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annotate env/lib/python3.7/site-packages/cwltool/schemas/v1.0/CommandLineTool.yml @ 2:6af9afd405e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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1 $base: "https://w3id.org/cwl/cwl#"
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2
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3 $namespaces:
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4 cwl: "https://w3id.org/cwl/cwl#"
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5
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6 $graph:
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7
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8 - name: CommandLineToolDoc
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9 type: documentation
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10 doc:
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11 - |
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12 # Common Workflow Language (CWL) Command Line Tool Description, v1.0.2
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13
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14 This version:
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15 * https://w3id.org/cwl/v1.0/
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16
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17 Current version:
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18 * https://w3id.org/cwl/
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19 - "\n\n"
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20 - {$include: contrib.md}
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21 - "\n\n"
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22 - |
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23 # Abstract
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24
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25 A Command Line Tool is a non-interactive executable program that reads
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26 some input, performs a computation, and terminates after producing some
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27 output. Command line programs are a flexible unit of code sharing and
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28 reuse, unfortunately the syntax and input/output semantics among command
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29 line programs is extremely heterogeneous. A common layer for describing
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30 the syntax and semantics of programs can reduce this incidental
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31 complexity by providing a consistent way to connect programs together.
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32 This specification defines the Common Workflow Language (CWL) Command
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33 Line Tool Description, a vendor-neutral standard for describing the
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34 syntax and input/output semantics of command line programs.
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35
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36 - {$include: intro.md}
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37
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38 - |
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39 ## Introduction to CWL Command Line Tool standard v1.0.2
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40
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41 This specification represents the third stable release from the CWL
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42 group. Since the initial v1.0 release, v1.0.2 introduces the following
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43 updates to the CWL Command Line Tool standard. Documents should continue
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44 to use `cwlVersion: v1.0` and existing v1.0 documents remain valid,
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45 however CWL documents that relied on previously undefined or
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46 underspecified behavior may have slightly different behavior in v1.0.2.
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47
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48 * 13 July 2016: Mark `baseCommand` as optional and update descriptive text.
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49 * 14 November 2016: Clarify [SoftwareRequirement](#SoftwareRequirement)
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50 `spec` fields.
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51 * 12 March 2017:
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52 * Mark `default` as not required for link checking.
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53 * Add note that files in InitialWorkDir must have path in output directory.
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54 * Add note that writable: true applies recursively.
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55 * 23 July 2017: (v1.0.1)
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56 * Add clarification about scattering over empty arrays.
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57 * Clarify interpretation of `secondaryFiles` on inputs.
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58 * Expanded discussion of semantics of `File` and `Directory` types
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59 * Fixed typo "EMACScript" to "ECMAScript"
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60 * Clarified application of input parameter default values when the input is `null` or undefined.
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61 * Clarified valid types and meaning of the format field on inputs versus outputs
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62 * Clarify that command line arguments must not interpreted as shell except when shellQuote: false
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63 * Clarify behavior of `entryname`
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64 * 10 August 2017: (v1.0.2)
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65 * Clarify behavior resolving expressions in `secondaryFile`
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66
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67 Since draft-3, v1.0 introduces the following changes and additions
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68 to the CWL Command Line Tool standard:
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69
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70 * The [Directory](#Directory) type.
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71 * Syntax simplifcations: denoted by the `map<>` syntax. Example: inputs
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72 contains a list of items, each with an id. Now one can specify
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73 a mapping of that identifier to the corresponding
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74 `CommandInputParamater`.
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75 ```
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76 inputs:
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77 - id: one
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78 type: string
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79 doc: First input parameter
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80 - id: two
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81 type: int
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82 doc: Second input parameter
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83 ```
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84 can be
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85 ```
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86 inputs:
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87 one:
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88 type: string
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89 doc: First input parameter
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90 two:
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91 type: int
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92 doc: Second input parameter
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93 ```
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94 * [InitialWorkDirRequirement](#InitialWorkDirRequirement): list of
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95 files and subdirectories to be present in the output directory prior
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96 to execution.
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97 * Shortcuts for specifying the standard [output](#stdout) and/or
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98 [error](#stderr) streams as a (streamable) File output.
