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annotate env/lib/python3.7/site-packages/cwltool/schemas/v1.0/Process.yml @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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1 $base: "https://w3id.org/cwl/cwl#"
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2
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3 $namespaces:
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4 cwl: "https://w3id.org/cwl/cwl#"
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5 sld: "https://w3id.org/cwl/salad#"
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6 rdfs: "http://www.w3.org/2000/01/rdf-schema#"
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7
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8 $graph:
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9
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10 - name: "Common Workflow Language, v1.0"
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11 type: documentation
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12 doc: {$include: concepts.md}
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13
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14 - $import: "salad/schema_salad/metaschema/metaschema_base.yml"
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15
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16 - name: BaseTypesDoc
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17 type: documentation
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18 doc: |
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19 ## Base types
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20 docChild:
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21 - "#CWLType"
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22 - "#Process"
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23
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24 - type: enum
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25 name: CWLVersion
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26 doc: "Version symbols for published CWL document versions."
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27 symbols:
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28 - cwl:draft-2
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29 - cwl:draft-3.dev1
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30 - cwl:draft-3.dev2
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31 - cwl:draft-3.dev3
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32 - cwl:draft-3.dev4
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33 - cwl:draft-3.dev5
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34 - cwl:draft-3
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35 - cwl:draft-4.dev1
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36 - cwl:draft-4.dev2
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37 - cwl:draft-4.dev3
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38 - cwl:v1.0.dev4
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39 - cwl:v1.0
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40
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41 - name: CWLType
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42 type: enum
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43 extends: "sld:PrimitiveType"
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44 symbols:
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45 - cwl:File
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46 - cwl:Directory
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47 doc:
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48 - "Extends primitive types with the concept of a file and directory as a builtin type."
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49 - "File: A File object"
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50 - "Directory: A Directory object"
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51
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52 - name: File
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53 type: record
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54 docParent: "#CWLType"
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55 doc: |
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56 Represents a file (or group of files when `secondaryFiles` is provided) that
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57 will be accessible by tools using standard POSIX file system call API such as
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58 open(2) and read(2).
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59
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60 Files are represented as objects with `class` of `File`. File objects have
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61 a number of properties that provide metadata about the file.
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62
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63 The `location` property of a File is a URI that uniquely identifies the
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64 file. Implementations must support the file:// URI scheme and may support
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65 other schemes such as http://. The value of `location` may also be a
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66 relative reference, in which case it must be resolved relative to the URI
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67 of the document it appears in. Alternately to `location`, implementations
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68 must also accept the `path` property on File, which must be a filesystem
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69 path available on the same host as the CWL runner (for inputs) or the
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70 runtime environment of a command line tool execution (for command line tool
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71 outputs).
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72
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73 If no `location` or `path` is specified, a file object must specify
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74 `contents` with the UTF-8 text content of the file. This is a "file
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75 literal". File literals do not correspond to external resources, but are
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76 created on disk with `contents` with when needed for a executing a tool.
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77 Where appropriate, expressions can return file literals to define new files
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78 on a runtime. The maximum size of `contents` is 64 kilobytes.
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79
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80 The `basename` property defines the filename on disk where the file is
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81 staged. This may differ from the resource name. If not provided,
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82 `basename` must be computed from the last path part of `location` and made
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83 available to expressions.
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84
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85 The `secondaryFiles` property is a list of File or Directory objects that
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86 must be staged in the same directory as the primary file. It is an error
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87 for file names to be duplicated in `secondaryFiles`.
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88
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89 The `size` property is the size in bytes of the File. It must be computed
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90 from the resource and made available to expressions. The `checksum` field
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91 contains a cryptographic hash of the file content for use it verifying file
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92 contents. Implementations may, at user option, enable or disable
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93 computation of the `checksum` field for performance or other reasons.
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94 However, the ability to compute output checksums is required to pass the
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95 CWL conformance test suite.
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96
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97 When executing a CommandLineTool, the files and secondary files may be
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98 staged to an arbitrary directory, but must use the value of `basename` for
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99 the filename. The `path` property must be file path in the context of the
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100 tool execution runtime (local to the compute node, or within the executing
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101 container). All computed properties should be available to expressions.
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102 File literals also must be staged and `path` must be set.
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103
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104 When collecting CommandLineTool outputs, `glob` matching returns file paths
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105 (with the `path` property) and the derived properties. This can all be
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106 modified by `outputEval`. Alternately, if the file `cwl.output.json` is
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107 present in the output, `outputBinding` is ignored.
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108
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109 File objects in the output must provide either a `location` URI or a `path`
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110 property in the context of the tool execution runtime (local to the compute
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111 node, or within the executing container).
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112
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113 When evaluating an ExpressionTool, file objects must be referenced via
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114 `location` (the expression tool does not have access to files on disk so
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115 `path` is meaningless) or as file literals. It is legal to return a file
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116 object with an existing `location` but a different `basename`. The
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117 `loadContents` field of ExpressionTool inputs behaves the same as on
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118 CommandLineTool inputs, however it is not meaningful on the outputs.
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119
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120 An ExpressionTool may forward file references from input to output by using
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121 the same value for `location`.
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122
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123 fields:
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124 - name: class
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125 type:
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126 type: enum
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127 name: File_class
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128 symbols:
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129 - cwl:File
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130 jsonldPredicate:
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131 _id: "@type"
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132 _type: "@vocab"
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133 doc: Must be `File` to indicate this object describes a file.
