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annotate env/lib/python3.9/site-packages/cwltool/argparser.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000 (2021-03-22)
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1 """Command line argument parsing for cwltool."""
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2
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3 import argparse
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4 import os
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5 from typing import (
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6 Any,
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7 AnyStr,
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8 Dict,
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9 List,
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10 MutableMapping,
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11 MutableSequence,
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12 Optional,
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13 Sequence,
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14 Union,
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15 cast,
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16 )
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17
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18 from schema_salad.ref_resolver import file_uri
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19
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20 from .loghandler import _logger
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21 from .process import Process, shortname
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22 from .resolver import ga4gh_tool_registries
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23 from .software_requirements import SOFTWARE_REQUIREMENTS_ENABLED
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24 from .utils import DEFAULT_TMP_PREFIX, onWindows
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25
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26
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27 def arg_parser() -> argparse.ArgumentParser:
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28 parser = argparse.ArgumentParser(
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29 description="Reference executor for Common Workflow Language standards. "
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30 "Not for production use."
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31 )
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32 parser.add_argument("--basedir", type=str)
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33 parser.add_argument(
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34 "--outdir",
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35 type=str,
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36 default=os.path.abspath("."),
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37 help="Output directory. The default is the current directory.",
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38 )
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39
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40 parser.add_argument(
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41 "--parallel",
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42 action="store_true",
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43 default=False,
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44 help="[experimental] Run jobs in parallel. ",
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45 )
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46 envgroup = parser.add_mutually_exclusive_group()
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47 envgroup.add_argument(
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48 "--preserve-environment",
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49 type=str,
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50 action="append",
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51 help="Preserve specific environment variable when running "
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52 "CommandLineTools without a software container. May be provided "
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53 "multiple times. The default is to preserve only the PATH.",
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54 metavar="ENVVAR",
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55 default=["PATH"],
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56 dest="preserve_environment",
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57 )
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58 envgroup.add_argument(
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59 "--preserve-entire-environment",
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60 action="store_true",
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61 help="Preserve all environment variables when running CommandLineTools "
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62 "without a software container.",
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63 default=False,
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64 dest="preserve_entire_environment",
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65 )
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66
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67 containergroup = parser.add_mutually_exclusive_group()
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68 containergroup.add_argument(
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69 "--rm-container",
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70 action="store_true",
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71 default=True,
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72 help="Delete Docker container used by jobs after they exit (default)",
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73 dest="rm_container",
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74 )
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75
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76 containergroup.add_argument(
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77 "--leave-container",
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78 action="store_false",
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79 default=True,
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80 help="Do not delete Docker container used by jobs after they exit",
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81 dest="rm_container",
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82 )
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83
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84 cidgroup = parser.add_argument_group(
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85 "Options for recording the Docker container identifier into a file."
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86 )
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87 cidgroup.add_argument(
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88 # Disabled as containerid is now saved by default
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89 "--record-container-id",
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90 action="store_true",
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91 default=False,
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92 help=argparse.SUPPRESS,
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93 dest="record_container_id",
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94 )
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95
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96 cidgroup.add_argument(
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97 "--cidfile-dir",
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98 type=str,
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99 help="Store the Docker container ID into a file in the specified directory.",
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100 default=None,
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101 dest="cidfile_dir",
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102 )
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103
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104 cidgroup.add_argument(
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105 "--cidfile-prefix",
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106 type=str,
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107 help="Specify a prefix to the container ID filename. "
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108 "Final file name will be followed by a timestamp. "
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109 "The default is no prefix.",
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110 default=None,
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111 dest="cidfile_prefix",
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112 )
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113
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114 parser.add_argument(
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115 "--tmpdir-prefix",
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116 type=str,
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117 help="Path prefix for temporary directories. If --tmpdir-prefix is not "
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118 "provided, then the prefix for temporary directories is influenced by "
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119 "the value of the TMPDIR, TEMP, or TMP environment variables. Taking "
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120 "those into consideration, the current default is {}.".format(
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121 DEFAULT_TMP_PREFIX
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122 ),
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123 default=DEFAULT_TMP_PREFIX,
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124 )
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125
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126 intgroup = parser.add_mutually_exclusive_group()
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127 intgroup.add_argument(
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128 "--tmp-outdir-prefix",
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129 type=str,
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130 help="Path prefix for intermediate output directories. Defaults to the "
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131 "value of --tmpdir-prefix.",
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132 default="",
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133 )
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134
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135 intgroup.add_argument(
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136 "--cachedir",
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137 type=str,
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138 default="",
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139 help="Directory to cache intermediate workflow outputs to avoid "
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140 "recomputing steps. Can be very helpful in the development and "
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141 "troubleshooting of CWL documents.",
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142 )
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143
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144 tmpgroup = parser.add_mutually_exclusive_group()
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145 tmpgroup.add_argument(
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146 "--rm-tmpdir",
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147 action="store_true",
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148 default=True,
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149 help="Delete intermediate temporary directories (default)",
