Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/planemo/options.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 """ Click definitions for various shared options and arguments.
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2 """
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3
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4 import functools
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5 import os
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6
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7 import click
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8 from galaxy.tools.deps import docker_util
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9 from .config import get_default_callback
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10
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11
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12 def force_option(what="files"):
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13 return click.option(
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14 "-f",
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15 "--force",
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16 is_flag=True,
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17 help="Overwrite existing %s if present." % what,
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18 )
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19
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20
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21 def test_data_option():
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22 return click.option(
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23 "--test_data",
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24 type=click.Path(exists=True, file_okay=False, resolve_path=True),
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25 help="test-data directory to for specified tool(s).",
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26 )
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27
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28
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29 def tool_data_table_option():
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30 return click.option(
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31 "--tool_data_table",
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32 type=click.Path(exists=True, file_okay=True, resolve_path=True),
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33 help="tool_data_table_conf.xml file to for specified tool(s).",
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34 )
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35
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36
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37 def galaxy_root_option():
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38 return click.option(
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39 "--galaxy_root",
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40 type=click.Path(exists=True, file_okay=False, resolve_path=True),
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41 help="Root of development galaxy directory to execute command with.",
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42 )
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43
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44
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45 def galaxy_port_option():
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46 return click.option(
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47 "--port",
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48 type=int,
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49 default=None,
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50 callback=get_default_callback("9090"),
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51 help="Port to serve Galaxy on (default is 9090).",
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52 )
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53
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54
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55 def galaxy_host_option():
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56 return click.option(
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57 "--host",
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58 type=str,
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59 default=None,
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60 callback=get_default_callback("127.0.0.1"),
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61 help=("Host to bind Galaxy to. Default is 127.0.0.1 that is "
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62 "restricted to localhost connections for security reasons "
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63 "set to 0.0.0.0 to bind Galaxy to all ports including "
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64 "potentially publicly accessible ones."),
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65 )
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66
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67
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68 def dependency_resolvers_option():
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69 return click.option(
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70 "--dependency_resolvers_config_file",
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71 type=click.Path(
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72 exists=True,
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73 file_okay=True,
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74 dir_okay=False,
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75 resolve_path=True
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76 ),
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77 help="Dependency resolver configuration for Galaxy to target.",
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78 )
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79
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80
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81 def brew_dependency_resolution():
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82 return click.option(
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83 "--brew_dependency_resolution",
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84 is_flag=True,
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85 help="Configure Galaxy to use plain brew dependency resolution.",
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86 )
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87
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88
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89 def shed_dependency_resolution():
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90 return click.option(
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91 "--shed_dependency_resolution",
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92 is_flag=True,
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93 help=("Configure Galaxy to use brewed Tool Shed dependency"
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94 " resolution."),
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95 )
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96
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97
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98 def job_config_option():
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99 return click.option(
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100 "--job_config_file",
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101 type=click.Path(
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102 exists=True,
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103 file_okay=True,
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104 dir_okay=False,
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105 resolve_path=True
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106 ),
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107 help="Job configuration file for Galaxy to target.",
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108 )
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109
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110
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111 def tool_dependency_dir_option():
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112 return click.option(
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113 "--tool_dependency_dir",
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114 type=click.Path(
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115 exists=True,
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116 file_okay=False,
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117 dir_okay=True,
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118 resolve_path=True
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119 ),
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120 help="Tool dependency dir for Galaxy to target.",
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121 )
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122
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123
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124 def install_galaxy_option():
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125 return click.option(
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126 "--install_galaxy",
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127 is_flag=True,
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128 help="Download and configure a disposable copy of Galaxy from github."
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129 )
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130
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131
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132 def no_cache_galaxy_option():
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133 return click.option(
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134 "--no_cache_galaxy",
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135 is_flag=True,
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136 help=("Skip caching of Galaxy source and dependencies obtained with "
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137 "--install_galaxy. Not caching this results in faster "
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138 "downloads (no git) - so is better on throw away instances such "
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139 "with TravisCI. ")
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140 )
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141
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142
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143 def brew_option():
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144 return click.option(
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145 "--brew",
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146 type=click.Path(exists=True, file_okay=True, dir_okay=False),
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147 help="Homebrew 'brew' executable to use."
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148 )
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149
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150
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151 def required_tool_arg():
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152 """ Decorate click method as requiring the path to a single tool.
