annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2.0-dev3/Process.yml @ 0:4f3585e2f14b draft default tip

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author shellac
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 sld: "https://w3id.org/cwl/salad#"
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7 rdfs: "http://www.w3.org/2000/01/rdf-schema#"
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8
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9 $graph:
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10
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11 - name: "Common Workflow Language, v1.2.0-dev3"
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12 type: documentation
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13 doc: {$include: concepts.md}
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14
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15 - $import: "salad/schema_salad/metaschema/metaschema_base.yml"
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16
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17 - name: BaseTypesDoc
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18 type: documentation
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19 doc: |
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20 ## Base types
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21 docChild:
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22 - "#CWLType"
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23 - "#Process"
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24
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25 - type: enum
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26 name: CWLVersion
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27 doc: "Version symbols for published CWL document versions."
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28 symbols:
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29 - cwl:draft-2
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30 - cwl:draft-3.dev1
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31 - cwl:draft-3.dev2
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32 - cwl:draft-3.dev3
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33 - cwl:draft-3.dev4
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34 - cwl:draft-3.dev5
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35 - cwl:draft-3
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36 - cwl:draft-4.dev1
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37 - cwl:draft-4.dev2
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38 - cwl:draft-4.dev3
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39 - cwl:v1.0.dev4
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40 - cwl:v1.0
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41 - cwl:v1.1.0-dev1 # a dash is required by the semver 2.0 rules
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42 - cwl:v1.1
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43 - cwl:v1.2.0-dev1
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44 - cwl:v1.2.0-dev2
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45 - cwl:v1.2.0-dev3
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46
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47 - name: CWLType
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48 type: enum
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49 extends: "sld:PrimitiveType"
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50 symbols:
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51 - cwl:File
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52 - cwl:Directory
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53 doc:
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54 - "Extends primitive types with the concept of a file and directory as a builtin type."
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55 - "File: A File object"
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56 - "Directory: A Directory object"
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57
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58 - name: File
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59 type: record
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60 docParent: "#CWLType"
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61 doc: |
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62 Represents a file (or group of files when `secondaryFiles` is provided) that
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63 will be accessible by tools using standard POSIX file system call API such as
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64 open(2) and read(2).
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65
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66 Files are represented as objects with `class` of `File`. File objects have
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67 a number of properties that provide metadata about the file.
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68
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69 The `location` property of a File is a URI that uniquely identifies the
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70 file. Implementations must support the file:// URI scheme and may support
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71 other schemes such as http://. The value of `location` may also be a
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72 relative reference, in which case it must be resolved relative to the URI
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73 of the document it appears in. Alternately to `location`, implementations
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74 must also accept the `path` property on File, which must be a filesystem
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75 path available on the same host as the CWL runner (for inputs) or the
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76 runtime environment of a command line tool execution (for command line tool
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77 outputs).
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78
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79 If no `location` or `path` is specified, a file object must specify
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80 `contents` with the UTF-8 text content of the file. This is a "file
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81 literal". File literals do not correspond to external resources, but are
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82 created on disk with `contents` with when needed for a executing a tool.
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83 Where appropriate, expressions can return file literals to define new files
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84 on a runtime. The maximum size of `contents` is 64 kilobytes.
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85
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86 The `basename` property defines the filename on disk where the file is
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87 staged. This may differ from the resource name. If not provided,
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88 `basename` must be computed from the last path part of `location` and made
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89 available to expressions.
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90
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91 The `secondaryFiles` property is a list of File or Directory objects that
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92 must be staged in the same directory as the primary file. It is an error
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93 for file names to be duplicated in `secondaryFiles`.
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94
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95 The `size` property is the size in bytes of the File. It must be computed
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96 from the resource and made available to expressions. The `checksum` field
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97 contains a cryptographic hash of the file content for use it verifying file
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98 contents. Implementations may, at user option, enable or disable
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99 computation of the `checksum` field for performance or other reasons.
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100 However, the ability to compute output checksums is required to pass the
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101 CWL conformance test suite.
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102
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103 When executing a CommandLineTool, the files and secondary files may be
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104 staged to an arbitrary directory, but must use the value of `basename` for
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105 the filename. The `path` property must be file path in the context of the
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106 tool execution runtime (local to the compute node, or within the executing
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107 container). All computed properties should be available to expressions.
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108 File literals also must be staged and `path` must be set.
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109
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110 When collecting CommandLineTool outputs, `glob` matching returns file paths
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111 (with the `path` property) and the derived properties. This can all be
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112 modified by `outputEval`. Alternately, if the file `cwl.output.json` is
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113 present in the output, `outputBinding` is ignored.
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114
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115 File objects in the output must provide either a `location` URI or a `path`
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116 property in the context of the tool execution runtime (local to the compute
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117 node, or within the executing container).
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118
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119 When evaluating an ExpressionTool, file objects must be referenced via
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120 `location` (the expression tool does not have access to files on disk so
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121 `path` is meaningless) or as file literals. It is legal to return a file
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122 object with an existing `location` but a different `basename`. The
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123 `loadContents` field of ExpressionTool inputs behaves the same as on
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124 CommandLineTool inputs, however it is not meaningful on the outputs.
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125
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126 An ExpressionTool may forward file references from input to output by using
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127 the same value for `location`.
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128
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129 fields:
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130 - name: class
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131 type:
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132 type: enum
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133 name: File_class
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134 symbols:
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135 - cwl:File
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136 jsonldPredicate:
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137 _id: "@type"
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138 _type: "@vocab"
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139 doc: Must be `File` to indicate this object describes a file.
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140 - name: location
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141 type: string?
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142 doc: |
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143 An IRI that identifies the file resource. This may be a relative
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144 reference, in which case it must be resolved using the base IRI of the
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145 document. The location may refer to a local or remote resource; the
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146 implementation must use the IRI to retrieve file content. If an
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147 implementation is unable to retrieve the file content stored at a
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148 remote resource (due to unsupported protocol, access denied, or other
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149 issue) it must signal an error.