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150 dest="rm_tmpdir",
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151 )
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152
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153 tmpgroup.add_argument(
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154 "--leave-tmpdir",
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155 action="store_false",
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156 default=True,
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157 help="Do not delete intermediate temporary directories",
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158 dest="rm_tmpdir",
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159 )
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160
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161 outgroup = parser.add_mutually_exclusive_group()
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162 outgroup.add_argument(
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163 "--move-outputs",
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164 action="store_const",
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165 const="move",
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166 default="move",
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167 help="Move output files to the workflow output directory and delete "
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168 "intermediate output directories (default).",
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169 dest="move_outputs",
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170 )
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171
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172 outgroup.add_argument(
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173 "--leave-outputs",
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174 action="store_const",
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175 const="leave",
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176 default="move",
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177 help="Leave output files in intermediate output directories.",
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178 dest="move_outputs",
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179 )
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180
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181 outgroup.add_argument(
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182 "--copy-outputs",
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183 action="store_const",
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184 const="copy",
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185 default="move",
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186 help="Copy output files to the workflow output directory and don't "
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187 "delete intermediate output directories.",
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188 dest="move_outputs",
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189 )
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190
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191 pullgroup = parser.add_mutually_exclusive_group()
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192 pullgroup.add_argument(
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193 "--enable-pull",
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194 default=True,
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195 action="store_true",
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196 help="Try to pull Docker images",
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197 dest="pull_image",
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198 )
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199
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200 pullgroup.add_argument(
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201 "--disable-pull",
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202 default=True,
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203 action="store_false",
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204 help="Do not try to pull Docker images",
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205 dest="pull_image",
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206 )
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207
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208 parser.add_argument(
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209 "--rdf-serializer",
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210 help="Output RDF serialization format used by --print-rdf (one of "
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211 "turtle (default), n3, nt, xml)",
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212 default="turtle",
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213 )
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214
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215 parser.add_argument(
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216 "--eval-timeout",
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217 help="Time to wait for a Javascript expression to evaluate before giving "
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218 "an error, default 20s.",
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219 type=float,
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220 default=20,
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221 )
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222
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223 provgroup = parser.add_argument_group(
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224 "Options for recording provenance information of the execution"
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225 )
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226 provgroup.add_argument(
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227 "--provenance",
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228 help="Save provenance to specified folder as a "
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229 "Research Object that captures and aggregates "
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230 "workflow execution and data products.",
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231 type=str,
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232 )
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233
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234 provgroup.add_argument(
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235 "--enable-user-provenance",
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236 default=False,
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237 action="store_true",
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238 help="Record user account info as part of provenance.",
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239 dest="user_provenance",
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240 )
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241 provgroup.add_argument(
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242 "--disable-user-provenance",
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243 default=False,
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244 action="store_false",
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245 help="Do not record user account info in provenance.",
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246 dest="user_provenance",
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247 )
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248 provgroup.add_argument(
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249 "--enable-host-provenance",
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250 default=False,
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251 action="store_true",
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252 help="Record host info as part of provenance.",
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253 dest="host_provenance",
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254 )
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255 provgroup.add_argument(
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256 "--disable-host-provenance",
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257 default=False,
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258 action="store_false",
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259 help="Do not record host info in provenance.",
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260 dest="host_provenance",
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261 )
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262 provgroup.add_argument(
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parents:
diff changeset
263 "--orcid",
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264 help="Record user ORCID identifier as part of "
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265 "provenance, e.g. https://orcid.org/0000-0002-1825-0097 "
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266 "or 0000-0002-1825-0097. Alternatively the environment variable "
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267 "ORCID may be set.",
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268 dest="orcid",
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269 default=os.environ.get("ORCID", ""),
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270 type=str,
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271 )
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272 provgroup.add_argument(
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273 "--full-name",
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274 help="Record full name of user as part of provenance, "
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275 "e.g. Josiah Carberry. You may need to use shell quotes to preserve "
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276 "spaces. Alternatively the environment variable CWL_FULL_NAME may "
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277 "be set.",
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278 dest="cwl_full_name",
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279 default=os.environ.get("CWL_FULL_NAME", ""),
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280 type=str,
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281 )
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282
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283 printgroup = parser.add_mutually_exclusive_group()
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284 printgroup.add_argument(
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285 "--print-rdf",
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286 action="store_true",
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287 help="Print corresponding RDF graph for workflow and exit",
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288 )
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289 printgroup.add_argument(
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290 "--print-dot",
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291 action="store_true",
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292 help="Print workflow visualization in graphviz format and exit",
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293 )
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294 printgroup.add_argument(
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295 "--print-pre",
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296 action="store_true",
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297 help="Print CWL document after preprocessing.",
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298 )
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299 printgroup.add_argument(
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300 "--print-deps", action="store_true", help="Print CWL document dependencies."
