annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2.0-dev4/CommandLineTool.yml @ 0:4f3585e2f14b draft default tip

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date Mon, 22 Mar 2021 18:12:50 +0000
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1 saladVersion: v1.1
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2 $base: "https://w3id.org/cwl/cwl#"
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3
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4 $namespaces:
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5 cwl: "https://w3id.org/cwl/cwl#"
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6
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7 $graph:
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8
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9 - name: CommandLineToolDoc
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10 type: documentation
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11 doc:
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12 - |
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13 # Common Workflow Language (CWL) Command Line Tool Description, v1.2.0-dev4
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14
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15 This version:
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16 * https://w3id.org/cwl/v1.2.0-dev4/
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17
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18 Current version:
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19 * https://w3id.org/cwl/
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20 - "\n\n"
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21 - {$include: contrib.md}
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22 - "\n\n"
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23 - |
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24 # Abstract
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25
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26 A Command Line Tool is a non-interactive executable program that reads
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27 some input, performs a computation, and terminates after producing some
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28 output. Command line programs are a flexible unit of code sharing and
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29 reuse, unfortunately the syntax and input/output semantics among command
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30 line programs is extremely heterogeneous. A common layer for describing
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31 the syntax and semantics of programs can reduce this incidental
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32 complexity by providing a consistent way to connect programs together.
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33 This specification defines the Common Workflow Language (CWL) Command
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34 Line Tool Description, a vendor-neutral standard for describing the
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35 syntax and input/output semantics of command line programs.
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36
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37 - {$include: intro.md}
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38
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39 - |
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40 ## Introduction to the CWL Command Line Tool standard v1.2.0-dev4
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41
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42 This specification represents the latest development release from the
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43 CWL group. Since the v1.1 release, v1.2.0-dev4 introduces the
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44 following updates to the CWL Command Line Tool standard.
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45 Documents should use `cwlVersion: v1.2.0-dev4` to make use of new
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46 syntax and features introduced in v1.2.0-dev4. Existing v1.1 documents
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47 should be trivially updatable by changing `cwlVersion`, however
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48 CWL documents that relied on previously undefined or
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49 underspecified behavior may have slightly different behavior in
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50 v1.2.0-dev4.
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51
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52 ## Changelog
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53
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54 * `coresMin` and `coresMax` of
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55 [ResourceRequirement](#ResourceRequirement) may now request fractional CPUs.
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56 * `ramMin`, `ramMax`, `tmpdirMin`, `tmpdirMax`, `outdirMin`, and `outdirMax` of
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57 [ResourceRequirement](#ResourceRequirement) now accept floating point values.
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58 * (CommandLineTool)[#CommandLineTool] can now express `intent`
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59 with an identifier for the type of computational operation.
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60 * Added conformance tests for order of operations evaluating `secondaryFiles` on input
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61 and ensure that input and output secondaryFiles expressions can return a File object.
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62 * Clarify there are no limits on the size of file literal `contents`.
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63 * When using `loadContents` it now must fail when attempting to
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64 load a file greater than 64 KiB instead of silently truncating
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65 the data.
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66 * Objects, arrays and numbers returned by parameter references
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67 or expressions in `Dirent.entry` that are not a `File` or
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68 `Directory` object (or array of such) are now specified to be
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69 JSON serialized to produce file contents.
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70 * Note that only enum and record types can be typedef-ed
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71 * Added conformance tests for order of operations evaluating `secondaryFiles` on input
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72 and ensure that input and output secondaryFiles expressions can return a File object.
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73 * Escaping in [string interpolation](#String_Interpolation) has
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74 been added to the specification along with conformance tests.
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75 * It is now possible to have an absolute path in the `entryname`
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76 field in
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77 [InitialWorkDirRequirement](#InitialWorkDirRequirement) when
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78 running in a mandatory container. Together with
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79 `DockerRequirement.dockerOutputDirectory` this it possible to
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80 control the locations of both input and output files when
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81 running in containers.
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82 * Specify default success/fail interpretation of exit codes when not given.
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83
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84 See also the [CWL Workflow Description, v1.2.0-dev4 changelog](Workflow.html#Changelog).
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85 For other changes since CWL v1.0, see the
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86 [CWL Command Line Tool Description, v1.1 changelog](https://www.commonwl.org/v1.1/CommandLineTool.html#Changelog)
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87
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88 ## Purpose
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89
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90 Standalone programs are a flexible and interoperable form of code reuse.
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91 Unlike monolithic applications, applications and analysis workflows which
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92 are composed of multiple separate programs can be written in multiple
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93 languages and execute concurrently on multiple hosts. However, POSIX
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94 does not dictate computer-readable grammar or semantics for program input
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95 and output, resulting in extremely diverse command line grammar and
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96 input/output semantics among programs. This is a particular problem in
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97 distributed computing (multi-node compute clusters) and virtualized
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98 environments (such as Docker containers) where it is often necessary to
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99 provision resources such as input files before executing the program.
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100
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101 Often this gap is filled by hard coding program invocation and
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102 implicitly assuming requirements will be met, or abstracting program
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103 invocation with wrapper scripts or descriptor documents. Unfortunately,
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104 where these approaches are application or platform specific it creates a
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105 significant barrier to reproducibility and portability, as methods
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106 developed for one platform must be manually ported to be used on new
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107 platforms. Similarly it creates redundant work, as wrappers for popular
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108 tools must be rewritten for each application or platform in use.
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109
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110 The Common Workflow Language Command Line Tool Description is designed to
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111 provide a common standard description of grammar and semantics for
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112 invoking programs used in data-intensive fields such as Bioinformatics,
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113 Chemistry, Physics, Astronomy, and Statistics. This specification
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114 attempts to define a precise data and execution model for Command Line Tools that
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115 can be implemented on a variety of computing platforms, ranging from a
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116 single workstation to cluster, grid, cloud, and high performance
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117 computing platforms. Details related to execution of these programs not
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118 laid out in this specification are open to interpretation by the computing
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119 platform implementing this specification.
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120
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121 - {$include: concepts.md}
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122 - {$include: invocation.md}
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123
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124
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125 - type: record
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126 name: EnvironmentDef
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127 doc: |
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128 Define an environment variable that will be set in the runtime environment
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129 by the workflow platform when executing the command line tool. May be the
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130 result of executing an expression, such as getting a parameter from input.
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131 fields:
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132 - name: envName
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133 type: string
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134 doc: The environment variable name
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135 - name: envValue
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136 type: [string, Expression]
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137 doc: The environment variable value
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138
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139 - type: record
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140 name: CommandLineBinding
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141 extends: InputBinding
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142 docParent: "#CommandInputParameter"
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143 doc: |
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144
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145 When listed under `inputBinding` in the input schema, the term
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146 "value" refers to the the corresponding value in the input object. For
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147 binding objects listed in `CommandLineTool.arguments`, the term "value"
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148 refers to the effective value after evaluating `valueFrom`.
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149
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150 The binding behavior when building the command line depends on the data
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151 type of the value. If there is a mismatch between the type described by
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152 the input schema and the effective value, such as resulting from an
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153 expression evaluation, an implementation must use the data type of the
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154 effective value.
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155
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156 - **string**: Add `prefix` and the string to the command line.
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157
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158 - **number**: Add `prefix` and decimal representation to command line.
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159
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160 - **boolean**: If true, add `prefix` to the command line. If false, add
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161 nothing.