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150
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151 If the `location` field is not provided, the `contents` field must be
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152 provided. The implementation must assign a unique identifier for
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153 the `location` field.
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154
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155 If the `path` field is provided but the `location` field is not, an
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156 implementation may assign the value of the `path` field to `location`,
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157 then follow the rules above.
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158 jsonldPredicate:
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159 _id: "@id"
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160 _type: "@id"
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161 - name: path
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162 type: string?
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163 doc: |
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164 The local host path where the File is available when a CommandLineTool is
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165 executed. This field must be set by the implementation. The final
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166 path component must match the value of `basename`. This field
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167 must not be used in any other context. The command line tool being
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168 executed must be able to to access the file at `path` using the POSIX
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169 `open(2)` syscall.
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170
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171 As a special case, if the `path` field is provided but the `location`
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172 field is not, an implementation may assign the value of the `path`
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173 field to `location`, and remove the `path` field.
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174
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175 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
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176 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
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177 `<space>`, `<tab>`, and `<newline>`) or characters
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178 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
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179 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
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180 then implementations may terminate the process with a
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181 `permanentFailure`.
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182 jsonldPredicate:
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183 "_id": "cwl:path"
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184 "_type": "@id"
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185 - name: basename
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186 type: string?
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187 doc: |
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188 The base name of the file, that is, the name of the file without any
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189 leading directory path. The base name must not contain a slash `/`.
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190
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191 If not provided, the implementation must set this field based on the
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192 `location` field by taking the final path component after parsing
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193 `location` as an IRI. If `basename` is provided, it is not required to
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194 match the value from `location`.
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195
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196 When this file is made available to a CommandLineTool, it must be named
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197 with `basename`, i.e. the final component of the `path` field must match
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198 `basename`.
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199 jsonldPredicate: "cwl:basename"
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200 - name: dirname
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201 type: string?
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202 doc: |
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203 The name of the directory containing file, that is, the path leading up
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204 to the final slash in the path such that `dirname + '/' + basename ==
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205 path`.
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206
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207 The implementation must set this field based on the value of `path`
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208 prior to evaluating parameter references or expressions in a
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209 CommandLineTool document. This field must not be used in any other
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210 context.
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211 - name: nameroot
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212 type: string?
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213 doc: |
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214 The basename root such that `nameroot + nameext == basename`, and
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215 `nameext` is empty or begins with a period and contains at most one
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216 period. For the purposess of path splitting leading periods on the
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217 basename are ignored; a basename of `.cshrc` will have a nameroot of
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218 `.cshrc`.
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219
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220 The implementation must set this field automatically based on the value
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221 of `basename` prior to evaluating parameter references or expressions.
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222 - name: nameext
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223 type: string?
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224 doc: |
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225 The basename extension such that `nameroot + nameext == basename`, and
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226 `nameext` is empty or begins with a period and contains at most one
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227 period. Leading periods on the basename are ignored; a basename of
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228 `.cshrc` will have an empty `nameext`.
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229
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230 The implementation must set this field automatically based on the value
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231 of `basename` prior to evaluating parameter references or expressions.
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232 - name: checksum
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233 type: string?
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234 doc: |
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235 Optional hash code for validating file integrity. Currently must be in the form
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236 "sha1$ + hexadecimal string" using the SHA-1 algorithm.
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237 - name: size
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238 type: long?
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239 doc: Optional file size
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240 - name: "secondaryFiles"
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241 type:
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242 - "null"
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243 - type: array
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244 items: [File, Directory]
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245 jsonldPredicate:
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246 _id: "cwl:secondaryFiles"
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247 secondaryFilesDSL: true
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248 doc: |
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249 A list of additional files or directories that are associated with the
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250 primary file and must be transferred alongside the primary file.
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251 Examples include indexes of the primary file, or external references
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252 which must be included when loading primary document. A file object
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253 listed in `secondaryFiles` may itself include `secondaryFiles` for
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254 which the same rules apply.
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255 - name: format
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256 type: string?
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257 jsonldPredicate:
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258 _id: cwl:format
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259 _type: "@id"
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260 identity: true
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261 doc: |
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262 The format of the file: this must be an IRI of a concept node that
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263 represents the file format, preferrably defined within an ontology.
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264 If no ontology is available, file formats may be tested by exact match.
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265
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266 Reasoning about format compatability must be done by checking that an
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267 input file format is the same, `owl:equivalentClass` or
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268 `rdfs:subClassOf` the format required by the input parameter.
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269 `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if
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270 `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer
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271 `<C> owl:subclassOf <A>`.
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272
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273 File format ontologies may be provided in the "$schema" metadata at the
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274 root of the document. If no ontologies are specified in `$schema`, the
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275 runtime may perform exact file format matches.
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276 - name: contents
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277 type: string?
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278 doc: |
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279 File contents literal. Maximum of 64 KiB.
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280
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281 If neither `location` nor `path` is provided, `contents` must be
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282 non-null. The implementation must assign a unique identifier for the
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283 `location` field. When the file is staged as input to CommandLineTool,
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284 the value of `contents` must be written to a file.
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285
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286 If `loadContents` of `inputBinding` or `outputBinding` is true and
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287 `location` is valid, the implementation must read up to the first 64
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288 KiB of text from the file and place it in the "contents" field.
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289
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290
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291 - name: Directory
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292 type: record
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293 docAfter: "#File"
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294 doc: |
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295 Represents a directory to present to a command line tool.
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296
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297 Directories are represented as objects with `class` of `Directory`. Directory objects have
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298 a number of properties that provide metadata about the directory.
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299
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300 The `location` property of a Directory is a URI that uniquely identifies
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301 the directory. Implementations must support the file:// URI scheme and may
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302 support other schemes such as http://. Alternately to `location`,
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303 implementations must also accept the `path` property on Directory, which
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304 must be a filesystem path available on the same host as the CWL runner (for
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305 inputs) or the runtime environment of a command line tool execution (for
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306 command line tool outputs).