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301 )
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302 printgroup.add_argument(
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303 "--print-input-deps",
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304 action="store_true",
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parents:
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305 help="Print input object document dependencies.",
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306 )
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307 printgroup.add_argument(
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308 "--pack",
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309 action="store_true",
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310 help="Combine components into single document and print.",
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311 )
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312 printgroup.add_argument(
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313 "--version", action="store_true", help="Print version and exit"
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314 )
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315 printgroup.add_argument(
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316 "--validate", action="store_true", help="Validate CWL document only."
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317 )
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318 printgroup.add_argument(
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319 "--print-supported-versions",
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320 action="store_true",
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321 help="Print supported CWL specs.",
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322 )
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323 printgroup.add_argument(
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324 "--print-subgraph",
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325 action="store_true",
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326 help="Print workflow subgraph that will execute. Can combined with "
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327 "--target or --single-step",
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328 )
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329 printgroup.add_argument(
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330 "--print-targets", action="store_true", help="Print targets (output parameters)"
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331 )
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332 printgroup.add_argument(
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333 "--make-template", action="store_true", help="Generate a template input object"
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334 )
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335
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336 strictgroup = parser.add_mutually_exclusive_group()
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337 strictgroup.add_argument(
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338 "--strict",
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339 action="store_true",
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340 help="Strict validation (unrecognized or out of place fields are error)",
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341 default=True,
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342 dest="strict",
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343 )
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344 strictgroup.add_argument(
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345 "--non-strict",
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346 action="store_false",
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347 help="Lenient validation (ignore unrecognized fields)",
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348 default=True,
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349 dest="strict",
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350 )
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351
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352 parser.add_argument(
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353 "--skip-schemas",
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354 action="store_true",
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355 help="Skip loading of schemas",
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356 default=False,
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357 dest="skip_schemas",
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358 )
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359
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360 doccachegroup = parser.add_mutually_exclusive_group()
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361 doccachegroup.add_argument(
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362 "--no-doc-cache",
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363 action="store_false",
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364 help="Disable disk cache for documents loaded over HTTP",
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365 default=True,
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366 dest="doc_cache",
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367 )
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368 doccachegroup.add_argument(
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369 "--doc-cache",
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370 action="store_true",
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371 help="Enable disk cache for documents loaded over HTTP",
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372 default=True,
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373 dest="doc_cache",
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374 )
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375
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376 volumegroup = parser.add_mutually_exclusive_group()
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377 volumegroup.add_argument("--verbose", action="store_true", help="Default logging")
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378 volumegroup.add_argument(
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379 "--quiet", action="store_true", help="Only print warnings and errors."