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153 """
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154 arg_type = click.Path(
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155 exists=True,
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156 file_okay=True,
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157 dir_okay=False,
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158 readable=True,
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159 resolve_path=True,
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160 )
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161 return click.argument("path", metavar="TOOL_PATH", type=arg_type)
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162
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163
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164 def _optional_tools_default(ctx, param, value):
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165 if param.name == "paths" and len(value) == 0:
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166 return [os.path.abspath(os.getcwd())]
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167 else:
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168 return value
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169
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170
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171 def optional_tools_arg(multiple=False):
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172 """ Decorate click method as optionally taking in the path to a tool
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173 or directory of tools. If no such argument is given the current working
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174 directory will be treated as a directory of tools.
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175 """
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176 arg_type = click.Path(
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177 exists=True,
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178 file_okay=True,
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179 dir_okay=True,
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180 readable=True,
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181 resolve_path=True,
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182 )
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183 name = "paths" if multiple else "path"
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184 nargs = -1 if multiple else 1
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185 return click.argument(
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186 name,
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187 metavar="TOOL_PATH",
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188 type=arg_type,
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189 nargs=nargs,
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190 callback=_optional_tools_default,
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191 )
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192
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193
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194 class ProjectOrRepositry(click.Path):
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195
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196 def __init__(self, **kwds):
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197 super(ProjectOrRepositry, self).__init__(**kwds)
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198
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199 def convert(self, value, param, ctx):
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200 if value and value.startswith("git:") or value.startswith("git+"):
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201 return value
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202 else:
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203 return super(ProjectOrRepositry, self).convert(value, param, ctx)
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204
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205
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206 def shed_project_arg(multiple=True):
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207 arg_type = ProjectOrRepositry(
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208 exists=True,
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209 file_okay=False,
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210 dir_okay=True,
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211 writable=True,
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212 resolve_path=True,
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213 )
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214 name = "paths" if multiple else "path"
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215 nargs = -1 if multiple else 1
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216 return click.argument(
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217 name,
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218 metavar="PROJECT",
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219 default=".",
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220 type=arg_type,
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221 nargs=nargs,
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222 callback=_optional_tools_default,
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223 )
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224
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225
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226 def optional_project_arg(exists=True):
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227 arg_type = click.Path(
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228 exists=exists,
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229 file_okay=False,
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230 dir_okay=True,
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231 writable=True,
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232 resolve_path=True,
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233 )
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234 return click.argument(
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235 "path",
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236 metavar="PROJECT",
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237 default=".",
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238 type=arg_type
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239 )
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240
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241
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242 def no_cleanup_option():
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243 return click.option(
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244 "--no_cleanup",
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245 is_flag=True,
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246 help=("Do not cleanup temp files created for and by Galaxy.")
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247 )
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248
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249
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250 def docker_cmd_option():
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251 return click.option(
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252 "--docker_cmd",
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253 default=docker_util.DEFAULT_DOCKER_COMMAND,
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254 help="Command used to launch docker (defaults to docker)."
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255 )
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256
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257
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258 def docker_sudo_option():
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259 return click.option(
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260 "--docker_sudo",
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261 is_flag=True,
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262 help="Flag to use sudo when running docker."
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263 )
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264
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265
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266 def docker_sudo_cmd_option():
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267 return click.option(
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268 "--docker_sudo_cmd",
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269 default=None,
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270 help="sudo command to use when --docker_sudo is enabled " +
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271 "(defaults to sudo).",
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272 callback=get_default_callback(docker_util.DEFAULT_SUDO_COMMAND),
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273 )
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274
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275
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276 def docker_host_option():
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277 return click.option(
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278 "--docker_host",
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279 default=None,
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280 help="Docker host to target when executing docker commands " +
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281 "(defaults to localhost).",
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282 callback=get_default_callback(docker_util.DEFAULT_HOST),
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283 )
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284
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285
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286 def shed_owner_option():
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287 return click.option(
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288 "--owner",
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289 help="Tool Shed repository owner (username)."
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290 )
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291
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292
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293 def shed_name_option():
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294 return click.option(
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295 "--name",
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296 help="Tool Shed repository name (defaults to the inferred "
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297 "tool directory name)."
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298 )
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299
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300
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301 def validate_shed_target_callback(ctx, param, value):
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302 target = get_default_callback("toolshed")(ctx, param, value)
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303 if target is None:
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304 ctx.fail("default_shed_target set to None, must specify a value for "
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305 "--shed_target to run this command.")
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306 return target
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307
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308
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309 def shed_target_option():
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310 return click.option(
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311 "-t",
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312 "--shed_target",
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313 help="Tool Shed to target (this can be 'toolshed', 'testtoolshed', "
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314 "'local' (alias for http://localhost:9009/), an arbitrary url "
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315 "or mappings defined ~/.planemo.yml.",
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316 default=None,
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317 callback=validate_shed_target_callback,
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318 )
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319
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320
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321 def shed_key_option():
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322 return click.option(
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323 "--shed_key",
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324 help=("API key for Tool Shed access. An API key is required unless "
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325 "e-mail and password is specified. This key can be specified "
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326 "with either --shed_key or --shed_key_from_env.")