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99 * [SoftwareRequirement](#SoftwareRequirement) for describing software
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100 dependencies of a tool.
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101 * The common `description` field has been renamed to `doc`.
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102
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103
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104 ## Purpose
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105
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106 Standalone programs are a flexible and interoperable form of code reuse.
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107 Unlike monolithic applications, applications and analysis workflows which
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108 are composed of multiple separate programs can be written in multiple
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109 languages and execute concurrently on multiple hosts. However, POSIX
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110 does not dictate computer-readable grammar or semantics for program input
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111 and output, resulting in extremely heterogeneous command line grammar and
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112 input/output semantics among program. This is a particular problem in
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113 distributed computing (multi-node compute clusters) and virtualized
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114 environments (such as Docker containers) where it is often necessary to
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115 provision resources such as input files before executing the program.
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116
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117 Often this gap is filled by hard coding program invocation and
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118 implicitly assuming requirements will be met, or abstracting program
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119 invocation with wrapper scripts or descriptor documents. Unfortunately,
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120 where these approaches are application or platform specific it creates a
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121 significant barrier to reproducibility and portability, as methods
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122 developed for one platform must be manually ported to be used on new
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123 platforms. Similarly it creates redundant work, as wrappers for popular
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124 tools must be rewritten for each application or platform in use.
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125
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126 The Common Workflow Language Command Line Tool Description is designed to
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127 provide a common standard description of grammar and semantics for
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128 invoking programs used in data-intensive fields such as Bioinformatics,
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129 Chemistry, Physics, Astronomy, and Statistics. This specification
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130 defines a precise data and execution model for Command Line Tools that
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131 can be implemented on a variety of computing platforms, ranging from a
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132 single workstation to cluster, grid, cloud, and high performance
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133 computing platforms.
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134
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135 - {$include: concepts.md}
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136 - {$include: invocation.md}
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137
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138
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139 - type: record
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140 name: EnvironmentDef
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141 doc: |
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142 Define an environment variable that will be set in the runtime environment
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143 by the workflow platform when executing the command line tool. May be the
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144 result of executing an expression, such as getting a parameter from input.
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145 fields:
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146 - name: envName
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147 type: string
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148 doc: The environment variable name
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149 - name: envValue
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150 type: [string, Expression]
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151 doc: The environment variable value
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152
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153 - type: record
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154 name: CommandLineBinding
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155 extends: InputBinding
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156 doc: |
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157
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158 When listed under `inputBinding` in the input schema, the term
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159 "value" refers to the the corresponding value in the input object. For
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160 binding objects listed in `CommandLineTool.arguments`, the term "value"
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161 refers to the effective value after evaluating `valueFrom`.
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162
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163 The binding behavior when building the command line depends on the data
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164 type of the value. If there is a mismatch between the type described by
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165 the input schema and the effective value, such as resulting from an
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166 expression evaluation, an implementation must use the data type of the
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167 effective value.
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168
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169 - **string**: Add `prefix` and the string to the command line.
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170
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171 - **number**: Add `prefix` and decimal representation to command line.
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172
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173 - **boolean**: If true, add `prefix` to the command line. If false, add
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174 nothing.
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175
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176 - **File**: Add `prefix` and the value of
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177 [`File.path`](#File) to the command line.
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178
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179 - **array**: If `itemSeparator` is specified, add `prefix` and the join
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180 the array into a single string with `itemSeparator` separating the
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181 items. Otherwise first add `prefix`, then recursively process
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182 individual elements.
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183
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184 - **object**: Add `prefix` only, and recursively add object fields for
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185 which `inputBinding` is specified.
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186
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187 - **null**: Add nothing.
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188
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189 fields:
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190 - name: position
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191 type: int?
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192 doc: "The sorting key. Default position is 0."
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193 - name: prefix
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194 type: string?
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195 doc: "Command line prefix to add before the value."
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196 - name: separate
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197 type: boolean?
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198 doc: |
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199 If true (default), then the prefix and value must be added as separate
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200 command line arguments; if false, prefix and value must be concatenated
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201 into a single command line argument.
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202 - name: itemSeparator
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203 type: string?
