, a user is needed to execute the tests. " | |
| 160 "This can be different the --api_key which is assumed to be an admin key. " | |
| 161 "If --api_key is a valid user (e.g. it is not a master API key) this does " | |
| 162 "not need to be specified and --api_key will be reused." | |
| 163 ) | |
| 164 command_parser.add_argument( | |
| 165 "--test_user", | |
| 166 dest="test_user", | |
| 167 help="If testing tools, a user is needed to execute the tests. " | |
| 168 "If --api_key is a master api key (i.e. not tied to a real user) and " | |
| 169 "--test_user_api_key isn't specified, this user email will be used. This " | |
| 170 "user will be created if needed." | |
| 171 ) | |
| 172 command_parser.add_argument( | |
| 173 "--parallel_tests", | |
| 174 dest="parallel_tests", | |
| 175 default=1, | |
| 176 type=int, | |
| 177 help="Specify the maximum number of tests that will be run in parallel." | |
| 178 ) | |
| 179 | |
| 180 # OPTIONS UNIQUE TO INSTALL | |
| 181 | |
| 182 install_command_parser.add_argument( | |
| 183 "--section", | |
| 184 dest="tool_panel_section_id", | |
| 185 help="Galaxy tool panel section ID where the tool will " | |
| 186 "be installed (the section must exist in Galaxy; " | |
| 187 "only applicable if the tools file is not provided).") | |
| 188 install_command_parser.add_argument( | |
| 189 "--section_label", | |
| 190 default=None, | |
| 191 dest="tool_panel_section_label", | |
| 192 help="Galaxy tool panel section label where tool will be installed " | |
| 193 "(if the section does not exist, it will be created; " | |
| 194 "only applicable if the tools file is not provided).") | |
| 195 | |
| 196 install_command_parser.add_argument( | |
| 197 "--latest", | |
| 198 action="store_true", | |
| 199 dest="force_latest_revision", | |
| 200 help="Will override the revisions in the tools file and always install the latest revision.") | |
| 201 | |
| 202 # OPTIONS UNIQUE TO TEST | |
| 203 # Same test_json as above but language modified for test instead of install/update. | |
| 204 test_command_parser.add_argument( | |
| 205 "--test_json", | |
| 206 default="tool_test_output.json", | |
| 207 dest="test_json", | |
| 208 help="Record tool test output to specified file. " | |
| 209 "This file can be turned into reports with ``planemo test_reports <output.json>``." | |
| 210 ) | |
| 211 | |
| 212 test_command_parser.add_argument( | |
| 213 "--test_user_api_key", | |
| 214 dest="test_user_api_key", | |
| 215 help="A user is needed to execute the tests. " | |
| 216 "This can be different the --api_key which is assumed to be an admin key. " | |
| 217 "If --api_key is a valid user (e.g. it is not a master API key) this does " | |
| 218 "not need to be specified and --api_key will be reused." | |
| 219 ) | |
| 220 test_command_parser.add_argument( | |
| 221 "--test_user", | |
| 222 dest="test_user", | |
| 223 help="A user is needed to execute the tests. " | |
| 224 "If --api_key is a master api key (i.e. not tied to a real user) and " | |
| 225 "--test_user_api_key isn't specified, this user email will be used. This " | |
| 226 "user will be created if needed." | |
| 227 ) | |
| 228 test_command_parser.add_argument( | |
| 229 "--parallel_tests", | |
| 230 dest="parallel_tests", | |
| 231 default=1, | |
| 232 type=int, | |
| 233 help="Specify the maximum number of tests that will be run in parallel." | |
| 234 ) | |
| 235 | |
| 236 return shed_parser |