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162
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163 - **File**: Add `prefix` and the value of
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164 [`File.path`](#File) to the command line.
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165
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166 - **Directory**: Add `prefix` and the value of
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167 [`Directory.path`](#Directory) to the command line.
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168
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169 - **array**: If `itemSeparator` is specified, add `prefix` and the join
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170 the array into a single string with `itemSeparator` separating the
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171 items. Otherwise first add `prefix`, then recursively process
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172 individual elements.
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173 If the array is empty, it does not add anything to command line.
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174
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175 - **object**: Add `prefix` only, and recursively add object fields for
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176 which `inputBinding` is specified.
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177
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178 - **null**: Add nothing.
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179
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180 fields:
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181 - name: position
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182 type: [ "null", int, Expression ]
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183 doc: |
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184 The sorting key. Default position is 0. If the inputBinding is
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185 associated with an input parameter, then the value of `self` in the
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186 expression will be the value of the input parameter. Input parameter
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187 defaults (as specified by the `InputParameter.default` field) must be
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188 applied before evaluating the expression. Expressions must return a
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189 single value of type int or a null.
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190 - name: prefix
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191 type: string?
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192 doc: "Command line prefix to add before the value."
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193 - name: separate
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194 type: boolean?
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195 default: true
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196 doc: |
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197 If true (default), then the prefix and value must be added as separate
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198 command line arguments; if false, prefix and value must be concatenated
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199 into a single command line argument.
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200 - name: itemSeparator
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201 type: string?
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202 doc: |
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203 Join the array elements into a single string with the elements
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204 separated by by `itemSeparator`.
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205 - name: valueFrom
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206 type:
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207 - "null"
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208 - string
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209 - Expression
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210 jsonldPredicate: "cwl:valueFrom"
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211 doc: |
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212 If `valueFrom` is a constant string value, use this as the value and
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213 apply the binding rules above.
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214
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215 If `valueFrom` is an expression, evaluate the expression to yield the
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216 actual value to use to build the command line and apply the binding
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217 rules above. If the inputBinding is associated with an input
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218 parameter, the value of `self` in the expression will be the value of
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219 the input parameter. Input parameter defaults (as specified by the
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220 `InputParameter.default` field) must be applied before evaluating the
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221 expression.
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222
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223 If the value of the associated input parameter is `null`, `valueFrom` is
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224 not evaluated and nothing is added to the command line.
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225
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226 When a binding is part of the `CommandLineTool.arguments` field,
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227 the `valueFrom` field is required.
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228
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229 - name: shellQuote
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230 type: boolean?
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231 default: true
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232 doc: |
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233 If `ShellCommandRequirement` is in the requirements for the current command,
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234 this controls whether the value is quoted on the command line (default is true).
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235 Use `shellQuote: false` to inject metacharacters for operations such as pipes.
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236
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237 If `shellQuote` is true or not provided, the implementation must not
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238 permit interpretation of any shell metacharacters or directives.
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239
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240
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241 - type: record
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242 name: CommandOutputBinding
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243 extends: LoadContents
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244 doc: |
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245 Describes how to generate an output parameter based on the files produced
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246 by a CommandLineTool.
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247
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248 The output parameter value is generated by applying these operations in the
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249 following order:
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250
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251 - glob
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252 - loadContents
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253 - outputEval
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254 - secondaryFiles
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255 fields:
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256 - name: glob
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257 type:
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258 - "null"
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259 - string
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260 - Expression
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261 - type: array
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262 items: string
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263 doc: |
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264 Find files or directories relative to the output directory, using POSIX
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265 glob(3) pathname matching. If an array is provided, find files or
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266 directories that match any pattern in the array. If an expression is
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267 provided, the expression must return a string or an array of strings,
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268 which will then be evaluated as one or more glob patterns. Must only
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269 match and return files/directories which actually exist.
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270
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271 If the value of glob is a relative path pattern (does not
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272 begin with a slash '/') then it is resolved relative to the
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273 output directory. If the value of the glob is an absolute
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274 path pattern (it does begin with a slash '/') then it must
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275 refer to a path within the output directory. It is an error
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276 if any glob resolves to a path outside the output directory.
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277 Specifically this means globs that resolve to paths outside the output
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278 directory are illegal.
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279
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280 A glob may match a path within the output directory which is
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281 actually a symlink to another file. In this case, the
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282 expected behavior is for the resulting File/Directory object to take the
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283 `basename` (and corresponding `nameroot` and `nameext`) of the
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284 symlink. The `location` of the File/Directory is implementation
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285 dependent, but logically the File/Directory should have the same content
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286 as the symlink target. Platforms may stage output files/directories to
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287 cloud storage that lack the concept of a symlink. In
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288 this case file content and directories may be duplicated, or (to avoid
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289 duplication) the File/Directory `location` may refer to the symlink
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290 target.
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291
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292 It is an error if a symlink in the output directory (or any
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293 symlink in a chain of links) refers to any file or directory
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294 that is not under an input or output directory.
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295
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296 Implementations may shut down a container before globbing
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297 output, so globs and expressions must not assume access to the
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298 container filesystem except for declared input and output.
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299
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300 - name: outputEval
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301 type: Expression?
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302 doc: |
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303 Evaluate an expression to generate the output value. If
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304 `glob` was specified, the value of `self` must be an array
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305 containing file objects that were matched. If no files were
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306 matched, `self` must be a zero length array; if a single file
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307 was matched, the value of `self` is an array of a single
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308 element. The exit code of the process is
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309 available in the expression as `runtime.exitCode`.
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310
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311 Additionally if `loadContents` is true, the file must be a
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312 UTF-8 text file 64 KiB or smaller, and the implementation must
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313 read the entire contents of the file (or file array) and place
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314 it in the `contents` field of the File object for use in
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315 `outputEval`. If the size of the file is greater than 64 KiB,
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316 the implementation must raise a fatal error.
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317
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318 If a tool needs to return a large amount of structured data to
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319 the workflow, loading the output object from `cwl.output.json`
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320 bypasses `outputEval` and is not subject to the 64 KiB
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321 `loadContents` limit.
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322
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323 - name: CommandLineBindable
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324 type: record
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325 fields:
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326 inputBinding:
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327 type: CommandLineBinding?
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328 jsonldPredicate: "cwl:inputBinding"
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329 doc: Describes how to turn this object into command line arguments.