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204 doc: |
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205 Join the array elements into a single string with the elements
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206 separated by by `itemSeparator`.
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207 - name: valueFrom
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208 type:
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209 - "null"
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210 - string
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211 - Expression
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212 jsonldPredicate: "cwl:valueFrom"
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213 doc: |
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214 If `valueFrom` is a constant string value, use this as the value and
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215 apply the binding rules above.
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216
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217 If `valueFrom` is an expression, evaluate the expression to yield the
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218 actual value to use to build the command line and apply the binding
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219 rules above. If the inputBinding is associated with an input
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220 parameter, the value of `self` in the expression will be the value of
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221 the input parameter. Input parameter defaults (as specified by the
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222 `InputParameter.default` field) must be applied before evaluating the
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223 expression.
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224
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225 When a binding is part of the `CommandLineTool.arguments` field,
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226 the `valueFrom` field is required.
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227
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228 - name: shellQuote
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229 type: boolean?
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230 doc: |
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231 If `ShellCommandRequirement` is in the requirements for the current command,
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232 this controls whether the value is quoted on the command line (default is true).
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233 Use `shellQuote: false` to inject metacharacters for operations such as pipes.
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234
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235 If `shellQuote` is true or not provided, the implementation must not
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236 permit interpretation of any shell metacharacters or directives.
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237
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238 - type: record
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239 name: CommandOutputBinding
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240 extends: OutputBinding
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241 doc: |
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242 Describes how to generate an output parameter based on the files produced
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243 by a CommandLineTool.
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244
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245 The output parameter value is generated by applying these operations in the
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246 following order:
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247
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248 - glob
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249 - loadContents
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250 - outputEval
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251 - secondaryFiles
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252 fields:
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253 - name: glob
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254 type:
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255 - "null"
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256 - string
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257 - Expression
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258 - type: array
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259 items: string
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260 doc: |
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261 Find files relative to the output directory, using POSIX glob(3)
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262 pathname matching. If an array is provided, find files that match any
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263 pattern in the array. If an expression is provided, the expression must
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264 return a string or an array of strings, which will then be evaluated as
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265 one or more glob patterns. Must only match and return files which
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266 actually exist.
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267 - name: loadContents
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268 type:
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269 - "null"
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270 - boolean
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271 jsonldPredicate: "cwl:loadContents"
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272 doc: |
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273 For each file matched in `glob`, read up to
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274 the first 64 KiB of text from the file and place it in the `contents`
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275 field of the file object for manipulation by `outputEval`.
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276 - name: outputEval
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277 type:
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278 - "null"
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279 - string
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280 - Expression
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281 doc: |
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282 Evaluate an expression to generate the output value. If `glob` was
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283 specified, the value of `self` must be an array containing file objects
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284 that were matched. If no files were matched, `self` must be a zero
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285 length array; if a single file was matched, the value of `self` is an
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286 array of a single element. Additionally, if `loadContents` is `true`,
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287 the File objects must include up to the first 64 KiB of file contents
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288 in the `contents` field.