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327 )
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328
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329
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330 def shed_key_from_env_option():
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331 return click.option(
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332 "--shed_key_from_env",
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333 help="Environment variable to read API key for Tool Shed access from."
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334 )
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335
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336
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337 def shed_email_option():
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338 return click.option(
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339 "--shed_email",
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340 help="E-mail for Tool Shed auth (required unless shed_key is "
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341 "specified)."
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342 )
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343
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344
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345 def shed_password_option():
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346 return click.option(
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347 "--shed_password",
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348 help="Password for Tool Shed auth (required unless shed_key is "
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349 "specified)."
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350 )
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351
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352
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353 def shed_skip_upload():
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354 return click.option(
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355 "--skip_upload",
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356 is_flag=True,
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357 help=("Skip upload contents as part of operation, only update "
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358 "metadata.")
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359 )
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360
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361
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362 def shed_skip_metadata():
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363 return click.option(
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364 "--skip_metadata",
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365 is_flag=True,
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366 help=("Skip metadata update as part of operation, only upload "
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367 "new contents.")
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368 )
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369
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370
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371 def shed_message_option():
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372 return click.option(
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373 "-m",
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374 "--message",
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375 help="Commit message for tool shed upload."
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376 )
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377
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378
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379 def shed_force_create_option():
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380 return click.option(
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381 "--force_repository_creation",
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382 help=("If a repository cannot be found for the specified user/repo "
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383 "name pair, then automatically create the repository in the "
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384 "toolshed."),
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385 is_flag=True,
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386 default=False
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387 )
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388
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389
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390 def shed_check_diff_option():
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391 return click.option(
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392 "--check_diff",
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393 is_flag=True,
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394 help=("Skip uploading if the shed_diff detects there would be no "
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395 "'difference' (only attributes populated by the shed would "
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396 "be updated.)")
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397 )
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398
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399
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400 def shed_upload_options():
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401 return _compose(
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402 shed_message_option(),
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403 shed_force_create_option(),
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404 shed_check_diff_option(),
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405 )
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406
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407
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408 def shed_realization_options():
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409 return _compose(
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410 shed_project_arg(multiple=True),
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411 recursive_shed_option(),
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412 shed_fail_fast_option(),
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413 )
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414
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415
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416 def shed_repo_options():
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417 return _compose(
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418 shed_owner_option(),
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419 shed_name_option(),
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420 )
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421
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422
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423 def shed_publish_options():
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424 """ Common options for commands that require publishing to a
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425 a shed.
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426 """
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427 return _compose(
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428 shed_realization_options(),
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429 shed_repo_options(),
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430 shed_target_options(),
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431 )
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432
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433
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434 def shed_read_options():
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435 """ Common options that require read access to mapped repositories
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436 in a shed.
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437 """
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438 return _compose(
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439 shed_realization_options(),
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440 shed_repo_options(),
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441 shed_target_options(),
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442 )
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443
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444
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445 def shed_target_options():
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446 """ Common options for commands that require read-only
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447 interactions with a shed.
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448 """
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449 return _compose(
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450 shed_email_option(),
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451 shed_key_option(),
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452 shed_key_from_env_option(),
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453 shed_password_option(),
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454 shed_target_option(),
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455 )
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456
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457
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458 def galaxy_run_options():
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459 return _compose(
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460 galaxy_target_options(),
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461 galaxy_port_option(),
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462 galaxy_host_option(),
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463 )
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464
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465
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466 def galaxy_config_options():
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467 return _compose(
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468 test_data_option(),
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469 tool_data_table_option(),
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470 dependency_resolvers_option(),
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471 tool_dependency_dir_option(),
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472 brew_dependency_resolution(),
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473 shed_dependency_resolution(),
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474 )
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475
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476
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477 def galaxy_target_options():
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478 return _compose(
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479 galaxy_root_option(),
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480 install_galaxy_option(),
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481 no_cache_galaxy_option(),
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482 no_cleanup_option(),
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483 job_config_option(),
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484 )
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485
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486
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487 def galaxy_serve_options():
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488 return _compose(
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489 galaxy_run_options(),
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490 galaxy_config_options(),
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491 )
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492
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493
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494 def shed_fail_fast_option():
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495 return click.option(
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496 "--fail_fast",
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497 is_flag=True,
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498 default=False,
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499 help="If multiple repositories are specified and an error occurs "
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500 "stop immediately instead of processing remaining repositories."