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330
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331 - name: CommandInputRecordField
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332 type: record
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333 extends: [InputRecordField, CommandLineBindable]
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334 specialize:
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335 - specializeFrom: InputRecordSchema
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336 specializeTo: CommandInputRecordSchema
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337 - specializeFrom: InputEnumSchema
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338 specializeTo: CommandInputEnumSchema
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339 - specializeFrom: InputArraySchema
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340 specializeTo: CommandInputArraySchema
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341 - specializeFrom: InputBinding
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342 specializeTo: CommandLineBinding
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343
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344
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345 - name: CommandInputRecordSchema
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346 type: record
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347 extends: [InputRecordSchema, CommandInputSchema, CommandLineBindable]
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348 specialize:
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349 - specializeFrom: InputRecordField
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350 specializeTo: CommandInputRecordField
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351 - specializeFrom: InputBinding
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352 specializeTo: CommandLineBinding
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353
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354
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355 - name: CommandInputEnumSchema
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356 type: record
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357 extends: [InputEnumSchema, CommandInputSchema, CommandLineBindable]
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358 specialize:
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359 - specializeFrom: InputBinding
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360 specializeTo: CommandLineBinding
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361
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362
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363 - name: CommandInputArraySchema
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364 type: record
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365 extends: [InputArraySchema, CommandInputSchema, CommandLineBindable]
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366 specialize:
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367 - specializeFrom: InputRecordSchema
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368 specializeTo: CommandInputRecordSchema
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369 - specializeFrom: InputEnumSchema
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370 specializeTo: CommandInputEnumSchema
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371 - specializeFrom: InputArraySchema
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372 specializeTo: CommandInputArraySchema
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373 - specializeFrom: InputBinding
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374 specializeTo: CommandLineBinding
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375
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376
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377 - name: CommandOutputRecordField
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378 type: record
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379 extends: OutputRecordField
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380 specialize:
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381 - specializeFrom: OutputRecordSchema
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382 specializeTo: CommandOutputRecordSchema
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383 - specializeFrom: OutputEnumSchema
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384 specializeTo: CommandOutputEnumSchema
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385 - specializeFrom: OutputArraySchema
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386 specializeTo: CommandOutputArraySchema
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387 fields:
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388 - name: outputBinding
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389 type: CommandOutputBinding?
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390 jsonldPredicate: "cwl:outputBinding"
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391 doc: |
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392 Describes how to generate this output object based on the files
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393 produced by a CommandLineTool
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394
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395
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396 - name: CommandOutputRecordSchema
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397 type: record
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398 extends: OutputRecordSchema
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399 specialize:
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400 - specializeFrom: OutputRecordField
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401 specializeTo: CommandOutputRecordField
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402
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403
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404 - name: CommandOutputEnumSchema
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405 type: record
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406 extends: OutputEnumSchema
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407 specialize:
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408 - specializeFrom: OutputRecordSchema
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409 specializeTo: CommandOutputRecordSchema
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410 - specializeFrom: OutputEnumSchema
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411 specializeTo: CommandOutputEnumSchema
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412 - specializeFrom: OutputArraySchema
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413 specializeTo: CommandOutputArraySchema
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414
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415
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416 - name: CommandOutputArraySchema
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417 type: record
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418 extends: OutputArraySchema
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419 specialize:
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420 - specializeFrom: OutputRecordSchema
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421 specializeTo: CommandOutputRecordSchema
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422 - specializeFrom: OutputEnumSchema
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423 specializeTo: CommandOutputEnumSchema
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424 - specializeFrom: OutputArraySchema
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425 specializeTo: CommandOutputArraySchema
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426
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427
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428 - type: record
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429 name: CommandInputParameter
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430 extends: InputParameter
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431 doc: An input parameter for a CommandLineTool.
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432 fields:
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433 - name: type
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434 type:
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435 - CWLType
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436 - stdin
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437 - CommandInputRecordSchema
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438 - CommandInputEnumSchema
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439 - CommandInputArraySchema
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440 - string
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441 - type: array
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442 items:
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443 - CWLType
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444 - CommandInputRecordSchema
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445 - CommandInputEnumSchema
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446 - CommandInputArraySchema
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447 - string
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448 jsonldPredicate:
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449 "_id": "sld:type"
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450 "_type": "@vocab"
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451 refScope: 2
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452 typeDSL: True
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453 doc: |
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454 Specify valid types of data that may be assigned to this parameter.
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455 - name: inputBinding
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456 type: CommandLineBinding?
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457 doc: |
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458 Describes how to turns the input parameters of a process into
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459 command line arguments.
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460 jsonldPredicate: "cwl:inputBinding"
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461
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462 - type: record
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463 name: CommandOutputParameter
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464 extends: OutputParameter
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465 doc: An output parameter for a CommandLineTool.
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466 fields:
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467 - name: type
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468 type:
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469 - CWLType
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470 - stdout
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471 - stderr
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472 - CommandOutputRecordSchema
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473 - CommandOutputEnumSchema
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474 - CommandOutputArraySchema
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475 - string
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476 - type: array
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477 items:
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478 - CWLType
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479 - CommandOutputRecordSchema
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480 - CommandOutputEnumSchema
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481 - CommandOutputArraySchema
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482 - string
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483 jsonldPredicate:
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484 "_id": "sld:type"
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485 "_type": "@vocab"
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486 refScope: 2
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487 typeDSL: True
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488 doc: |
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489 Specify valid types of data that may be assigned to this parameter.
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490 - name: outputBinding
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491 type: CommandOutputBinding?
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492 jsonldPredicate: "cwl:outputBinding"
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493 doc: Describes how to generate this output object based on the files
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494 produced by a CommandLineTool
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495
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496 - name: stdin
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497 type: enum
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498 symbols: [ "cwl:stdin" ]
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499 docParent: "#CommandOutputParameter"
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500 doc: |
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501 Only valid as a `type` for a `CommandLineTool` input with no
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502 `inputBinding` set. `stdin` must not be specified at the `CommandLineTool`
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503 level.
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504
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505 The following
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506 ```
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507 inputs:
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508 an_input_name:
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509 type: stdin
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510 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
511 is equivalent to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
512 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
513 inputs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
514 an_input_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
515 type: File
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
516 streamable: true
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
517
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
518 stdin: ${inputs.an_input_name.path}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
519 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
520
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
521 - name: stdout
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
522 type: enum
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
523 symbols: [ "cwl:stdout" ]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
524 docParent: "#CommandOutputParameter"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
525 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
526 Only valid as a `type` for a `CommandLineTool` output with no
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
527 `outputBinding` set.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
528
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
529 The following
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
530 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
531 outputs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
532 an_output_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
533 type: stdout
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
534
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
535 stdout: a_stdout_file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
536 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
537 is equivalent to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
538 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
539 outputs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
540 an_output_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
541 type: File
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
542 streamable: true
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
543 outputBinding:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
544 glob: a_stdout_file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
545
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
546 stdout: a_stdout_file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
547 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
548
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
549 If there is no `stdout` name provided, a random filename will be created.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
550 For example, the following
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
551 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
552 outputs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
553 an_output_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
554 type: stdout
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
555 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
556 is equivalent to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
557 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
558 outputs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
559 an_output_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
560 type: File
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
561 streamable: true
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
562 outputBinding:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
563 glob: random_stdout_filenameABCDEFG
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
564
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
565 stdout: random_stdout_filenameABCDEFG
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
566 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
567
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
568
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
569 - name: stderr
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
570 type: enum
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
571 symbols: [ "cwl:stderr" ]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
572 docParent: "#CommandOutputParameter"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
573 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
574 Only valid as a `type` for a `CommandLineTool` output with no
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
575 `outputBinding` set.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
576
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
577 The following
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
578 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
579 outputs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
580 an_output_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
581 type: stderr
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
582
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
583 stderr: a_stderr_file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
584 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
585 is equivalent to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
586 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
587 outputs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
588 an_output_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
589 type: File
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
590 streamable: true
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
591 outputBinding:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
592 glob: a_stderr_file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
593
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
594 stderr: a_stderr_file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
595 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
596
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
597 If there is no `stderr` name provided, a random filename will be created.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
598 For example, the following
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
599 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
600 outputs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
601 an_output_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
602 type: stderr
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
603 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
604 is equivalent to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
605 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
606 outputs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
607 an_output_name:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
608 type: File
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
609 streamable: true
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
610 outputBinding:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
611 glob: random_stderr_filenameABCDEFG
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
612
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
613 stderr: random_stderr_filenameABCDEFG
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
614 ```
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
615
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
616
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
617 - type: record
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
618 name: CommandLineTool
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
619 extends: Process
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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620 documentRoot: true
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
621 specialize:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
622 - specializeFrom: InputParameter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
623 specializeTo: CommandInputParameter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
624 - specializeFrom: OutputParameter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
625 specializeTo: CommandOutputParameter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
626 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
627 This defines the schema of the CWL Command Line Tool Description document.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
628
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
629 fields:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
630 - name: class
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
631 jsonldPredicate:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
632 "_id": "@type"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
633 "_type": "@vocab"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
634 type: string
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
635 - name: baseCommand
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
636 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
637 Specifies the program to execute. If an array, the first element of
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
638 the array is the command to execute, and subsequent elements are
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
639 mandatory command line arguments. The elements in `baseCommand` must
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
640 appear before any command line bindings from `inputBinding` or
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
641 `arguments`.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
642
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
643 If `baseCommand` is not provided or is an empty array, the first
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
644 element of the command line produced after processing `inputBinding` or
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diff changeset
645 `arguments` must be used as the program to execute.