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289
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290
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291 - name: CommandInputRecordField
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292 type: record
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293 extends: InputRecordField
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294 specialize:
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295 - specializeFrom: InputRecordSchema
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296 specializeTo: CommandInputRecordSchema
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297 - specializeFrom: InputEnumSchema
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298 specializeTo: CommandInputEnumSchema
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299 - specializeFrom: InputArraySchema
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300 specializeTo: CommandInputArraySchema
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301 - specializeFrom: InputBinding
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302 specializeTo: CommandLineBinding
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303
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304
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305 - name: CommandInputRecordSchema
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306 type: record
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307 extends: InputRecordSchema
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308 specialize:
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309 - specializeFrom: InputRecordField
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310 specializeTo: CommandInputRecordField
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311
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312
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313 - name: CommandInputEnumSchema
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314 type: record
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315 extends: InputEnumSchema
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316 specialize:
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317 - specializeFrom: InputBinding
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318 specializeTo: CommandLineBinding
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319
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320
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321 - name: CommandInputArraySchema
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322 type: record
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323 extends: InputArraySchema
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324 specialize:
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325 - specializeFrom: InputRecordSchema
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326 specializeTo: CommandInputRecordSchema
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327 - specializeFrom: InputEnumSchema
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328 specializeTo: CommandInputEnumSchema
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329 - specializeFrom: InputArraySchema
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330 specializeTo: CommandInputArraySchema
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331 - specializeFrom: InputBinding
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332 specializeTo: CommandLineBinding
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333
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334
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335 - name: CommandOutputRecordField
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336 type: record
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337 extends: OutputRecordField
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338 specialize:
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339 - specializeFrom: OutputRecordSchema
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340 specializeTo: CommandOutputRecordSchema
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341 - specializeFrom: OutputEnumSchema
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342 specializeTo: CommandOutputEnumSchema
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343 - specializeFrom: OutputArraySchema
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344 specializeTo: CommandOutputArraySchema
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345 - specializeFrom: OutputBinding
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346 specializeTo: CommandOutputBinding
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347
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348
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349 - name: CommandOutputRecordSchema
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350 type: record
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351 extends: OutputRecordSchema
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352 specialize:
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353 - specializeFrom: OutputRecordField
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354 specializeTo: CommandOutputRecordField
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355
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356
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357 - name: CommandOutputEnumSchema
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358 type: record
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359 extends: OutputEnumSchema
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360 specialize:
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361 - specializeFrom: OutputRecordSchema
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362 specializeTo: CommandOutputRecordSchema
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363 - specializeFrom: OutputEnumSchema
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364 specializeTo: CommandOutputEnumSchema
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365 - specializeFrom: OutputArraySchema
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366 specializeTo: CommandOutputArraySchema
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367 - specializeFrom: OutputBinding
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368 specializeTo: CommandOutputBinding
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369
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370
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371 - name: CommandOutputArraySchema
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372 type: record
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373 extends: OutputArraySchema
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374 specialize:
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375 - specializeFrom: OutputRecordSchema
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376 specializeTo: CommandOutputRecordSchema
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377 - specializeFrom: OutputEnumSchema
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378 specializeTo: CommandOutputEnumSchema
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379 - specializeFrom: OutputArraySchema
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380 specializeTo: CommandOutputArraySchema
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381 - specializeFrom: OutputBinding
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382 specializeTo: CommandOutputBinding
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383
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384
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385 - type: record
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386 name: CommandInputParameter
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387 extends: InputParameter
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388 doc: An input parameter for a CommandLineTool.
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389 specialize:
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390 - specializeFrom: InputRecordSchema
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391 specializeTo: CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
392 - specializeFrom: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
393 specializeTo: CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
394 - specializeFrom: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
395 specializeTo: CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
396 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
397 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
398
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
399 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
400 name: CommandOutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
401 extends: OutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
402 doc: An output parameter for a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
403 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
404 - specializeFrom: OutputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
405 specializeTo: CommandOutputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
406 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
407 - name: type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
408 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
409 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
410 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
411 - stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
412 - stderr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
413 - CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
414 - CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
415 - CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
416 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
417 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
418 items:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
419 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
420 - CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
421 - CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
422 - CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
423 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
424 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
425 "_id": "sld:type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
426 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
427 refScope: 2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
428 typeDSL: True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
429 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
430 Specify valid types of data that may be assigned to this parameter.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
431
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
432 - name: stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
433 type: enum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
434 symbols: [ "cwl:stdout" ]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
435 docParent: "#CommandOutputParameter"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
436 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
437 Only valid as a `type` for a `CommandLineTool` output with no
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
438 `outputBinding` set.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
439
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
440 The following
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
441 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
442 outputs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
443 an_output_name:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
444 type: stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
445
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
446 stdout: a_stdout_file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
447 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
448 is equivalent to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
449 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
450 outputs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
451 an_output_name:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
452 type: File
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
453 streamable: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
454 outputBinding:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
455 glob: a_stdout_file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
456
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
457 stdout: a_stdout_file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
458 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
459
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
460 If there is no `stdout` name provided, a random filename will be created.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
461 For example, the following
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
462 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
463 outputs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
464 an_output_name:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
465 type: stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
466 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