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307
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308 A Directory object may have a `listing` field. This is a list of File and
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309 Directory objects that are contained in the Directory. For each entry in
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310 `listing`, the `basename` property defines the name of the File or
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311 Subdirectory when staged to disk. If `listing` is not provided, the
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312 implementation must have some way of fetching the Directory listing at
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313 runtime based on the `location` field.
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314
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315 If a Directory does not have `location`, it is a Directory literal. A
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316 Directory literal must provide `listing`. Directory literals must be
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317 created on disk at runtime as needed.
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318
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319 The resources in a Directory literal do not need to have any implied
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320 relationship in their `location`. For example, a Directory listing may
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321 contain two files located on different hosts. It is the responsibility of
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322 the runtime to ensure that those files are staged to disk appropriately.
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323 Secondary files associated with files in `listing` must also be staged to
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324 the same Directory.
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325
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326 When executing a CommandLineTool, Directories must be recursively staged
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327 first and have local values of `path` assigend.
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328
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329 Directory objects in CommandLineTool output must provide either a
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330 `location` URI or a `path` property in the context of the tool execution
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331 runtime (local to the compute node, or within the executing container).
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332
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333 An ExpressionTool may forward file references from input to output by using
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334 the same value for `location`.
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335
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336 Name conflicts (the same `basename` appearing multiple times in `listing`
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337 or in any entry in `secondaryFiles` in the listing) is a fatal error.
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338
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339 fields:
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340 - name: class
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341 type:
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342 type: enum
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343 name: Directory_class
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344 symbols:
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345 - cwl:Directory
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346 jsonldPredicate:
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347 _id: "@type"
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348 _type: "@vocab"
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349 doc: Must be `Directory` to indicate this object describes a Directory.
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350 - name: location
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351 type: string?
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352 doc: |
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353 An IRI that identifies the directory resource. This may be a relative
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354 reference, in which case it must be resolved using the base IRI of the
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355 document. The location may refer to a local or remote resource. If
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356 the `listing` field is not set, the implementation must use the
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357 location IRI to retrieve directory listing. If an implementation is
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358 unable to retrieve the directory listing stored at a remote resource (due to
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359 unsupported protocol, access denied, or other issue) it must signal an
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360 error.
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361
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362 If the `location` field is not provided, the `listing` field must be
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363 provided. The implementation must assign a unique identifier for
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364 the `location` field.
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365
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366 If the `path` field is provided but the `location` field is not, an
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367 implementation may assign the value of the `path` field to `location`,
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368 then follow the rules above.
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369 jsonldPredicate:
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370 _id: "@id"
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371 _type: "@id"
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parents:
diff changeset
372 - name: path
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parents:
diff changeset
373 type: string?
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parents:
diff changeset
374 doc: |
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parents:
diff changeset
375 The local path where the Directory is made available prior to executing a
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parents:
diff changeset
376 CommandLineTool. This must be set by the implementation. This field
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parents:
diff changeset
377 must not be used in any other context. The command line tool being
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parents:
diff changeset
378 executed must be able to to access the directory at `path` using the POSIX
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parents:
diff changeset
379 `opendir(2)` syscall.
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parents:
diff changeset
380
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parents:
diff changeset
381 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
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parents:
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382 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
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parents:
diff changeset
383 `<space>`, `<tab>`, and `<newline>`) or characters
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parents:
diff changeset
384 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
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shellac
parents:
diff changeset
385 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
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parents:
diff changeset
386 then implementations may terminate the process with a
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parents:
diff changeset
387 `permanentFailure`.
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parents:
diff changeset
388 jsonldPredicate:
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parents:
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389 _id: "cwl:path"
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parents:
diff changeset
390 _type: "@id"
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parents:
diff changeset
391 - name: basename
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parents:
diff changeset
392 type: string?
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diff changeset
393 doc: |
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394 The base name of the directory, that is, the name of the file without any
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parents:
diff changeset
395 leading directory path. The base name must not contain a slash `/`.
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parents:
diff changeset
396
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diff changeset
397 If not provided, the implementation must set this field based on the
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398 `location` field by taking the final path component after parsing
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parents:
diff changeset
399 `location` as an IRI. If `basename` is provided, it is not required to
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parents:
diff changeset
400 match the value from `location`.
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parents:
diff changeset
401
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parents:
diff changeset
402 When this file is made available to a CommandLineTool, it must be named
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parents:
diff changeset
403 with `basename`, i.e. the final component of the `path` field must match
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parents:
diff changeset
404 `basename`.
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parents:
diff changeset
405 jsonldPredicate: "cwl:basename"
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parents:
diff changeset
406 - name: listing
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parents:
diff changeset
407 type:
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parents:
diff changeset
408 - "null"
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parents:
diff changeset
409 - type: array
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parents:
diff changeset
410 items: [File, Directory]
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parents:
diff changeset
411 doc: |
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parents:
diff changeset
412 List of files or subdirectories contained in this directory. The name
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parents:
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413 of each file or subdirectory is determined by the `basename` field of
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parents:
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414 each `File` or `Directory` object. It is an error if a `File` shares a
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
415 `basename` with any other entry in `listing`. If two or more
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parents:
diff changeset
416 `Directory` object share the same `basename`, this must be treated as
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parents:
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417 equivalent to a single subdirectory with the listings recursively
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parents:
diff changeset
418 merged.
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419 jsonldPredicate:
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420 _id: "cwl:listing"
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parents:
diff changeset
421
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parents:
diff changeset
422 - name: Labeled
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parents:
diff changeset
423 type: record
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parents:
diff changeset
424 abstract: true
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parents:
diff changeset
425 fields:
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parents:
diff changeset
426 - name: label
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parents:
diff changeset
427 type:
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parents:
diff changeset
428 - "null"
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parents:
diff changeset
429 - string
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parents:
diff changeset
430 jsonldPredicate: "rdfs:label"
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parents:
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431 doc: "A short, human-readable label of this object."