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646
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diff changeset
647 If the program includes a path separator character it must
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parents:
diff changeset
648 be an absolute path, otherwise it is an error. If the program does not
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parents:
diff changeset
649 include a path separator, search the `$PATH` variable in the runtime
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parents:
diff changeset
650 environment of the workflow runner find the absolute path of the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
651 executable.
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parents:
diff changeset
652 type:
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parents:
diff changeset
653 - string?
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parents:
diff changeset
654 - string[]?
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diff changeset
655 jsonldPredicate:
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parents:
diff changeset
656 "_id": "cwl:baseCommand"
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diff changeset
657 "_container": "@list"
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parents:
diff changeset
658 - name: arguments
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diff changeset
659 doc: |
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parents:
diff changeset
660 Command line bindings which are not directly associated with input
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diff changeset
661 parameters. If the value is a string, it is used as a string literal
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parents:
diff changeset
662 argument. If it is an Expression, the result of the evaluation is used
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parents:
diff changeset
663 as an argument.
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parents:
diff changeset
664 type:
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parents:
diff changeset
665 - "null"
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parents:
diff changeset
666 - type: array
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parents:
diff changeset
667 items: [string, Expression, CommandLineBinding]
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parents:
diff changeset
668 jsonldPredicate:
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parents:
diff changeset
669 "_id": "cwl:arguments"
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parents:
diff changeset
670 "_container": "@list"
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parents:
diff changeset
671 - name: stdin
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parents:
diff changeset
672 type: ["null", string, Expression]
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parents:
diff changeset
673 jsonldPredicate: "https://w3id.org/cwl/cwl#stdin"
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parents:
diff changeset
674 doc: |
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parents:
diff changeset
675 A path to a file whose contents must be piped into the command's
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
676 standard input stream.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
677 - name: stderr
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parents:
diff changeset
678 type: ["null", string, Expression]
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parents:
diff changeset
679 jsonldPredicate: "https://w3id.org/cwl/cwl#stderr"
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parents:
diff changeset
680 doc: |
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parents:
diff changeset
681 Capture the command's standard error stream to a file written to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
682 the designated output directory.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
683
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diff changeset
684 If `stderr` is a string, it specifies the file name to use.
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parents:
diff changeset
685
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parents:
diff changeset
686 If `stderr` is an expression, the expression is evaluated and must
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
687 return a string with the file name to use to capture stderr. If the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
688 return value is not a string, or the resulting path contains illegal
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
689 characters (such as the path separator `/`) it is an error.
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parents:
diff changeset
690 - name: stdout
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parents:
diff changeset
691 type: ["null", string, Expression]
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parents:
diff changeset
692 jsonldPredicate: "https://w3id.org/cwl/cwl#stdout"
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parents:
diff changeset
693 doc: |
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parents:
diff changeset
694 Capture the command's standard output stream to a file written to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
695 the designated output directory.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
696
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parents:
diff changeset
697 If `stdout` is a string, it specifies the file name to use.
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shellac
parents:
diff changeset
698
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shellac
parents:
diff changeset
699 If `stdout` is an expression, the expression is evaluated and must
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
700 return a string with the file name to use to capture stdout. If the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
701 return value is not a string, or the resulting path contains illegal
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
702 characters (such as the path separator `/`) it is an error.
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shellac
parents:
diff changeset
703 - name: successCodes
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parents:
diff changeset
704 type: int[]?
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parents:
diff changeset
705 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
706 Exit codes that indicate the process completed successfully.
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shellac
parents:
diff changeset
707
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parents:
diff changeset
708 If not specified, only exit code 0 is considered success.
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parents:
diff changeset
709
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parents:
diff changeset
710 - name: temporaryFailCodes
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shellac
parents:
diff changeset
711 type: int[]?
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parents:
diff changeset
712 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
713 Exit codes that indicate the process failed due to a possibly
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
714 temporary condition, where executing the process with the same
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
715 runtime environment and inputs may produce different results.
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shellac
parents:
diff changeset
716
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
717 If not specified, no exit codes are considered temporary failure.
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shellac
parents:
diff changeset
718
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
719 - name: permanentFailCodes
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
720 type: int[]?
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
721 doc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
722 Exit codes that indicate the process failed due to a permanent logic
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
723 error, where executing the process with the same runtime environment and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
724 same inputs is expected to always fail.
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shellac
parents:
diff changeset
725
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
726 If not specified, all exit codes except 0 are considered permanent failure.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
727
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
728
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
729 - type: record
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
730 name: DockerRequirement
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
731 extends: ProcessRequirement
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
732 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
733 Indicates that a workflow component should be run in a
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
734 [Docker](http://docker.com) or Docker-compatible (such as
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
735 [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
736 specifies how to fetch or build the image.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
737
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
738 If a CommandLineTool lists `DockerRequirement` under
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
739 `hints` (or `requirements`), it may (or must) be run in the specified Docker
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
740 container.
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shellac
parents:
diff changeset
741
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shellac
parents:
diff changeset
742 The platform must first acquire or install the correct Docker image as
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
743 specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`.
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shellac
parents:
diff changeset
744
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shellac
parents:
diff changeset
745 The platform must execute the tool in the container using `docker run` with
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
746 the appropriate Docker image and tool command line.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
747
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shellac
parents:
diff changeset
748 The workflow platform may provide input files and the designated output
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shellac
parents:
diff changeset
749 directory through the use of volume bind mounts. The platform should rewrite
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
750 file paths in the input object to correspond to the Docker bind mounted
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
751 locations. That is, the platform should rewrite values in the parameter context
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
752 such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths
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shellac
parents:
diff changeset
753 within the container. The platform must ensure that `runtime.outdir` and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
754 `runtime.tmpdir` are distinct directories.
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shellac
parents:
diff changeset
755
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
756 When running a tool contained in Docker, the workflow platform must not
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
757 assume anything about the contents of the Docker container, such as the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
758 presence or absence of specific software, except to assume that the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
759 generated command line represents a valid command within the runtime
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
760 environment of the container.
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shellac
parents:
diff changeset
761
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shellac
parents:
diff changeset
762 A container image may specify an
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
763 [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
764 and/or
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
765 [CMD](https://docs.docker.com/engine/reference/builder/#cmd).