467 is equivalent to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
468 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
469 outputs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
470 an_output_name:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
471 type: File
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
472 streamable: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
473 outputBinding:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
474 glob: random_stdout_filenameABCDEFG
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
475
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
476 stdout: random_stdout_filenameABCDEFG
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
477 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
478
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
479
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
480 - name: stderr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
481 type: enum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
482 symbols: [ "cwl:stderr" ]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
483 docParent: "#CommandOutputParameter"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
484 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
485 Only valid as a `type` for a `CommandLineTool` output with no
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
486 `outputBinding` set.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
487
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
488 The following
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
489 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
490 outputs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
491 an_output_name:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
492 type: stderr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
493
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
494 stderr: a_stderr_file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
495 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
496 is equivalent to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
497 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
498 outputs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
499 an_output_name:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
500 type: File
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
501 streamable: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
502 outputBinding:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
503 glob: a_stderr_file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
504
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
505 stderr: a_stderr_file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
506 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
507
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
508 If there is no `stderr` name provided, a random filename will be created.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
509 For example, the following
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
510 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
511 outputs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
512 an_output_name:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
513 type: stderr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
514 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
515 is equivalent to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
516 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
517 outputs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
518 an_output_name:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
519 type: File
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
520 streamable: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
521 outputBinding:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
522 glob: random_stderr_filenameABCDEFG
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
523
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
524 stderr: random_stderr_filenameABCDEFG
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
525 ```
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
526
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
527
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
528 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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diff changeset
529 name: CommandLineTool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
530 extends: Process
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
531 documentRoot: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
532 specialize:
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diff changeset
533 - specializeFrom: InputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
534 specializeTo: CommandInputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
535 - specializeFrom: OutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
536 specializeTo: CommandOutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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537 doc: |
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diff changeset
538 This defines the schema of the CWL Command Line Tool Description document.
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539
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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540 fields:
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parents:
diff changeset
541 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
542 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
543 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
544 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
545 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
546 - name: baseCommand
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
547 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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548 Specifies the program to execute. If an array, the first element of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
549 the array is the command to execute, and subsequent elements are
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
550 mandatory command line arguments. The elements in `baseCommand` must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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551 appear before any command line bindings from `inputBinding` or
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diff changeset
552 `arguments`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
553
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
554 If `baseCommand` is not provided or is an empty array, the first
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
555 element of the command line produced after processing `inputBinding` or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
556 `arguments` must be used as the program to execute.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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557
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
558 If the program includes a path separator character it must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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559 be an absolute path, otherwise it is an error. If the program does not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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560 include a path separator, search the `$PATH` variable in the runtime
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
561 environment of the workflow runner find the absolute path of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
562 executable.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
563 type:
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diff changeset
564 - string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
565 - string[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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566 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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567 "_id": "cwl:baseCommand"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
568 "_container": "@list"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
569 - name: arguments
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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570 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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571 Command line bindings which are not directly associated with input parameters.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
572 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
573 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
574 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
575 items: [string, Expression, CommandLineBinding]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
576 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
577 "_id": "cwl:arguments"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
578 "_container": "@list"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
579 - name: stdin
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
580 type: ["null", string, Expression]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
581 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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582 A path to a file whose contents must be piped into the command's
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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diff changeset
583 standard input stream.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
584 - name: stderr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
585 type: ["null", string, Expression]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
586 jsonldPredicate: "https://w3id.org/cwl/cwl#stderr"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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587 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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588 Capture the command's standard error stream to a file written to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
589 the designated output directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
590
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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591 If `stderr` is a string, it specifies the file name to use.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
592
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
593 If `stderr` is an expression, the expression is evaluated and must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
594 return a string with the file name to use to capture stderr. If the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
595 return value is not a string, or the resulting path contains illegal
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
596 characters (such as the path separator `/`) it is an error.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
597 - name: stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
598 type: ["null", string, Expression]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
599 jsonldPredicate: "https://w3id.org/cwl/cwl#stdout"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
600 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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diff changeset
601 Capture the command's standard output stream to a file written to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
602 the designated output directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
603
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
604 If `stdout` is a string, it specifies the file name to use.
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shellac
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diff changeset
605
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
606 If `stdout` is an expression, the expression is evaluated and must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
607 return a string with the file name to use to capture stdout. If the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
608 return value is not a string, or the resulting path contains illegal
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
609 characters (such as the path separator `/`) it is an error.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
610 - name: successCodes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
611 type: int[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
612 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
613 Exit codes that indicate the process completed successfully.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
614
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
615 - name: temporaryFailCodes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
616 type: int[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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617 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
618 Exit codes that indicate the process failed due to a possibly
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
619 temporary condition, where executing the process with the same
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
620 runtime environment and inputs may produce different results.