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380 )
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381 volumegroup.add_argument(
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382 "--debug", action="store_true", help="Print even more logging"
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383 )
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384
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385 parser.add_argument(
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386 "--strict-memory-limit",
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387 action="store_true",
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388 help="When running with "
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diff changeset
389 "software containers and the Docker engine, pass either the "
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390 "calculated memory allocation from ResourceRequirements or the "
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391 "default of 1 gigabyte to Docker's --memory option.",
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392 )
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diff changeset
393
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394 parser.add_argument(
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parents:
diff changeset
395 "--timestamps",
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diff changeset
396 action="store_true",
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397 help="Add timestamps to the errors, warnings, and notifications.",
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398 )
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diff changeset
399 parser.add_argument(
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diff changeset
400 "--js-console", action="store_true", help="Enable javascript console output"
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401 )
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diff changeset
402 parser.add_argument(
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parents:
diff changeset
403 "--disable-js-validation",
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parents:
diff changeset
404 action="store_true",
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parents:
diff changeset
405 help="Disable javascript validation.",
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parents:
diff changeset
406 )
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diff changeset
407 parser.add_argument(
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diff changeset
408 "--js-hint-options-file",
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409 type=str,
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410 help="File of options to pass to jshint. "
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diff changeset
411 'This includes the added option "includewarnings". ',
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412 )
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413 dockergroup = parser.add_mutually_exclusive_group()
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414 dockergroup.add_argument(
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415 "--user-space-docker-cmd",
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416 metavar="CMD",
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417 help="(Linux/OS X only) Specify the path to udocker. Implies --udocker",
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418 )
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419 dockergroup.add_argument(
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420 "--udocker",
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421 help="(Linux/OS X only) Use the udocker runtime for running containers "
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422 "(equivalent to --user-space-docker-cmd=udocker).",
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423 action="store_const",
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424 const="udocker",
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425 dest="user_space_docker_cmd",
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426 )
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diff changeset
427
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428 dockergroup.add_argument(
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429 "--singularity",
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parents:
diff changeset
430 action="store_true",
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431 default=False,
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432 help="[experimental] Use "
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diff changeset
433 "Singularity runtime for running containers. "
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434 "Requires Singularity v2.6.1+ and Linux with kernel "
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435 "version v3.18+ or with overlayfs support "
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diff changeset
436 "backported.",
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437 )
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438 dockergroup.add_argument(
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439 "--no-container",
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diff changeset
440 action="store_false",
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441 default=True,
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442 help="Do not execute jobs in a "
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443 "Docker container, even when `DockerRequirement` "
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diff changeset
444 "is specified under `hints`.",
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445 dest="use_container",
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446 )
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447
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448 dependency_resolvers_configuration_help = argparse.SUPPRESS
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449 dependencies_directory_help = argparse.SUPPRESS
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450 use_biocontainers_help = argparse.SUPPRESS
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451 conda_dependencies = argparse.SUPPRESS
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452
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453 if SOFTWARE_REQUIREMENTS_ENABLED:
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454 dependency_resolvers_configuration_help = "Dependency resolver "
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455 "configuration file describing how to adapt 'SoftwareRequirement' "
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diff changeset
456 "packages to current system."
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457 dependencies_directory_help = (
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458 "Defaut root directory used by dependency resolvers configuration."
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459 )
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460 use_biocontainers_help = "Use biocontainers for tools without an "
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461 "explicitly annotated Docker container."
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462 conda_dependencies = (
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463 "Short cut to use Conda to resolve 'SoftwareRequirement' packages."