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shellac
parents:
diff changeset
766 Command line arguments will be appended after all elements of
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shellac
parents:
diff changeset
767 ENTRYPOINT, and will override all elements specified using CMD (in
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shellac
parents:
diff changeset
768 other words, CMD is only used when the CommandLineTool definition
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
769 produces an empty command line).
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
770
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parents:
diff changeset
771 Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility
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parents:
diff changeset
772 concerns of the implicit hidden execution point (For further discussion, see
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parents:
diff changeset
773 [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable
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parents:
diff changeset
774 CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD.
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shellac
parents:
diff changeset
775 CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the
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parents:
diff changeset
776 `requirements` section.
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parents:
diff changeset
777
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parents:
diff changeset
778 ## Interaction with other requirements
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shellac
parents:
diff changeset
779
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parents:
diff changeset
780 If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
781 DockerRequirement, the environment variables must be provided to Docker
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parents:
diff changeset
782 using `--env` or `--env-file` and interact with the container's preexisting
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
783 environment as defined by Docker.
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parents:
diff changeset
784
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parents:
diff changeset
785 fields:
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parents:
diff changeset
786 - name: class
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
787 type: string
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parents:
diff changeset
788 doc: "Always 'DockerRequirement'"
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parents:
diff changeset
789 jsonldPredicate:
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parents:
diff changeset
790 "_id": "@type"
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parents:
diff changeset
791 "_type": "@vocab"
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parents:
diff changeset
792 - name: dockerPull
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parents:
diff changeset
793 type: string?
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parents:
diff changeset
794 doc: |
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parents:
diff changeset
795 Specify a Docker image to retrieve using `docker pull`. Can contain the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
796 immutable digest to ensure an exact container is used:
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parents:
diff changeset
797 `dockerPull: ubuntu@sha256:45b23dee08af5e43a7fea6c4cf9c25ccf269ee113168c19722f87876677c5cb2`
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parents:
diff changeset
798 - name: dockerLoad
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parents:
diff changeset
799 type: string?
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parents:
diff changeset
800 doc: "Specify a HTTP URL from which to download a Docker image using `docker load`."
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parents:
diff changeset
801 - name: dockerFile
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parents:
diff changeset
802 type: string?
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parents:
diff changeset
803 doc: "Supply the contents of a Dockerfile which will be built using `docker build`."
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parents:
diff changeset
804 - name: dockerImport
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parents:
diff changeset
805 type: string?
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parents:
diff changeset
806 doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import."
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parents:
diff changeset
807 - name: dockerImageId
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parents:
diff changeset
808 type: string?
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parents:
diff changeset
809 doc: |
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parents:
diff changeset
810 The image id that will be used for `docker run`. May be a
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parents:
diff changeset
811 human-readable image name or the image identifier hash. May be skipped
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parents:
diff changeset
812 if `dockerPull` is specified, in which case the `dockerPull` image id
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parents:
diff changeset
813 must be used.
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parents:
diff changeset
814 - name: dockerOutputDirectory
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parents:
diff changeset
815 type: string?
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parents:
diff changeset
816 doc: |
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parents:
diff changeset
817 Set the designated output directory to a specific location inside the
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shellac
parents:
diff changeset
818 Docker container.
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parents:
diff changeset
819
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parents:
diff changeset
820
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parents:
diff changeset
821 - type: record
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parents:
diff changeset
822 name: SoftwareRequirement
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parents:
diff changeset
823 extends: ProcessRequirement
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parents:
diff changeset
824 doc: |
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parents:
diff changeset
825 A list of software packages that should be configured in the environment of
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parents:
diff changeset
826 the defined process.
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parents:
diff changeset
827 fields:
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parents:
diff changeset
828 - name: class
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parents:
diff changeset
829 type: string
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
830 doc: "Always 'SoftwareRequirement'"
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parents:
diff changeset
831 jsonldPredicate:
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parents:
diff changeset
832 "_id": "@type"
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parents:
diff changeset
833 "_type": "@vocab"
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parents:
diff changeset
834 - name: packages
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parents:
diff changeset
835 type: SoftwarePackage[]
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parents:
diff changeset
836 doc: "The list of software to be configured."
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parents:
diff changeset
837 jsonldPredicate:
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parents:
diff changeset
838 mapSubject: package
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parents:
diff changeset
839 mapPredicate: specs
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parents:
diff changeset
840
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parents:
diff changeset
841 - name: SoftwarePackage
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parents:
diff changeset
842 type: record
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parents:
diff changeset
843 fields:
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parents:
diff changeset
844 - name: package
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parents:
diff changeset
845 type: string
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parents:
diff changeset
846 doc: |
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parents:
diff changeset
847 The name of the software to be made available. If the name is
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
848 common, inconsistent, or otherwise ambiguous it should be combined with
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shellac
parents:
diff changeset
849 one or more identifiers in the `specs` field.
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parents:
diff changeset
850 - name: version
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parents:
diff changeset
851 type: string[]?
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parents:
diff changeset
852 doc: |
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parents:
diff changeset
853 The (optional) versions of the software that are known to be
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
854 compatible.
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parents:
diff changeset
855 - name: specs
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parents:
diff changeset
856 type: string[]?
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parents:
diff changeset
857 jsonldPredicate: {_type: "@id", noLinkCheck: true}
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parents:
diff changeset
858 doc: |
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parents:
diff changeset
859 One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
860 identifying resources for installing or enabling the software named in
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
861 the `package` field. Implementations may provide resolvers which map
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parents:
diff changeset
862 these software identifer IRIs to some configuration action; or they can
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parents:
diff changeset
863 use only the name from the `package` field on a best effort basis.
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parents:
diff changeset
864
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parents:
diff changeset
865 For example, the IRI https://packages.debian.org/bowtie could
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parents:
diff changeset
866 be resolved with `apt-get install bowtie`. The IRI
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parents:
diff changeset
867 https://anaconda.org/bioconda/bowtie could be resolved with `conda
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parents:
diff changeset
868 install -c bioconda bowtie`.
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parents:
diff changeset
869
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parents:
diff changeset
870 IRIs can also be system independent and used to map to a specific
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parents:
diff changeset
871 software installation or selection mechanism.
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parents:
diff changeset
872 Using [RRID](https://www.identifiers.org/rrid/) as an example:
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parents:
diff changeset
873 https://identifiers.org/rrid/RRID:SCR_005476
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parents:
diff changeset
874 could be fulfilled using the above mentioned Debian or bioconda
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shellac
parents:
diff changeset
875 package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
876 or any other mechanism the platform chooses. IRIs can also be from
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shellac
parents:
diff changeset
877 identifer sources that are discipline specific yet still system
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shellac
parents:
diff changeset
878 independent. As an example, the equivalent [ELIXIR Tools and Data
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shellac
parents:
diff changeset
879 Service Registry](https://bio.tools) IRI to the previous RRID example is
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
880 https://bio.tools/tool/bowtie2/version/2.2.8.
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parents:
diff changeset
881 If supported by a given registry, implementations are encouraged to
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parents:
diff changeset
882 query these system independent sofware identifier IRIs directly for
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
883 links to packaging systems.