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501 )
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502
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503
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504 def lint_xsd_option():
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505 return click.option(
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506 "--xsd",
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507 is_flag=True,
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508 default=False,
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509 help=("Include experimental tool XSD validation in linting "
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510 "process (requires xmllint on PATH or lxml installed).")
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511 )
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512
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513
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514 def report_level_option():
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515 return click.option(
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516 "--report_level",
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517 type=click.Choice(["all", "warn", "error"]),
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518 default="all",
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519 )
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520
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521
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522 def skip_option():
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523 return click.option(
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524 "-s",
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525 "--skip",
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526 default=None,
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527 help=("Comma-separated list of lint tests to skip (e.g send ."
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528 "--skip 'citations,xml_order' to skip linting of citations "
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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diff changeset
529 "and best-practice XML ordering.")
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530 )
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parents:
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531
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532
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533 def fail_level_option():
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parents:
diff changeset
534 return click.option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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535 "--fail_level",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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536 type=click.Choice(['warn', 'error']),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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537 default="warn"
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538 )
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parents:
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539
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540
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541 def recursive_shed_option():
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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542 return recursive_option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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543 "Recursively perform command for nested repository directories.",
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544 )
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parents:
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545
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parents:
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546
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547 def recursive_option(help="Recursively perform command for subdirectories."):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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548 return click.option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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549 "-r",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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550 "--recursive",
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551 is_flag=True,
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552 help=help,
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553 )
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parents:
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554
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555
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556 def test_options():
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557 return _compose(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
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558 click.option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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559 "--update_test_data",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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560 is_flag=True,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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561 help="Update test-data directory with job outputs (normally"
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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562 " written to directory --job_output_files if specified.)"
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563 ),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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564 click.option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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565 "--test_output",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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566 type=click.Path(file_okay=True, resolve_path=True),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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567 callback=get_default_callback("tool_test_output.html"),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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568 help=("Output test report (HTML - for humans) defaults to "
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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569 "tool_test_output.html."),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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570 default=None,
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571 ),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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572 click.option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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573 "--test_output_text",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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574 type=click.Path(file_okay=True, resolve_path=True),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
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575 callback=get_default_callback(None),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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576 help=("Output test report (Basic text - for display in CI)"),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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577 default=None,
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578 ),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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579 click.option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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580 "--test_output_markdown",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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581 type=click.Path(file_okay=True, resolve_path=True),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
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582 callback=get_default_callback(None),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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583 help=("Output test report (Markdown style - for humans & "
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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584 "computers)"),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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585 default=None,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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586 ),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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587 click.option(
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588 "--test_output_xunit",
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589 type=click.Path(file_okay=True, resolve_path=True),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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590 callback=get_default_callback(None),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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591 help="Output test report (xUnit style - for computers).",
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diff changeset
592 default=None,
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parents:
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593 ),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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594 click.option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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595 "--test_output_json",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
diff changeset
596 type=click.Path(file_okay=True, resolve_path=True),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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597 callback=get_default_callback("tool_test_output.json"),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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598 help=("Output test report (planemo json) defaults to "
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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599 "tool_test_output.json."),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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diff changeset
600 default=None,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
diff changeset
601 ),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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602 click.option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
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603 "--job_output_files",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
diff changeset
604 type=click.Path(file_okay=False, resolve_path=True),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
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605 help="Write job outputs to specified directory.",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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diff changeset
606 default=None,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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607 ),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
diff changeset
608 click.option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
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609 "--summary",
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610 type=click.Choice(["none", "minimal", "compact"]),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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611 default="minimal",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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612 help=("Summary style printed to planemo's standard output (see "
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
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613 "output reports for more complete summary). Set to 'none' "
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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diff changeset
614 "to disable completely.")
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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615 )
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
parents:
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616 )
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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617
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618
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
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619 def _compose(*functions):
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620 def compose2(f, g):
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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621 return lambda x: f(g(x))
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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622 return functools.reduce(compose2, functions)
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parents:
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623
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624
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bcclaywell
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diff changeset
625 def dependencies_script_options():
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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626 return _compose(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
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627 click.option(
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
bcclaywell
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628 "--download_cache",
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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parents:
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629 type=click.Path(file_okay=False, resolve_path=True),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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630 callback=get_default_callback(None),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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631 help=("Directory to cache downloaded files, default is $DOWNLOAD_CACHE"),
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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632 default=None,
d67268158946 planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
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633 ),
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parents:
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634 )