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464 )
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465
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466 parser.add_argument(
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467 "--beta-dependency-resolvers-configuration",
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468 default=None,
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469 help=dependency_resolvers_configuration_help,
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470 )
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471 parser.add_argument(
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472 "--beta-dependencies-directory", default=None, help=dependencies_directory_help
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473 )
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474 parser.add_argument(
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diff changeset
475 "--beta-use-biocontainers",
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476 default=None,
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477 help=use_biocontainers_help,
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diff changeset
478 action="store_true",
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479 )
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480 parser.add_argument(
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diff changeset
481 "--beta-conda-dependencies",
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482 default=None,
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483 help=conda_dependencies,
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parents:
diff changeset
484 action="store_true",
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parents:
diff changeset
485 )
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486
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487 parser.add_argument(
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488 "--tool-help", action="store_true", help="Print command line help for tool"
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489 )
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490
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491 parser.add_argument(
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492 "--relative-deps",
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493 choices=["primary", "cwd"],
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494 default="primary",
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495 help="When using --print-deps, print paths "
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496 "relative to primary file or current working directory.",
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497 )
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498
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499 parser.add_argument(
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500 "--enable-dev",
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501 action="store_true",
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502 help="Enable loading and running unofficial development versions of "
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503 "the CWL standards.",
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504 default=False,
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505 )
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506
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507 parser.add_argument(
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508 "--enable-ext",
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509 action="store_true",
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510 help="Enable loading and running 'cwltool:' extensions to the CWL standards.",
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511 default=False,
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512 )
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513
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514 colorgroup = parser.add_mutually_exclusive_group()
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515 colorgroup.add_argument(
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516 "--enable-color",
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517 action="store_true",
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diff changeset
518 help="Enable logging color (default enabled)",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
519 default=not onWindows(),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
520 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
521 colorgroup.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
522 "--disable-color",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
523 action="store_false",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
524 dest="enable_color",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
525 help="Disable colored logging (default false)",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
526 default=onWindows(),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
527 )
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shellac
parents:
diff changeset
528
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shellac
parents:
diff changeset
529 parser.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
530 "--default-container",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
531 help="Specify a default software container to use for any "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
532 "CommandLineTool without a DockerRequirement.",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
533 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
534 parser.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
535 "--no-match-user",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
536 action="store_true",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
537 help="Disable passing the current uid to `docker run --user`",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
538 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
539 parser.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
540 "--custom-net",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
541 type=str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
542 help="Passed to `docker run` as the '--net' parameter when "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
543 "NetworkAccess is true, which is its default setting.",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
544 )
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shellac
parents:
diff changeset
545 parser.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
546 "--disable-validate",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
547 dest="do_validate",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
548 action="store_false",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
549 default=True,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
550 help=argparse.SUPPRESS,
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shellac
parents:
diff changeset
551 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
552
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shellac
parents:
diff changeset
553 reggroup = parser.add_mutually_exclusive_group()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
554 reggroup.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
555 "--enable-ga4gh-tool-registry",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
556 action="store_true",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
557 help="Enable tool resolution using GA4GH tool registry API",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
558 dest="enable_ga4gh_tool_registry",
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shellac
parents:
diff changeset
559 default=True,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
560 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
561 reggroup.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
562 "--disable-ga4gh-tool-registry",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
563 action="store_false",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
564 help="Disable tool resolution using GA4GH tool registry API",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
565 dest="enable_ga4gh_tool_registry",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
566 default=True,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
567 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
568
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
569 parser.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
570 "--add-ga4gh-tool-registry",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
571 action="append",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
572 help="Add a GA4GH tool registry endpoint to use for resolution, default %s"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
573 % ga4gh_tool_registries,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
574 dest="ga4gh_tool_registries",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
575 default=[],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
576 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
577
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
578 parser.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
579 "--on-error",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
580 help="Desired workflow behavior when a step fails. One of 'stop' (do "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
581 "not submit any more steps) or 'continue' (may submit other steps that "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
582 "are not downstream from the error). Default is 'stop'.",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
583 default="stop",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
584 choices=("stop", "continue"),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
585 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
586
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
587 checkgroup = parser.add_mutually_exclusive_group()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
588 checkgroup.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
589 "--compute-checksum",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
590 action="store_true",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
591 default=True,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
592 help="Compute checksum of contents while collecting outputs",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
593 dest="compute_checksum",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
594 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
595 checkgroup.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
596 "--no-compute-checksum",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
597 action="store_false",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
598 help="Do not compute checksum of contents while collecting outputs",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
599 dest="compute_checksum",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
600 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
601
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
602 parser.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
603 "--relax-path-checks",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
604 action="store_true",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
605 default=False,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
606 help="Relax requirements on path names to permit "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
607 "spaces and hash characters.",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
608 dest="relax_path_checks",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
609 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
610
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
611 parser.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
612 "--force-docker-pull",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
613 action="store_true",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
614 default=False,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
615 help="Pull latest software container image even if it is locally present",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
616 dest="force_docker_pull",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
617 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