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parents:
diff changeset
884
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parents:
diff changeset
885 A site specific IRI can be listed as well. For example, an academic
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shellac
parents:
diff changeset
886 computing cluster using Environement Modules could list the IRI
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parents:
diff changeset
887 `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
888 `module load bowtie-tbb/1.1.2` should be executed to make available
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parents:
diff changeset
889 `bowtie` version 1.1.2 compiled with the TBB library prior to running
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
890 the accompanying Workflow or CommandLineTool. Note that the example IRI
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
891 is specific to a particular institution and computing environment as
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
892 the Environment Modules system does not have a common namespace or
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
893 standardized naming convention.
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parents:
diff changeset
894
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shellac
parents:
diff changeset
895 This last example is the least portable and should only be used if
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
896 mechanisms based off of the `package` field or more generic IRIs are
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
897 unavailable or unsuitable. While harmless to other sites, site specific
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
898 software IRIs should be left out of shared CWL descriptions to avoid
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
899 clutter.
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shellac
parents:
diff changeset
900
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shellac
parents:
diff changeset
901 - name: Dirent
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shellac
parents:
diff changeset
902 type: record
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shellac
parents:
diff changeset
903 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
904 Define a file or subdirectory that must be staged to a particular
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
905 place prior to executing the command line tool. May be the result
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
906 of executing an expression, such as building a configuration file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
907 from a template.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
908
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
909 Usually files are staged within the [designated output directory](#Runtime_environment).
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
910 However, under certain circumstances, files may be staged at
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
911 arbitrary locations, see discussion for `entryname`.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
912
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
913 fields:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
914 - name: entryname
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
915 type: ["null", string, Expression]
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shellac
parents:
diff changeset
916 jsonldPredicate:
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shellac
parents:
diff changeset
917 _id: cwl:entryname
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shellac
parents:
diff changeset
918 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
919 The "target" name of the file or subdirectory. If `entry` is
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
920 a File or Directory, the `entryname` field overrides the value
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
921 of `basename` of the File or Directory object.
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shellac
parents:
diff changeset
922
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shellac
parents:
diff changeset
923 * Required when `entry` evaluates to file contents only
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
924 * Optional when `entry` evaluates to a File or Directory object with a `basename`
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
925 * Invalid when `entry` evaluates to an array of File or Directory objects.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
926
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shellac
parents:
diff changeset
927 If `entryname` is a relative path, it specifies a name within
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
928 the designated output directory. A relative path starting
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
929 with `../` or that resolves to location above the designated output directory is an error.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
930
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
931 If `entryname` is an absolute path (starts with a slash `/`)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
932 it is an error unless the following conditions are met:
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shellac
parents:
diff changeset
933
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
934 * `DockerRequirement` is present in `requirements`
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
935 * The program is will run inside a software container
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
936 where, from the perspective of the program, the root
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
937 filesystem is not shared with any other user or
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
938 running program.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
939
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shellac
parents:
diff changeset
940 In this case, and the above conditions are met, then
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
941 `entryname` may specify the absolute path within the container
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
942 where the file or directory must be placed.
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shellac
parents:
diff changeset
943
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
944 - name: entry
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shellac
parents:
diff changeset
945 type: [string, Expression]
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shellac
parents:
diff changeset
946 jsonldPredicate:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
947 _id: cwl:entry
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shellac
parents:
diff changeset
948 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
949 If the value is a string literal or an expression which evaluates to a
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
950 string, a new text file must be created with the string as the file contents.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
951
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
952 If the value is an expression that evaluates to a `File` or
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
953 `Directory` object, or an array of `File` or `Directory`
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
954 objects, this indicates the referenced file or directory
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
955 should be added to the designated output directory prior to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
956 executing the tool.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
957
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shellac
parents:
diff changeset
958 If the value is an expression that evaluates to `null`,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
959 nothing is added to the designated output directory, the entry
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
960 has no effect.
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shellac
parents:
diff changeset
961
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shellac
parents:
diff changeset
962 If the value is an expression that evaluates to some other
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
963 array, number, or object not consisting of `File` or
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
964 `Directory` objects, a new file must be created with the value
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
965 serialized to JSON text as the file contents. The JSON
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
966 serialization behavior should match the behavior of string
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
967 interpolation of [Parameter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
968 references](#Parameter_references).
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
969
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shellac
parents:
diff changeset
970 - name: writable
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
971 type: boolean?
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
972 default: false
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
973 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
974 If true, the File or Directory (or array of Files or
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
975 Directories) declared in `entry` must be writable by the tool.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
976
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
977 Changes to the file or directory must be isolated and not
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
978 visible by any other CommandLineTool process. This may be
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
979 implemented by making a copy of the original file or
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
980 directory.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
981
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
982 Default false (files and directories read-only by default).
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
983
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
984 A directory marked as `writable: true` implies that all files and
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
985 subdirectories are recursively writable as well.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
986
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
987 If `writable` is false, the file may be made available using a
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
988 bind mount or file system link to avoid unnecessary copying of
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
989 the input file. Command line tools may receive an error on
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
990 attempting to rename or delete files or directories that are
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
991 not explicitly marked as writable.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
992
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
993
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
994 - name: InitialWorkDirRequirement
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
995 type: record
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
996 extends: ProcessRequirement
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shellac
parents:
diff changeset
997 doc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
998 Define a list of files and subdirectories that must be staged by
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
999 the workflow platform prior to executing the command line tool.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1000
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1001 Normally files are staged within the designated output directory.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1002 However, when running inside containers, files may be staged at
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1003 arbitrary locations, see discussion for `Dirent.entryname`.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1004 Together with `DockerRequirement.dockerOutputDirectory` this it
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1005 possible to control the locations of both input and output files
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1006 when running in containers.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1007
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1008 fields:
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shellac
parents:
diff changeset
1009 - name: class
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shellac
parents:
diff changeset
1010 type: string
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1011 doc: InitialWorkDirRequirement
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1012 jsonldPredicate:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1013 "_id": "@type"
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shellac
parents:
diff changeset
1014 "_type": "@vocab"
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shellac
parents:
diff changeset
1015 - name: listing
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shellac
parents:
diff changeset
1016 type:
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shellac
parents:
diff changeset
1017 - Expression
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shellac
parents:
diff changeset
1018 - type: array
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shellac
parents:
diff changeset
1019 items:
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shellac
parents:
diff changeset
1020 - "null"
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shellac
parents:
diff changeset
1021 - Dirent
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shellac
parents:
diff changeset
1022 - Expression
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shellac
parents:
diff changeset
1023 - File
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shellac
parents:
diff changeset
1024 - Directory
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shellac
parents:
diff changeset
1025 - type: array
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shellac
parents:
diff changeset
1026 items:
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shellac
parents:
diff changeset
1027 - File
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shellac
parents:
diff changeset
1028 - Directory
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shellac
parents:
diff changeset
1029 jsonldPredicate:
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shellac
parents:
diff changeset
1030 _id: "cwl:listing"
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shellac
parents:
diff changeset
1031 doc: |
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shellac
parents:
diff changeset
1032 The list of files or subdirectories that must be staged prior
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shellac
parents:
diff changeset
1033 to executing the command line tool.
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shellac
parents:
diff changeset
1034
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shellac
parents:
diff changeset
1035 Return type of each expression must validate as `["null",
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shellac
parents:
diff changeset
1036 File, Directory, Dirent, {type: array, items: [File,
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shellac
parents:
diff changeset
1037 Directory]}]`.
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shellac
parents:
diff changeset
1038
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shellac
parents:
diff changeset
1039 Each `File` or `Directory` that is returned by an Expression
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shellac
parents:
diff changeset
1040 must be added to the designated output directory prior to
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shellac
parents:
diff changeset
1041 executing the tool.