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parents:
diff changeset
432
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shellac
parents:
diff changeset
433
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shellac
parents:
diff changeset
434 - name: Identified
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parents:
diff changeset
435 type: record
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parents:
diff changeset
436 abstract: true
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parents:
diff changeset
437 fields:
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shellac
parents:
diff changeset
438 - name: id
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shellac
parents:
diff changeset
439 type: string?
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parents:
diff changeset
440 jsonldPredicate: "@id"
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parents:
diff changeset
441 doc: "The unique identifier for this object."
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shellac
parents:
diff changeset
442
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
443
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
444 - name: LoadListingEnum
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
445 type: enum
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
446 symbols: [no_listing, shallow_listing, deep_listing]
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shellac
parents:
diff changeset
447 doc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
448 - |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
449 Specify the desired behavior for loading the `listing` field of
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
450 a Directory object for use by expressions.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
451 - "no_listing: Do not load the directory listing."
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
452 - "shallow_listing: Only load the top level listing, do not recurse into subdirectories."
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
453 - "deep_listing: Load the directory listing and recursively load all subdirectories as well."
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shellac
parents:
diff changeset
454
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shellac
parents:
diff changeset
455
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shellac
parents:
diff changeset
456 - name: LoadContents
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shellac
parents:
diff changeset
457 type: record
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
458 abstract: true
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
459 fields:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
460 - name: loadContents
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shellac
parents:
diff changeset
461 type: boolean?
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parents:
diff changeset
462 jsonldPredicate: "cwl:loadContents"
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parents:
diff changeset
463 doc: |
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464 Only valid when `type: File` or is an array of `items: File`.
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parents:
diff changeset
465
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parents:
diff changeset
466 Read up to the first 64 KiB of text from the file and place it in the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
467 "contents" field of the file object for use by expressions.
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parents:
diff changeset
468 - name: loadListing
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
469 type: LoadListingEnum?
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parents:
diff changeset
470 jsonldPredicate: "cwl:loadListing"
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parents:
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471 doc: |
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
472 Only valid when `type: Directory` or is an array of `items: Directory`.
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shellac
parents:
diff changeset
473
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
474 Specify the desired behavior for loading the `listing` field of
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
475 a Directory object for use by expressions.
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shellac
parents:
diff changeset
476
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shellac
parents:
diff changeset
477 The order of precedence for loadListing is:
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parents:
diff changeset
478
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parents:
diff changeset
479 1. `loadListing` on an individual parameter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
480 2. Inherited from `LoadListingRequirement`
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parents:
diff changeset
481 3. By default: `no_listing`
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parents:
diff changeset
482
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parents:
diff changeset
483 - name: FieldBase
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
484 type: record
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
485 extends: Labeled
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parents:
diff changeset
486 abstract: true
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parents:
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487 fields:
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parents:
diff changeset
488 secondaryFiles:
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parents:
diff changeset
489 type:
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parents:
diff changeset
490 - "null"
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parents:
diff changeset
491 - SecondaryFileSchema
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parents:
diff changeset
492 - type: array
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
493 items: SecondaryFileSchema
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parents:
diff changeset
494 jsonldPredicate:
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parents:
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495 _id: "cwl:secondaryFiles"
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parents:
diff changeset
496 secondaryFilesDSL: true
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parents:
diff changeset
497 doc: |
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diff changeset
498 Only valid when `type: File` or is an array of `items: File`.
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parents:
diff changeset
499
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parents:
diff changeset
500 Provides a pattern or expression specifying files or
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parents:
diff changeset
501 directories that should be included alongside the primary
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parents:
diff changeset
502 file. Secondary files may be required or optional. When not
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parents:
diff changeset
503 explicitly specified, secondary files specified for `inputs`
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parents:
diff changeset
504 are required and `outputs` are optional. An implementation
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parents:
diff changeset
505 must include matching Files and Directories in the
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parents:
diff changeset
506 `secondaryFiles` property of the primary file. These Files
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parents:
diff changeset
507 and Directories must be transferred and staged alongside the
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parents:
diff changeset
508 primary file. An implementation may fail workflow execution
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parents:
diff changeset
509 if a required secondary file does not exist.
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parents:
diff changeset
510
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parents:
diff changeset
511 If the value is an expression, the value of `self` in the expression
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parents:
diff changeset
512 must be the primary input or output File object to which this binding
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parents:
diff changeset
513 applies. The `basename`, `nameroot` and `nameext` fields must be
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parents:
diff changeset
514 present in `self`. For `CommandLineTool` outputs the `path` field must
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parents:
diff changeset
515 also be present. The expression must return a filename string relative
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parents:
diff changeset
516 to the path to the primary File, a File or Directory object with either
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parents:
diff changeset
517 `path` or `location` and `basename` fields set, or an array consisting
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parents:
diff changeset
518 of strings or File or Directory objects. It is legal to reference an
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parents:
diff changeset
519 unchanged File or Directory object taken from input as a secondaryFile.
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parents:
diff changeset
520 The expression may return "null" in which case there is no secondaryFile
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parents:
diff changeset
521 from that expression.
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parents:
diff changeset
522
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parents:
diff changeset
523 To work on non-filename-preserving storage systems, portable tool
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parents:
diff changeset
524 descriptions should avoid constructing new values from `location`, but
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parents:
diff changeset
525 should construct relative references using `basename` or `nameroot`
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parents:
diff changeset
526 instead.
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parents:
diff changeset
527
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parents:
diff changeset
528 If a value in `secondaryFiles` is a string that is not an expression,
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parents:
diff changeset
529 it specifies that the following pattern should be applied to the path
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parents:
diff changeset
530 of the primary file to yield a filename relative to the primary File:
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parents:
diff changeset
531
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parents:
diff changeset
532 1. If string ends with `?` character, remove the last `?` and mark
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parents:
diff changeset
533 the resulting secondary file as optional.