618 parser.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
619 "--no-read-only",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
620 action="store_true",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
621 default=False,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
622 help="Do not set root directory in the container as read-only",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
623 dest="no_read_only",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
624 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
625
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
626 parser.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
627 "--overrides",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
628 type=str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
629 default=None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
630 help="Read process requirement overrides from file.",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
631 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
632
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
633 subgroup = parser.add_mutually_exclusive_group()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
634 subgroup.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
635 "--target",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
636 "-t",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
637 action="append",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
638 help="Only execute steps that contribute to listed targets (can be "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
639 "provided more than once).",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
640 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
641 subgroup.add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
642 "--single-step",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
643 type=str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
644 default=None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
645 help="Only executes a single step in a workflow. The input object must "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
646 "match that step's inputs. Can be combined with --print-subgraph.",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
647 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
648
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649 parser.add_argument(
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650 "--mpi-config-file",
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651 type=str,
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652 default=None,
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653 help="Platform specific configuration for MPI (parallel launcher, its "
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654 "flag etc). See README section 'Running MPI-based tools' for details "
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diff changeset
655 "of the format.",
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656 )
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657
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658 parser.add_argument(
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659 "workflow",
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660 type=str,
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661 nargs="?",
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662 default=None,
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663 metavar="cwl_document",
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664 help="path or URL to a CWL Workflow, "
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665 "CommandLineTool, or ExpressionTool. If the `inputs_object` has a "
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666 "`cwl:tool` field indicating the path or URL to the cwl_document, "
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667 " then the `cwl_document` argument is optional.",
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668 )
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669 parser.add_argument(
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670 "job_order",
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671 nargs=argparse.REMAINDER,
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672 metavar="inputs_object",
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673 help="path or URL to a YAML or JSON "
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674 "formatted description of the required input values for the given "
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675 "`cwl_document`.",
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676 )
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677
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678 return parser
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679
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680
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681 def get_default_args() -> Dict[str, Any]:
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682 """Get default values of cwltool's command line options."""
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683 ap = arg_parser()
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684 args = ap.parse_args([])
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685 return vars(args)
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686
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687
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688 class FSAction(argparse.Action):
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689 objclass = None # type: str
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690
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691 def __init__(
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692 self, option_strings: List[str], dest: str, nargs: Any = None, **kwargs: Any
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693 ) -> None:
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694 """Fail if nargs is used."""
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695 if nargs is not None:
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696 raise ValueError("nargs not allowed")
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697 super().__init__(option_strings, dest, **kwargs)
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698
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699 def __call__(
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700 self,
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701 parser: argparse.ArgumentParser,
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702 namespace: argparse.Namespace,
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703 values: Union[AnyStr, Sequence[Any], None],
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704 option_string: Optional[str] = None,
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parents:
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705 ) -> None:
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parents:
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706 setattr(
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707 namespace,
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708 self.dest,
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709 {
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710 "class": self.objclass,
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711 "location": file_uri(str(os.path.abspath(cast(AnyStr, values)))),
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712 },
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713 )
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714
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715
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716 class FSAppendAction(argparse.Action):
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717 objclass = None # type: str
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718
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719 def __init__(
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720 self, option_strings: List[str], dest: str, nargs: Any = None, **kwargs: Any
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721 ) -> None:
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722 """Initialize."""
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723 if nargs is not None:
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724 raise ValueError("nargs not allowed")
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725 super().__init__(option_strings, dest, **kwargs)
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diff changeset
726
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727 def __call__(
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728 self,
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729 parser: argparse.ArgumentParser,
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diff changeset
730 namespace: argparse.Namespace,
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731 values: Union[AnyStr, Sequence[Any], None],
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diff changeset
732 option_string: Optional[str] = None,
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parents:
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733 ) -> None:
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734 g = getattr(namespace, self.dest)
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735 if not g:
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736 g = []
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737 setattr(namespace, self.dest, g)
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738 g.append(
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739 {
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740 "class": self.objclass,
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741 "location": file_uri(str(os.path.abspath(cast(AnyStr, values)))),
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742 }
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743 )
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744
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745
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746 class FileAction(FSAction):
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747 objclass = "File"
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748
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749
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750 class DirectoryAction(FSAction):
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751 objclass = "Directory"
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752
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753
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754 class FileAppendAction(FSAppendAction):
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755 objclass = "File"
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756
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757
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758 class DirectoryAppendAction(FSAppendAction):
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759 objclass = "Directory"
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760
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761
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762 def add_argument(
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763 toolparser: argparse.ArgumentParser,
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764 name: str,
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765 inptype: Any,
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766 records: List[str],
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767 description: str = "",
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768 default: Any = None,
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769 input_required: bool = True,
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770 ) -> None:
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771 if len(name) == 1:
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772 flag = "-"
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773 else:
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774 flag = "--"
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775
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776 # if input_required is false, don't make the command line
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777 # parameter required.