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shellac
parents:
diff changeset
1042
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shellac
parents:
diff changeset
1043 Each `Dirent` record that is listed or returned by an
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shellac
parents:
diff changeset
1044 expression specifies a file to be created or staged in the
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shellac
parents:
diff changeset
1045 designated output directory prior to executing the tool.
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shellac
parents:
diff changeset
1046
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shellac
parents:
diff changeset
1047 Expressions may return null, in which case they have no effect.
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shellac
parents:
diff changeset
1048
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shellac
parents:
diff changeset
1049 Files or Directories which are listed in the input parameters
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shellac
parents:
diff changeset
1050 and appear in the `InitialWorkDirRequirement` listing must
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shellac
parents:
diff changeset
1051 have their `path` set to their staged location. If the same
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shellac
parents:
diff changeset
1052 File or Directory appears more than once in the
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shellac
parents:
diff changeset
1053 `InitialWorkDirRequirement` listing, the implementation must
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shellac
parents:
diff changeset
1054 choose exactly one value for `path`; how this value is chosen
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shellac
parents:
diff changeset
1055 is undefined.
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shellac
parents:
diff changeset
1056
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shellac
parents:
diff changeset
1057
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shellac
parents:
diff changeset
1058 - name: EnvVarRequirement
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shellac
parents:
diff changeset
1059 type: record
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shellac
parents:
diff changeset
1060 extends: ProcessRequirement
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shellac
parents:
diff changeset
1061 doc: |
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shellac
parents:
diff changeset
1062 Define a list of environment variables which will be set in the
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shellac
parents:
diff changeset
1063 execution environment of the tool. See `EnvironmentDef` for details.
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shellac
parents:
diff changeset
1064 fields:
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shellac
parents:
diff changeset
1065 - name: class
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shellac
parents:
diff changeset
1066 type: string
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shellac
parents:
diff changeset
1067 doc: "Always 'EnvVarRequirement'"
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shellac
parents:
diff changeset
1068 jsonldPredicate:
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shellac
parents:
diff changeset
1069 "_id": "@type"
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shellac
parents:
diff changeset
1070 "_type": "@vocab"
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shellac
parents:
diff changeset
1071 - name: envDef
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shellac
parents:
diff changeset
1072 type: EnvironmentDef[]
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shellac
parents:
diff changeset
1073 doc: The list of environment variables.
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shellac
parents:
diff changeset
1074 jsonldPredicate:
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shellac
parents:
diff changeset
1075 mapSubject: envName
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shellac
parents:
diff changeset
1076 mapPredicate: envValue
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shellac
parents:
diff changeset
1077
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shellac
parents:
diff changeset
1078
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shellac
parents:
diff changeset
1079 - type: record
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shellac
parents:
diff changeset
1080 name: ShellCommandRequirement
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shellac
parents:
diff changeset
1081 extends: ProcessRequirement
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shellac
parents:
diff changeset
1082 doc: |
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shellac
parents:
diff changeset
1083 Modify the behavior of CommandLineTool to generate a single string
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shellac
parents:
diff changeset
1084 containing a shell command line. Each item in the argument list must be
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shellac
parents:
diff changeset
1085 joined into a string separated by single spaces and quoted to prevent
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shellac
parents:
diff changeset
1086 intepretation by the shell, unless `CommandLineBinding` for that argument
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shellac
parents:
diff changeset
1087 contains `shellQuote: false`. If `shellQuote: false` is specified, the
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shellac
parents:
diff changeset
1088 argument is joined into the command string without quoting, which allows
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shellac
parents:
diff changeset
1089 the use of shell metacharacters such as `|` for pipes.
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shellac
parents:
diff changeset
1090 fields:
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shellac
parents:
diff changeset
1091 - name: class
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shellac
parents:
diff changeset
1092 type: string
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shellac
parents:
diff changeset
1093 doc: "Always 'ShellCommandRequirement'"
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shellac
parents:
diff changeset
1094 jsonldPredicate:
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shellac
parents:
diff changeset
1095 "_id": "@type"
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shellac
parents:
diff changeset
1096 "_type": "@vocab"
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shellac
parents:
diff changeset
1097
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shellac
parents:
diff changeset
1098
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shellac
parents:
diff changeset
1099 - type: record
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shellac
parents:
diff changeset
1100 name: ResourceRequirement
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shellac
parents:
diff changeset
1101 extends: ProcessRequirement
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shellac
parents:
diff changeset
1102 doc: |
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shellac
parents:
diff changeset
1103 Specify basic hardware resource requirements.
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shellac
parents:
diff changeset
1104
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shellac
parents:
diff changeset
1105 "min" is the minimum amount of a resource that must be reserved to
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shellac
parents:
diff changeset
1106 schedule a job. If "min" cannot be satisfied, the job should not
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shellac
parents:
diff changeset
1107 be run.
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shellac
parents:
diff changeset
1108
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shellac
parents:
diff changeset
1109 "max" is the maximum amount of a resource that the job shall be
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shellac
parents:
diff changeset
1110 allocated. If a node has sufficient resources, multiple jobs may
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shellac
parents:
diff changeset
1111 be scheduled on a single node provided each job's "max" resource
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shellac
parents:
diff changeset
1112 requirements are met. If a job attempts to exceed its resource
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shellac
parents:
diff changeset
1113 allocation, an implementation may deny additional resources, which
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shellac
parents:
diff changeset
1114 may result in job failure.
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shellac
parents:
diff changeset
1115
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shellac
parents:
diff changeset
1116 If both "min" and "max" are specified, an implementation may
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shellac
parents:
diff changeset
1117 choose to allocate any amount between "min" and "max", with the
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shellac
parents:
diff changeset
1118 actual allocation provided in the `runtime` object.
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shellac
parents:
diff changeset
1119
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shellac
parents:
diff changeset
1120 If "min" is specified but "max" is not, then "max" == "min"
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shellac
parents:
diff changeset
1121 If "max" is specified by "min" is not, then "min" == "max".
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parents:
diff changeset
1122
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parents:
diff changeset
1123 It is an error if max < min.
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shellac
parents:
diff changeset
1124
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shellac
parents:
diff changeset
1125 It is an error if the value of any of these fields is negative.
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shellac
parents:
diff changeset
1126
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shellac
parents:
diff changeset
1127 If neither "min" nor "max" is specified for a resource, use the default values below.
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shellac
parents:
diff changeset
1128
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shellac
parents:
diff changeset
1129 fields:
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shellac
parents:
diff changeset
1130 - name: class
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shellac
parents:
diff changeset
1131 type: string
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shellac
parents:
diff changeset
1132 doc: "Always 'ResourceRequirement'"
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shellac
parents:
diff changeset
1133 jsonldPredicate:
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parents:
diff changeset
1134 "_id": "@type"
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parents:
diff changeset
1135 "_type": "@vocab"
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shellac
parents:
diff changeset
1136 - name: coresMin
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shellac
parents:
diff changeset
1137 type: ["null", long, float, Expression]
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shellac
parents:
diff changeset
1138 doc: |
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shellac
parents:
diff changeset
1139 Minimum reserved number of CPU cores (default is 1).
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shellac
parents:
diff changeset
1140
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shellac
parents:
diff changeset
1141 May be a fractional value to indicate to a scheduling
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shellac
parents:
diff changeset
1142 algorithm that one core can be allocated to multiple
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shellac
parents:
diff changeset
1143 jobs. For example, a value of 0.25 indicates that up to 4
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shellac
parents:
diff changeset
1144 jobs may run in parallel on 1 core. A value of 1.25 means
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shellac
parents:
diff changeset
1145 that up to 3 jobs can run on a 4 core system (4/1.25 ≈ 3).