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parents:
diff changeset
534 2. If string begins with one or more caret `^` characters, for each
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parents:
diff changeset
535 caret, remove the last file extension from the path (the last
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
536 period `.` and all following characters). If there are no file
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parents:
diff changeset
537 extensions, the path is unchanged.
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parents:
diff changeset
538 3. Append the remainder of the string to the end of the file path.
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parents:
diff changeset
539
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parents:
diff changeset
540 streamable:
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parents:
diff changeset
541 type: boolean?
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parents:
diff changeset
542 doc: |
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parents:
diff changeset
543 Only valid when `type: File` or is an array of `items: File`.
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parents:
diff changeset
544
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parents:
diff changeset
545 A value of `true` indicates that the file is read or written
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parents:
diff changeset
546 sequentially without seeking. An implementation may use this flag to
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parents:
diff changeset
547 indicate whether it is valid to stream file contents using a named
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parents:
diff changeset
548 pipe. Default: `false`.
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parents:
diff changeset
549
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parents:
diff changeset
550
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parents:
diff changeset
551 - name: InputFormat
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parents:
diff changeset
552 type: record
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parents:
diff changeset
553 abstract: true
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parents:
diff changeset
554 fields:
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parents:
diff changeset
555 format:
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parents:
diff changeset
556 type:
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parents:
diff changeset
557 - "null"
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parents:
diff changeset
558 - string
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parents:
diff changeset
559 - type: array
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parents:
diff changeset
560 items: string
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parents:
diff changeset
561 - Expression
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parents:
diff changeset
562 jsonldPredicate:
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parents:
diff changeset
563 _id: cwl:format
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parents:
diff changeset
564 _type: "@id"
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parents:
diff changeset
565 identity: true
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parents:
diff changeset
566 doc: |
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parents:
diff changeset
567 Only valid when `type: File` or is an array of `items: File`.
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parents:
diff changeset
568
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parents:
diff changeset
569 This must be one or more IRIs of concept nodes
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parents:
diff changeset
570 that represents file formats which are allowed as input to this
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parents:
diff changeset
571 parameter, preferrably defined within an ontology. If no ontology is
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parents:
diff changeset
572 available, file formats may be tested by exact match.
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parents:
diff changeset
573
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parents:
diff changeset
574
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parents:
diff changeset
575 - name: OutputFormat
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parents:
diff changeset
576 type: record
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parents:
diff changeset
577 abstract: true
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parents:
diff changeset
578 fields:
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parents:
diff changeset
579 format:
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parents:
diff changeset
580 type:
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parents:
diff changeset
581 - "null"
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parents:
diff changeset
582 - string
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parents:
diff changeset
583 - Expression
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parents:
diff changeset
584 jsonldPredicate:
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parents:
diff changeset
585 _id: cwl:format
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parents:
diff changeset
586 _type: "@id"
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parents:
diff changeset
587 identity: true
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parents:
diff changeset
588 doc: |
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diff changeset
589 Only valid when `type: File` or is an array of `items: File`.
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parents:
diff changeset
590
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parents:
diff changeset
591 This is the file format that will be assigned to the output
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parents:
diff changeset
592 File object.
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parents:
diff changeset
593
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parents:
diff changeset
594
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parents:
diff changeset
595 - name: Parameter
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parents:
diff changeset
596 type: record
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parents:
diff changeset
597 extends: [FieldBase, sld:Documented, Identified]
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parents:
diff changeset
598 abstract: true
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parents:
diff changeset
599 doc: |
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parents:
diff changeset
600 Define an input or output parameter to a process.
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parents:
diff changeset
601
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parents:
diff changeset
602
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parents:
diff changeset
603 - type: enum
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parents:
diff changeset
604 name: Expression
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parents:
diff changeset
605 doc: |
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parents:
diff changeset
606 'Expression' is not a real type. It indicates that a field must allow
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parents:
diff changeset
607 runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement)
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shellac
parents:
diff changeset
608 is declared and supported by the platform, the field must also allow
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parents:
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609 Javascript expressions.
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parents:
diff changeset
610 symbols:
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parents:
diff changeset
611 - cwl:ExpressionPlaceholder
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parents:
diff changeset
612
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parents:
diff changeset
613
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parents:
diff changeset
614 - name: InputBinding
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parents:
diff changeset
615 type: record
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parents:
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616 fields:
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parents:
diff changeset
617 - name: loadContents
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parents:
diff changeset
618 type:
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parents:
diff changeset
619 - "null"
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parents:
diff changeset
620 - boolean
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621 jsonldPredicate: "cwl:loadContents"
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parents:
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622 doc: |
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diff changeset
623 Use of `loadContents` in `InputBinding` is deprecated.
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parents:
diff changeset
624 Preserved for v1.0 backwards compatability. Will be removed in
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parents:
diff changeset
625 CWL v2.0. Use `InputParameter.loadContents` instead.
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parents:
diff changeset
626
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parents:
diff changeset
627 Only valid when `type: File` or is an array of `items: File`.
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parents:
diff changeset
628
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parents:
diff changeset
629 Read up to the first 64 KiB of text from the file and place it in the
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parents:
diff changeset
630 "contents" field of the file object for use by expressions.
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parents:
diff changeset
631
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parents:
diff changeset
632
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parents:
diff changeset
633 - name: IOSchema
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parents:
diff changeset
634 extends: [Labeled, sld:Documented]
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parents:
diff changeset
635 type: record
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parents:
diff changeset
636 abstract: true
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diff changeset
637 fields:
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parents:
diff changeset
638 - name: name
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parents:
diff changeset
639 type: string?