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778 required = default is None and input_required
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779 if isinstance(inptype, MutableSequence):
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parents:
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780 if inptype[0] == "null":
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parents:
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781 required = False
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782 if len(inptype) == 2:
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parents:
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783 inptype = inptype[1]
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parents:
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784 else:
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parents:
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785 _logger.debug("Can't make command line argument from %s", inptype)
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parents:
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786 return None
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parents:
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787
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parents:
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788 ahelp = description.replace("%", "%%")
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parents:
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789 action = None # type: Optional[Union[argparse.Action, str]]
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parents:
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790 atype = None # type: Any
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791
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792 if inptype == "File":
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793 action = cast(argparse.Action, FileAction)
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parents:
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794 elif inptype == "Directory":
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parents:
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795 action = cast(argparse.Action, DirectoryAction)
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parents:
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796 elif isinstance(inptype, MutableMapping) and inptype["type"] == "array":
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parents:
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797 if inptype["items"] == "File":
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parents:
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798 action = cast(argparse.Action, FileAppendAction)
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parents:
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799 elif inptype["items"] == "Directory":
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800 action = cast(argparse.Action, DirectoryAppendAction)
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801 else:
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802 action = "append"
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803 elif isinstance(inptype, MutableMapping) and inptype["type"] == "enum":
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parents:
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804 atype = str
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parents:
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805 elif isinstance(inptype, MutableMapping) and inptype["type"] == "record":
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parents:
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806 records.append(name)
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parents:
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807 for field in inptype["fields"]:
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parents:
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808 fieldname = name + "." + shortname(field["name"])
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parents:
diff changeset
809 fieldtype = field["type"]
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parents:
diff changeset
810 fielddescription = field.get("doc", "")
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parents:
diff changeset
811 add_argument(toolparser, fieldname, fieldtype, records, fielddescription)
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parents:
diff changeset
812 return
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shellac
parents:
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813 elif inptype == "string":
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parents:
diff changeset
814 atype = str
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parents:
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815 elif inptype == "int":
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parents:
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816 atype = int
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parents:
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817 elif inptype == "double":
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parents:
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818 atype = float
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parents:
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819 elif inptype == "float":
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parents:
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820 atype = float
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821 elif inptype == "boolean":
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parents:
diff changeset
822 action = "store_true"
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parents:
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823 else:
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824 _logger.debug("Can't make command line argument from %s", inptype)
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parents:
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825 return None
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parents:
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826
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parents:
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827 if inptype != "boolean":
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parents:
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828 typekw = {"type": atype}
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parents:
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829 else:
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parents:
diff changeset
830 typekw = {}
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parents:
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831
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parents:
diff changeset
832 toolparser.add_argument(
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parents:
diff changeset
833 flag + name,
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parents:
diff changeset
834 required=required,
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parents:
diff changeset
835 help=ahelp,
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parents:
diff changeset
836 action=action, # type: ignore
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parents:
diff changeset
837 default=default,
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parents:
diff changeset
838 **typekw
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parents:
diff changeset
839 )
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parents:
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840
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841
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parents:
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842 def generate_parser(
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parents:
diff changeset
843 toolparser: argparse.ArgumentParser,
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parents:
diff changeset
844 tool: Process,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
845 namemap: Dict[str, str],
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parents:
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846 records: List[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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847 input_required: bool = True,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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848 ) -> argparse.ArgumentParser:
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shellac
parents:
diff changeset
849 toolparser.description = tool.tool.get("doc", None)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
850 toolparser.add_argument("job_order", nargs="?", help="Job input json file")
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shellac
parents:
diff changeset
851 namemap["job_order"] = "job_order"
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parents:
diff changeset
852
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parents:
diff changeset
853 for inp in tool.tool["inputs"]:
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shellac
parents:
diff changeset
854 name = shortname(inp["id"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
855 namemap[name.replace("-", "_")] = name
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
856 inptype = inp["type"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
857 description = inp.get("doc", "")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
858 default = inp.get("default", None)
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shellac
parents:
diff changeset
859 add_argument(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
860 toolparser, name, inptype, records, description, default, input_required
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
861 )
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parents:
diff changeset
862
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shellac
parents:
diff changeset
863 return toolparser