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shellac
parents:
diff changeset
1146
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shellac
parents:
diff changeset
1147 Processes can only share a core allocation if the sum of each
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shellac
parents:
diff changeset
1148 of their `ramMax`, `tmpdirMax`, and `outdirMax` requests also
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1149 do not exceed the capacity of the node.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1150
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1151 Processes sharing a core must have the same level of isolation
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1152 (typically a container or VM) that they would normally.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1153
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1154 The reported number of CPU cores reserved for the process,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1155 which is available to expressions on the CommandLineTool as
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1156 `runtime.cores`, must be a non-zero integer, and may be
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1157 calculated by rounding up the cores request to the next whole
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1158 number.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1159
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1160 Scheduling systems may allocate fractional CPU resources by
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1161 setting quotas or scheduling weights. Scheduling systems that
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1162 do not support fractional CPUs may round up the request to the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1163 next whole number.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1164
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1165 - name: coresMax
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1166 type: ["null", long, float, Expression]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1167 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1168 Maximum reserved number of CPU cores.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1169
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1170 See `coresMin` for discussion about fractional CPU requests.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1171
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1172 - name: ramMin
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1173 type: ["null", long, float, Expression]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1174 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1175 Minimum reserved RAM in mebibytes (2**20) (default is 256)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1176
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1177 May be a fractional value. If so, the actual RAM request must
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1178 be rounded up to the next whole number. The reported amount of
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1179 RAM reserved for the process, which is available to
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1180 expressions on the CommandLineTool as `runtime.ram`, must be a
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1181 non-zero integer.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1182
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1183 - name: ramMax
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1184 type: ["null", long, float, Expression]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1185 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1186 Maximum reserved RAM in mebibytes (2**20)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1187
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1188 See `ramMin` for discussion about fractional RAM requests.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1189
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1190 - name: tmpdirMin
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1191 type: ["null", long, float, Expression]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1192 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1193 Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1194
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1195 May be a fractional value. If so, the actual storage request
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1196 must be rounded up to the next whole number. The reported
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1197 amount of storage reserved for the process, which is available
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1198 to expressions on the CommandLineTool as `runtime.tmpdirSize`,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1199 must be a non-zero integer.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1200
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1201 - name: tmpdirMax
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1202 type: ["null", long, float, Expression]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1203 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1204 Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1205
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1206 See `tmpdirMin` for discussion about fractional storage requests.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1207
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1208 - name: outdirMin
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1209 type: ["null", long, float, Expression]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1210 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1211 Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1212
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1213 May be a fractional value. If so, the actual storage request
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1214 must be rounded up to the next whole number. The reported
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1215 amount of storage reserved for the process, which is available
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1216 to expressions on the CommandLineTool as `runtime.outdirSize`,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1217 must be a non-zero integer.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1218
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1219 - name: outdirMax
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1220 type: ["null", long, float, Expression]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1221 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1222 Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1223
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1224 See `outdirMin` for discussion about fractional storage requests.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1225
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1226
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1227 - type: record
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1228 name: WorkReuse
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1229 extends: ProcessRequirement
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1230 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1231 For implementations that support reusing output from past work (on
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1232 the assumption that same code and same input produce same
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1233 results), control whether to enable or disable the reuse behavior
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1234 for a particular tool or step (to accomodate situations where that
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1235 assumption is incorrect). A reused step is not executed but
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1236 instead returns the same output as the original execution.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1237
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1238 If `WorkReuse` is not specified, correct tools should assume it
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1239 is enabled by default.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1240 fields:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1241 - name: class
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1242 type: string
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1243 doc: "Always 'WorkReuse'"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1244 jsonldPredicate:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1245 "_id": "@type"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1246 "_type": "@vocab"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1247 - name: enableReuse
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1248 type: [boolean, Expression]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1249 default: true
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1250
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1251
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1252 - type: record
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1253 name: NetworkAccess
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1254 extends: ProcessRequirement
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1255 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1256 Indicate whether a process requires outgoing IPv4/IPv6 network
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1257 access. Choice of IPv4 or IPv6 is implementation and site
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1258 specific, correct tools must support both.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1259
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1260 If `networkAccess` is false or not specified, tools must not
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1261 assume network access, except for localhost (the loopback device).
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1262
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1263 If `networkAccess` is true, the tool must be able to make outgoing
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1264 connections to network resources. Resources may be on a private
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1265 subnet or the public Internet. However, implementations and sites
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1266 may apply their own security policies to restrict what is
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1267 accessible by the tool.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1268
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1269 Enabling network access does not imply a publically routable IP
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1270 address or the ability to accept inbound connections.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1271
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1272 fields:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1273 - name: class
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1274 type: string
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
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1275 doc: "Always 'NetworkAccess'"
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1276 jsonldPredicate:
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1277 "_id": "@type"
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1278 "_type": "@vocab"
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1279 - name: networkAccess
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1280 type: [boolean, Expression]
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1281
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1282 - name: InplaceUpdateRequirement
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1283 type: record
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1284 extends: cwl:ProcessRequirement
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1285 doc: |
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1286
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1287 If `inplaceUpdate` is true, then an implementation supporting this
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1288 feature may permit tools to directly update files with `writable:
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1289 true` in InitialWorkDirRequirement. That is, as an optimization,
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1290 files may be destructively modified in place as opposed to copied
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1291 and updated.
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1292
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1293 An implementation must ensure that only one workflow step may
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1294 access a writable file at a time. It is an error if a file which
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1295 is writable by one workflow step file is accessed (for reading or
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1296 writing) by any other workflow step running independently.
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1297 However, a file which has been updated in a previous completed
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1298 step may be used as input to multiple steps, provided it is
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1299 read-only in every step.
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1300
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1301 Workflow steps which modify a file must produce the modified file
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1302 as output. Downstream steps which futher process the file must
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1303 use the output of previous steps, and not refer to a common input
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1304 (this is necessary for both ordering and correctness).
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1305
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1306 Workflow authors should provide this in the `hints` section. The
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1307 intent of this feature is that workflows produce the same results
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1308 whether or not InplaceUpdateRequirement is supported by the
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1309 implementation, and this feature is primarily available as an
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1310 optimization for particular environments.
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1311
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1312 Users and implementers should be aware that workflows that
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1313 destructively modify inputs may not be repeatable or reproducible.
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1314 In particular, enabling this feature implies that WorkReuse should
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1315 not be enabled.
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1316
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1317 fields:
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1318 class:
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1319 type: string
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1320 doc: "Always 'InplaceUpdateRequirement'"
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1321 jsonldPredicate:
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1322 "_id": "@type"
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1323 "_type": "@vocab"
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1324 inplaceUpdate:
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1325 type: boolean
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1326
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1327 - type: record
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1328 name: ToolTimeLimit
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1329 extends: ProcessRequirement
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1330 doc: |
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1331 Set an upper limit on the execution time of a CommandLineTool.
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1332 A CommandLineTool whose execution duration exceeds the time
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1333 limit may be preemptively terminated and considered failed.
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