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parents:
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640 jsonldPredicate: "@id"
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parents:
diff changeset
641 doc: "The identifier for this type"
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parents:
diff changeset
642
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parents:
diff changeset
643 - name: InputSchema
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parents:
diff changeset
644 extends: [IOSchema]
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diff changeset
645 type: record
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diff changeset
646 abstract: true
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parents:
diff changeset
647
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parents:
diff changeset
648 - name: OutputSchema
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parents:
diff changeset
649 extends: [IOSchema]
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diff changeset
650 type: record
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diff changeset
651 abstract: true
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diff changeset
652
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diff changeset
653
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parents:
diff changeset
654 - name: InputRecordField
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parents:
diff changeset
655 type: record
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parents:
diff changeset
656 extends: [sld:RecordField, FieldBase, InputFormat, LoadContents]
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diff changeset
657 specialize:
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diff changeset
658 - specializeFrom: "sld:RecordSchema"
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diff changeset
659 specializeTo: InputRecordSchema
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diff changeset
660 - specializeFrom: "sld:EnumSchema"
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diff changeset
661 specializeTo: InputEnumSchema
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diff changeset
662 - specializeFrom: "sld:ArraySchema"
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663 specializeTo: InputArraySchema
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diff changeset
664 - specializeFrom: "sld:PrimitiveType"
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diff changeset
665 specializeTo: CWLType
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parents:
diff changeset
666
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parents:
diff changeset
667
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parents:
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668 - name: InputRecordSchema
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parents:
diff changeset
669 type: record
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diff changeset
670 extends: ["sld:RecordSchema", InputSchema]
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671 specialize:
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672 - specializeFrom: "sld:RecordField"
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673 specializeTo: InputRecordField
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674
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diff changeset
675
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parents:
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676 - name: InputEnumSchema
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diff changeset
677 type: record
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678 extends: ["sld:EnumSchema", InputSchema]
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679
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680
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parents:
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681 - name: InputArraySchema
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parents:
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682 type: record
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683 extends: ["sld:ArraySchema", InputSchema]
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684 specialize:
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diff changeset
685 - specializeFrom: "sld:RecordSchema"
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686 specializeTo: InputRecordSchema
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parents:
diff changeset
687 - specializeFrom: "sld:EnumSchema"
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688 specializeTo: InputEnumSchema
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diff changeset
689 - specializeFrom: "sld:ArraySchema"
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690 specializeTo: InputArraySchema
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parents:
diff changeset
691 - specializeFrom: "sld:PrimitiveType"
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692 specializeTo: CWLType
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693
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diff changeset
694
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parents:
diff changeset
695 - name: OutputRecordField
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diff changeset
696 type: record
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diff changeset
697 extends: [sld:RecordField, FieldBase, OutputFormat]
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diff changeset
698 specialize:
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diff changeset
699 - specializeFrom: "sld:RecordSchema"
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diff changeset
700 specializeTo: OutputRecordSchema
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parents:
diff changeset
701 - specializeFrom: "sld:EnumSchema"
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parents:
diff changeset
702 specializeTo: OutputEnumSchema
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parents:
diff changeset
703 - specializeFrom: "sld:ArraySchema"
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diff changeset
704 specializeTo: OutputArraySchema
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parents:
diff changeset
705 - specializeFrom: "sld:PrimitiveType"
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parents:
diff changeset
706 specializeTo: CWLType
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parents:
diff changeset
707
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diff changeset
708
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parents:
diff changeset
709 - name: OutputRecordSchema
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parents:
diff changeset
710 type: record
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diff changeset
711 extends: ["sld:RecordSchema", "#OutputSchema"]
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712 docParent: "#OutputParameter"
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713 specialize:
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diff changeset
714 - specializeFrom: "sld:RecordField"
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parents:
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715 specializeTo: OutputRecordField
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parents:
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716
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717
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718 - name: OutputEnumSchema
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parents:
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719 type: record
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diff changeset
720 extends: ["sld:EnumSchema", OutputSchema]
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diff changeset
721 docParent: "#OutputParameter"
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diff changeset
722
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parents:
diff changeset
723
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parents:
diff changeset
724 - name: OutputArraySchema
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parents:
diff changeset
725 type: record
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diff changeset
726 extends: ["sld:ArraySchema", OutputSchema]
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727 docParent: "#OutputParameter"
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diff changeset
728 specialize:
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diff changeset
729 - specializeFrom: "sld:RecordSchema"
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730 specializeTo: OutputRecordSchema
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diff changeset
731 - specializeFrom: "sld:EnumSchema"
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732 specializeTo: OutputEnumSchema
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733 - specializeFrom: "sld:ArraySchema"
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734 specializeTo: OutputArraySchema
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diff changeset
735 - specializeFrom: "sld:PrimitiveType"
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parents:
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736 specializeTo: CWLType
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parents:
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737
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738
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parents:
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739 - name: InputParameter
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parents:
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740 type: record
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741 abstract: true
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742 extends: [Parameter, InputFormat, LoadContents]
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743 fields:
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parents:
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744 - name: default
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parents:
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745 type: Any?
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parents:
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746 jsonldPredicate:
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747 _id: sld:default
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748 noLinkCheck: true
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749 doc: |
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750 The default value to use for this parameter if the parameter is missing
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751 from the input object, or if the value of the parameter in the input
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752 object is `null`. Default values are applied before evaluating expressions
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parents:
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753 (e.g. dependent `valueFrom` fields).
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parents:
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754
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755
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756 - name: OutputParameter
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parents:
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757 type: record
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758 extends: [Parameter, OutputFormat]
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759 abstract: true
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760
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761
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762 - type: record
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763 name: ProcessRequirement
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764 abstract: true
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765 doc: |
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766 A process requirement declares a prerequisite that may or must be fulfilled
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767 before executing a process. See [`Process.hints`](#process) and
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768 [`Process.requirements`](#process).
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769
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770 Process requirements are the primary mechanism for specifying extensions to
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771 the CWL core specification.
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772
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773
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774 - type: record
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775 name: Process
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776 extends: [Identified, Labeled, sld:Documented]
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777 abstract: true
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778 doc: |
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779
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780 The base executable type in CWL is the `Process` object defined by the
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781 document. Note that the `Process` object is abstract and cannot be
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782 directly executed.