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diff changeset
621
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
622 - name: permanentFailCodes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
623 type: int[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
624 doc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
625 Exit codes that indicate the process failed due to a permanent logic
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
626 error, where executing the process with the same runtime environment and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
627 same inputs is expected to always fail.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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628
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
629
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
630 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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631 name: DockerRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
632 extends: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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633 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
634 Indicates that a workflow component should be run in a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
635 [Docker](http://docker.com) container, and specifies how to fetch or build
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parents:
diff changeset
636 the image.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
637
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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638 If a CommandLineTool lists `DockerRequirement` under
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
639 `hints` (or `requirements`), it may (or must) be run in the specified Docker
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
640 container.
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diff changeset
641
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
642 The platform must first acquire or install the correct Docker image as
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
643 specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`.
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644
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
645 The platform must execute the tool in the container using `docker run` with
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diff changeset
646 the appropriate Docker image and tool command line.
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647
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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648 The workflow platform may provide input files and the designated output
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
649 directory through the use of volume bind mounts. The platform may rewrite
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
650 file paths in the input object to correspond to the Docker bind mounted
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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651 locations.
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652
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
653 When running a tool contained in Docker, the workflow platform must not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
654 assume anything about the contents of the Docker container, such as the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
655 presence or absence of specific software, except to assume that the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
656 generated command line represents a valid command within the runtime
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diff changeset
657 environment of the container.
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658
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
659 ## Interaction with other requirements
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
660
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
661 If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
662 DockerRequirement, the environment variables must be provided to Docker
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
663 using `--env` or `--env-file` and interact with the container's preexisting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
664 environment as defined by Docker.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
665
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
666 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
667 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
668 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
669 doc: "Always 'DockerRequirement'"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
670 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
671 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
672 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
673 - name: dockerPull
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
674 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
675 doc: "Specify a Docker image to retrieve using `docker pull`."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
676 - name: dockerLoad
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
677 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
678 doc: "Specify a HTTP URL from which to download a Docker image using `docker load`."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
679 - name: dockerFile
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
680 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
681 doc: "Supply the contents of a Dockerfile which will be built using `docker build`."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
682 - name: dockerImport
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
683 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
684 doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
685 - name: dockerImageId
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
686 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
687 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
688 The image id that will be used for `docker run`. May be a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
689 human-readable image name or the image identifier hash. May be skipped
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
690 if `dockerPull` is specified, in which case the `dockerPull` image id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
691 must be used.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
692 - name: dockerOutputDirectory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
693 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
694 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
695 Set the designated output directory to a specific location inside the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
696 Docker container.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
697
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
698
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
699 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
700 name: SoftwareRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
701 extends: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
702 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
703 A list of software packages that should be configured in the environment of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
704 the defined process.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
705 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
706 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
707 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
708 doc: "Always 'SoftwareRequirement'"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
709 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
710 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
711 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
712 - name: packages
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
713 type: SoftwarePackage[]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
714 doc: "The list of software to be configured."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
715 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
716 mapSubject: package
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
717 mapPredicate: specs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
718
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
719 - name: SoftwarePackage
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
720 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
721 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
722 - name: package
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
723 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
724 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
725 The name of the software to be made available. If the name is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
726 common, inconsistent, or otherwise ambiguous it should be combined with
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
727 one or more identifiers in the `specs` field.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
728 - name: version
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
729 type: string[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
730 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
731 The (optional) versions of the software that are known to be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
732 compatible.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
733 - name: specs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
734 type: string[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
735 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
736 One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
737 identifying resources for installing or enabling the software named in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
738 the `package` field. Implementations may provide resolvers which map
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
739 these software identifer IRIs to some configuration action; or they can
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
740 use only the name from the `package` field on a best effort basis.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
741
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
742 For example, the IRI https://packages.debian.org/bowtie could
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
743 be resolved with `apt-get install bowtie`. The IRI
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
744 https://anaconda.org/bioconda/bowtie could be resolved with `conda
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
745 install -c bioconda bowtie`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
746
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
747 IRIs can also be system independent and used to map to a specific
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
748 software installation or selection mechanism.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
749 Using [RRID](https://www.identifiers.org/rrid/) as an example:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
750 https://identifiers.org/rrid/RRID:SCR_005476
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
751 could be fulfilled using the above mentioned Debian or bioconda
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
752 package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
753 or any other mechanism the platform chooses. IRIs can also be from
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
754 identifer sources that are discipline specific yet still system
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
755 independent. As an example, the equivalent [ELIXIR Tools and Data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
756 Service Registry](https://bio.tools) IRI to the previous RRID example is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
757 https://bio.tools/tool/bowtie2/version/2.2.8.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
758 If supported by a given registry, implementations are encouraged to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
759 query these system independent sofware identifier IRIs directly for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
760 links to packaging systems.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
761
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
762 A site specific IRI can be listed as well. For example, an academic
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
763 computing cluster using Environement Modules could list the IRI
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
764 `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
765 `module load bowtie-tbb/1.1.2` should be executed to make available
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
766 `bowtie` version 1.1.2 compiled with the TBB library prior to running
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
767 the accompanying Workflow or CommandLineTool. Note that the example IRI
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
768 is specific to a particular institution and computing environment as
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
769 the Environment Modules system does not have a common namespace or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
770 standardized naming convention.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
771
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
772 This last example is the least portable and should only be used if
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
773 mechanisms based off of the `package` field or more generic IRIs are
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
774 unavailable or unsuitable. While harmless to other sites, site specific
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
775 software IRIs should be left out of shared CWL descriptions to avoid
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
776 clutter.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
777
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
778 - name: Dirent
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
779 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
780 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
781 Define a file or subdirectory that must be placed in the designated output
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
782 directory prior to executing the command line tool. May be the result of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
783 executing an expression, such as building a configuration file from a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
784 template.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
785 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
786 - name: entryname
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
787 type: ["null", string, Expression]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
788 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
789 _id: cwl:entryname
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
790 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
791 The name of the file or subdirectory to create in the output directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
792 If `entry` is a File or Directory, the `entryname` field overrides the value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
793 of `basename` of the File or Directory object. Optional.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
794 - name: entry
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
795 type: [string, Expression]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
796 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
797 _id: cwl:entry
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
798 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
799 If the value is a string literal or an expression which evaluates to a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
800 string, a new file must be created with the string as the file contents.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
801
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
802 If the value is an expression that evaluates to a `File` object, this
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
803 indicates the referenced file should be added to the designated output
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
804 directory prior to executing the tool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
805
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
806 If the value is an expression that evaluates to a `Dirent` object, this
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
807 indicates that the File or Directory in `entry` should be added to the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
808 designated output directory with the name in `entryname`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
809
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
810 If `writable` is false, the file may be made available using a bind
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
811 mount or file system link to avoid unnecessary copying of the input
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
812 file.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
813 - name: writable
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
814 type: boolean?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
815 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
816 If true, the file or directory must be writable by the tool. Changes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
817 to the file or directory must be isolated and not visible by any other
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
818 CommandLineTool process. This may be implemented by making a copy of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
819 the original file or directory. Default false (files and directories
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
820 read-only by default).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
821
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
822 A directory marked as `writable: true` implies that all files and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
823 subdirectories are recursively writable as well.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
824
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
825
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
826 - name: InitialWorkDirRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
827 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
828 extends: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
829 doc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
830 Define a list of files and subdirectories that must be created by the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
831 workflow platform in the designated output directory prior to executing the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
832 command line tool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
833 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
834 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
835 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
836 doc: InitialWorkDirRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
837 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
838 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
839 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
840 - name: listing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
841 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
842 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
843 items: [File, Directory, Dirent, string, Expression]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
844 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
845 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
846 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
847 _id: "cwl:listing"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