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783
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784 fields:
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785 - name: inputs
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786 type:
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787 type: array
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788 items: InputParameter
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789 jsonldPredicate:
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790 _id: "cwl:inputs"
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791 mapSubject: id
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792 mapPredicate: type
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793 doc: |
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794 Defines the input parameters of the process. The process is ready to
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795 run when all required input parameters are associated with concrete
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796 values. Input parameters include a schema for each parameter which is
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797 used to validate the input object. It may also be used to build a user
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798 interface for constructing the input object.
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799
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800 When accepting an input object, all input parameters must have a value.
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801 If an input parameter is missing from the input object, it must be
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802 assigned a value of `null` (or the value of `default` for that
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803 parameter, if provided) for the purposes of validation and evaluation
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804 of expressions.
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805
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806 - name: outputs
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807 type:
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808 type: array
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809 items: OutputParameter
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810 jsonldPredicate:
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811 _id: "cwl:outputs"
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812 mapSubject: id
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813 mapPredicate: type
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814 doc: |
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815 Defines the parameters representing the output of the process. May be
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diff changeset
816 used to generate and/or validate the output object.
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817 - name: requirements
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818 type: ProcessRequirement[]?
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819 jsonldPredicate:
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820 _id: "cwl:requirements"
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821 mapSubject: class
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822 doc: |
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823 Declares requirements that apply to either the runtime environment or the
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diff changeset
824 workflow engine that must be met in order to execute this process. If
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diff changeset
825 an implementation cannot satisfy all requirements, or a requirement is
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diff changeset
826 listed which is not recognized by the implementation, it is a fatal
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827 error and the implementation must not attempt to run the process,
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828 unless overridden at user option.
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829 - name: hints
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830 type: Any[]?
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831 doc: |
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832 Declares hints applying to either the runtime environment or the
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diff changeset
833 workflow engine that may be helpful in executing this process. It is
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834 not an error if an implementation cannot satisfy all hints, however
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835 the implementation may report a warning.
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836 jsonldPredicate:
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diff changeset
837 _id: cwl:hints
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838 noLinkCheck: true
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839 mapSubject: class
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840 - name: cwlVersion
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diff changeset
841 type: CWLVersion?
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842 doc: |
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843 CWL document version. Always required at the document root. Not
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844 required for a Process embedded inside another Process.
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845 jsonldPredicate:
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846 "_id": "cwl:cwlVersion"
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847 "_type": "@vocab"
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848 - name: intent
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849 type: string[]?
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850 jsonldPredicate:
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851 _type: "@id"
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852 identity: true
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853 doc: |
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854 An identifier for the type of computational operation, of this Process.
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855 Especially useful for "class: Operation", but can also be used for
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856 CommandLineTool, Workflow, or ExpressionTool.
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857
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858 If provided, then this must be an IRI of a concept node that
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859 represents the type of operation, preferrably defined within an ontology.
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860
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861 For example, in the domain of bioinformatics, one can use an IRI from
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862 the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004),
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863 like [Alignment](http://edamontology.org/operation_2928),
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864 or [Clustering](http://edamontology.org/operation_3432); or a more
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865 specific Operation concept like
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866 [Split read mapping](http://edamontology.org/operation_3199).
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867
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868 - name: InlineJavascriptRequirement
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869 type: record
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870 extends: ProcessRequirement
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871 doc: |
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872 Indicates that the workflow platform must support inline Javascript expressions.
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873 If this requirement is not present, the workflow platform must not perform expression
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874 interpolatation.
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875 fields:
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876 - name: class
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877 type: string
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878 doc: "Always 'InlineJavascriptRequirement'"
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879 jsonldPredicate:
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880 "_id": "@type"
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881 "_type": "@vocab"
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882 - name: expressionLib
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883 type: string[]?
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884 doc: |
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885 Additional code fragments that will also be inserted
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886 before executing the expression code. Allows for function definitions that may
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diff changeset
887 be called from CWL expressions.
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parents:
diff changeset
888
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parents:
diff changeset
889
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parents:
diff changeset
890 - name: CommandInputSchema
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parents:
diff changeset
891 type: record
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parents:
diff changeset
892 abstract: true
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parents:
diff changeset
893
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parents:
diff changeset
894 - name: SchemaDefRequirement
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parents:
diff changeset
895 type: record
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parents:
diff changeset
896 extends: ProcessRequirement
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parents:
diff changeset
897 doc: |
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parents:
diff changeset
898 This field consists of an array of type definitions which must be used when
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
899 interpreting the `inputs` and `outputs` fields. When a `type` field
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shellac
parents:
diff changeset
900 contain a IRI, the implementation must check if the type is defined in
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shellac
parents:
diff changeset
901 `schemaDefs` and use that definition. If the type is not found in
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shellac
parents:
diff changeset
902 `schemaDefs`, it is an error. The entries in `schemaDefs` must be
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shellac
parents:
diff changeset
903 processed in the order listed such that later schema definitions may refer
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shellac
parents:
diff changeset
904 to earlier schema definitions.
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parents:
diff changeset
905 fields:
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parents:
diff changeset
906 - name: class
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parents:
diff changeset
907 type: string
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parents:
diff changeset
908 doc: "Always 'SchemaDefRequirement'"
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parents:
diff changeset
909 jsonldPredicate:
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parents:
diff changeset
910 "_id": "@type"
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parents:
diff changeset
911 "_type": "@vocab"
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parents:
diff changeset
912 - name: types
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parents:
diff changeset
913 type:
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parents:
diff changeset
914 type: array
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parents:
diff changeset
915 items: CommandInputSchema
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parents:
diff changeset
916 doc: The list of type definitions.
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parents:
diff changeset
917
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parents:
diff changeset
918 - name: SecondaryFileSchema
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parents:
diff changeset
919 type: record
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parents:
diff changeset
920 fields:
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parents:
diff changeset
921 - name: pattern
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parents:
diff changeset
922 type:
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parents:
diff changeset
923 - string
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parents:
diff changeset
924 - Expression
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parents:
diff changeset
925 doc: |
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parents:
diff changeset
926 Provides a pattern or expression specifying files or directories that
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shellac
parents:
diff changeset
927 should be included alongside the primary file.