848 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
849 The list of files or subdirectories that must be placed in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
850 designated output directory prior to executing the command line tool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
851
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
852 May be an expression. If so, the expression return value must validate
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
853 as `{type: array, items: [File, Directory]}`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
854
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
855 Files or Directories which are listed in the input parameters and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
856 appear in the `InitialWorkDirRequirement` listing must have their
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
857 `path` set to their staged location in the designated output directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
858 If the same File or Directory appears more than once in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
859 `InitialWorkDirRequirement` listing, the implementation must choose
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
860 exactly one value for `path`; how this value is chosen is undefined.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
861
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
862
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
863 - name: EnvVarRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
864 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
865 extends: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
866 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
867 Define a list of environment variables which will be set in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
868 execution environment of the tool. See `EnvironmentDef` for details.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
869 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
870 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
871 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
872 doc: "Always 'EnvVarRequirement'"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
873 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
874 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
875 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
876 - name: envDef
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
877 type: EnvironmentDef[]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
878 doc: The list of environment variables.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
879 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
880 mapSubject: envName
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
881 mapPredicate: envValue
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
882
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
883
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
884 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
885 name: ShellCommandRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
886 extends: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
887 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
888 Modify the behavior of CommandLineTool to generate a single string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
889 containing a shell command line. Each item in the argument list must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
890 joined into a string separated by single spaces and quoted to prevent
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
891 intepretation by the shell, unless `CommandLineBinding` for that argument
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
892 contains `shellQuote: false`. If `shellQuote: false` is specified, the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
893 argument is joined into the command string without quoting, which allows
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
894 the use of shell metacharacters such as `|` for pipes.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
895 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
896 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
897 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
898 doc: "Always 'ShellCommandRequirement'"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
899 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
900 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
901 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
902
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
903
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
904 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
905 name: ResourceRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
906 extends: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
907 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
908 Specify basic hardware resource requirements.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
909
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
910 "min" is the minimum amount of a resource that must be reserved to schedule
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
911 a job. If "min" cannot be satisfied, the job should not be run.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
912
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
913 "max" is the maximum amount of a resource that the job shall be permitted
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
914 to use. If a node has sufficient resources, multiple jobs may be scheduled
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
915 on a single node provided each job's "max" resource requirements are
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
916 met. If a job attempts to exceed its "max" resource allocation, an
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917 implementation may deny additional resources, which may result in job
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918 failure.
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919
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920 If "min" is specified but "max" is not, then "max" == "min"
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921 If "max" is specified by "min" is not, then "min" == "max".
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922
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923 It is an error if max < min.
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924
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925 It is an error if the value of any of these fields is negative.
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926
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927 If neither "min" nor "max" is specified for a resource, an implementation may provide a default.
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928
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929 fields:
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930 - name: class
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931 type: string
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932 doc: "Always 'ResourceRequirement'"
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933 jsonldPredicate:
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934 "_id": "@type"
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935 "_type": "@vocab"
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936 - name: coresMin
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937 type: ["null", long, string, Expression]
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938 doc: Minimum reserved number of CPU cores
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939
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940 - name: coresMax
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941 type: ["null", int, string, Expression]
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942 doc: Maximum reserved number of CPU cores
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diff changeset
943
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944 - name: ramMin
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945 type: ["null", long, string, Expression]
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946 doc: Minimum reserved RAM in mebibytes (2**20)
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947
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948 - name: ramMax
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diff changeset
949 type: ["null", long, string, Expression]
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950 doc: Maximum reserved RAM in mebibytes (2**20)
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diff changeset
951
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diff changeset
952 - name: tmpdirMin
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953 type: ["null", long, string, Expression]
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954 doc: Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
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955
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956 - name: tmpdirMax
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957 type: ["null", long, string, Expression]
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958 doc: Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
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959
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960 - name: outdirMin
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diff changeset
961 type: ["null", long, string, Expression]
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962 doc: Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
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963
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964 - name: outdirMax
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965 type: ["null", long, string, Expression]
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diff changeset
966 doc: Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)