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parents:
diff changeset
928
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parents:
diff changeset
929 If the value is an expression, the value of `self` in the
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shellac
parents:
diff changeset
930 expression must be the primary input or output File object to
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shellac
parents:
diff changeset
931 which this binding applies. The `basename`, `nameroot` and
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shellac
parents:
diff changeset
932 `nameext` fields must be present in `self`. For
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shellac
parents:
diff changeset
933 `CommandLineTool` inputs the `location` field must also be
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shellac
parents:
diff changeset
934 present. For `CommandLineTool` outputs the `path` field must
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
935 also be present. If secondary files were included on an input
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shellac
parents:
diff changeset
936 File object as part of the Process invocation, they must also
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shellac
parents:
diff changeset
937 be present in `secondaryFiles` on `self`.
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shellac
parents:
diff changeset
938
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parents:
diff changeset
939 The expression must return either: a filename string relative
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shellac
parents:
diff changeset
940 to the path to the primary File, a File or Directory object
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shellac
parents:
diff changeset
941 (`class: File` or 'class: Directory`) with either `location`
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shellac
parents:
diff changeset
942 (for inputs) or `path` (for outputs) and `basename` fields
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shellac
parents:
diff changeset
943 set, or an array consisting of strings or File or Directory
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shellac
parents:
diff changeset
944 objects as previously described.
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parents:
diff changeset
945
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parents:
diff changeset
946 It is legal to use `location` from a File or Directory object
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shellac
parents:
diff changeset
947 passed in as input, including `location` from secondary files
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shellac
parents:
diff changeset
948 on `self`. If an expression returns a File object with the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
949 same `location` but a different `basename` as a secondary file
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shellac
parents:
diff changeset
950 that was passed in, the expression result takes precedence.
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shellac
parents:
diff changeset
951 Setting the basename with an expression this way affects the
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shellac
parents:
diff changeset
952 `path` where the secondary file will be staged to in the
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shellac
parents:
diff changeset
953 CommandLineTool.
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parents:
diff changeset
954
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parents:
diff changeset
955 The expression may return "null" in which case there is no
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shellac
parents:
diff changeset
956 secondary file from that expression.
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parents:
diff changeset
957
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parents:
diff changeset
958 To work on non-filename-preserving storage systems, portable
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shellac
parents:
diff changeset
959 tool descriptions should treat `location` as an opaque
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shellac
parents:
diff changeset
960 identifier and avoid constructing new values from `location`,
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shellac
parents:
diff changeset
961 but should construct relative references using `basename` or
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
962 `nameroot` instead, or propagate `location` from defined inputs.
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shellac
parents:
diff changeset
963
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shellac
parents:
diff changeset
964 If a value in `secondaryFiles` is a string that is not an expression,
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shellac
parents:
diff changeset
965 it specifies that the following pattern should be applied to the path
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shellac
parents:
diff changeset
966 of the primary file to yield a filename relative to the primary File:
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shellac
parents:
diff changeset
967
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parents:
diff changeset
968 1. If string ends with `?` character, remove the last `?` and mark
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shellac
parents:
diff changeset
969 the resulting secondary file as optional.
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parents:
diff changeset
970 2. If string begins with one or more caret `^` characters, for each
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shellac
parents:
diff changeset
971 caret, remove the last file extension from the path (the last
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
972 period `.` and all following characters). If there are no file
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shellac
parents:
diff changeset
973 extensions, the path is unchanged.
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parents:
diff changeset
974 3. Append the remainder of the string to the end of the file path.
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shellac
parents:
diff changeset
975 - name: required
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parents:
diff changeset
976 type: ["null", boolean, Expression]
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parents:
diff changeset
977 doc: |
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parents:
diff changeset
978 An implementation must not fail workflow execution if `required` is
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parents:
diff changeset
979 set to `false` and the expected secondary file does not exist.
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shellac
parents:
diff changeset
980 Default value for `required` field is `true` for secondary files on
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shellac
parents:
diff changeset
981 input and `false` for secondary files on output.
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shellac
parents:
diff changeset
982 doc: |
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parents:
diff changeset
983 Secondary files are specified using the following micro-DSL for secondary files:
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parents:
diff changeset
984
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parents:
diff changeset
985 * If the value is a string, it is transformed to an object with two fields
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parents:
diff changeset
986 `pattern` and `required`
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parents:
diff changeset
987 * By default, the value of `required` is `null`
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shellac
parents:
diff changeset
988 (this indicates default behavior, which may be based on the context)
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shellac
parents:
diff changeset
989 * If the value ends with a question mark `?` the question mark is
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shellac
parents:
diff changeset
990 stripped off and the value of the field `required` is set to `False`
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shellac
parents:
diff changeset
991 * The remaining value is assigned to the field `pattern`
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shellac
parents:
diff changeset
992
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parents:
diff changeset
993 For implementation details and examples, please see
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
994 [this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files)
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parents:
diff changeset
995 in the Schema Salad specification.
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parents:
diff changeset
996
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parents:
diff changeset
997 - name: LoadListingRequirement
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parents:
diff changeset
998 type: record
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parents:
diff changeset
999 extends: ProcessRequirement
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shellac
parents:
diff changeset
1000 doc: |
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parents:
diff changeset
1001 Specify the desired behavior for loading the `listing` field of
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
1002 a Directory object for use by expressions.
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parents:
diff changeset
1003 fields:
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parents:
diff changeset
1004 class:
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parents:
diff changeset
1005 type: string
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parents:
diff changeset
1006 doc: "Always 'LoadListingRequirement'"
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parents:
diff changeset
1007 jsonldPredicate:
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parents:
diff changeset
1008 "_id": "@type"
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parents:
diff changeset
1009 "_type": "@vocab"
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shellac
parents:
diff changeset
1010 loadListing:
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parents:
diff changeset
1011 type: LoadListingEnum?
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parents:
diff changeset
1012 jsonldPredicate: "cwl:loadListing"