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134 - name: location
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135 type: string?
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136 doc: |
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137 An IRI that identifies the file resource. This may be a relative
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138 reference, in which case it must be resolved using the base IRI of the
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139 document. The location may refer to a local or remote resource; the
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140 implementation must use the IRI to retrieve file content. If an
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141 implementation is unable to retrieve the file content stored at a
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142 remote resource (due to unsupported protocol, access denied, or other
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143 issue) it must signal an error.
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144
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145 If the `location` field is not provided, the `contents` field must be
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146 provided. The implementation must assign a unique identifier for
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147 the `location` field.
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148
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149 If the `path` field is provided but the `location` field is not, an
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150 implementation may assign the value of the `path` field to `location`,
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151 then follow the rules above.
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152 jsonldPredicate:
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153 _id: "@id"
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154 _type: "@id"
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155 - name: path
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156 type: string?
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157 doc: |
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158 The local host path where the File is available when a CommandLineTool is
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159 executed. This field must be set by the implementation. The final
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160 path component must match the value of `basename`. This field
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161 must not be used in any other context. The command line tool being
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162 executed must be able to to access the file at `path` using the POSIX
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163 `open(2)` syscall.
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164
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165 As a special case, if the `path` field is provided but the `location`
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166 field is not, an implementation may assign the value of the `path`
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167 field to `location`, and remove the `path` field.
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168
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169 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
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170 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
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171 `<space>`, `<tab>`, and `<newline>`) or characters
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172 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
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173 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
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174 then implementations may terminate the process with a
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175 `permanentFailure`.
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176 jsonldPredicate:
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177 "_id": "cwl:path"
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178 "_type": "@id"
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179 - name: basename
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180 type: string?
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181 doc: |
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182 The base name of the file, that is, the name of the file without any
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183 leading directory path. The base name must not contain a slash `/`.
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184
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185 If not provided, the implementation must set this field based on the
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186 `location` field by taking the final path component after parsing
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187 `location` as an IRI. If `basename` is provided, it is not required to
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188 match the value from `location`.
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189
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190 When this file is made available to a CommandLineTool, it must be named
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191 with `basename`, i.e. the final component of the `path` field must match
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192 `basename`.
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193 jsonldPredicate: "cwl:basename"
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194 - name: dirname
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195 type: string?
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196 doc: |
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197 The name of the directory containing file, that is, the path leading up
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198 to the final slash in the path such that `dirname + '/' + basename ==
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199 path`.
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200
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201 The implementation must set this field based on the value of `path`
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202 prior to evaluating parameter references or expressions in a
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203 CommandLineTool document. This field must not be used in any other
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204 context.
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205 - name: nameroot
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206 type: string?
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207 doc: |
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208 The basename root such that `nameroot + nameext == basename`, and
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209 `nameext` is empty or begins with a period and contains at most one
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210 period. For the purposess of path splitting leading periods on the
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211 basename are ignored; a basename of `.cshrc` will have a nameroot of
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212 `.cshrc`.
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213
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214 The implementation must set this field automatically based on the value
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215 of `basename` prior to evaluating parameter references or expressions.
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216 - name: nameext
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217 type: string?
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218 doc: |
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219 The basename extension such that `nameroot + nameext == basename`, and
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220 `nameext` is empty or begins with a period and contains at most one
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221 period. Leading periods on the basename are ignored; a basename of
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222 `.cshrc` will have an empty `nameext`.
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223
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224 The implementation must set this field automatically based on the value
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225 of `basename` prior to evaluating parameter references or expressions.
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226 - name: checksum
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227 type: string?
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228 doc: |
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229 Optional hash code for validating file integrity. Currently must be in the form
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230 "sha1$ + hexadecimal string" using the SHA-1 algorithm.
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231 - name: size
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232 type: long?
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233 doc: Optional file size
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234 - name: "secondaryFiles"
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235 type:
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236 - "null"
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237 - type: array
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238 items: [File, Directory]
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239 jsonldPredicate: "cwl:secondaryFiles"
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240 doc: |
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241 A list of additional files or directories that are associated with the
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242 primary file and must be transferred alongside the primary file.
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243 Examples include indexes of the primary file, or external references
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244 which must be included when loading primary document. A file object
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245 listed in `secondaryFiles` may itself include `secondaryFiles` for
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246 which the same rules apply.
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247 - name: format
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248 type: string?
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249 jsonldPredicate:
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250 _id: cwl:format
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251 _type: "@id"
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252 identity: true
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253 doc: |
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254 The format of the file: this must be an IRI of a concept node that
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255 represents the file format, preferrably defined within an ontology.
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256 If no ontology is available, file formats may be tested by exact match.
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257
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258 Reasoning about format compatability must be done by checking that an
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259 input file format is the same, `owl:equivalentClass` or
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260 `rdfs:subClassOf` the format required by the input parameter.
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261 `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if
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262 `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer
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263 `<C> owl:subclassOf <A>`.
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264
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265 File format ontologies may be provided in the "$schema" metadata at the
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266 root of the document. If no ontologies are specified in `$schema`, the
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267 runtime may perform exact file format matches.
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268 - name: contents
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269 type: string?
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270 doc: |
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271 File contents literal. Maximum of 64 KiB.
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272
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273 If neither `location` nor `path` is provided, `contents` must be
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274 non-null. The implementation must assign a unique identifier for the
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275 `location` field. When the file is staged as input to CommandLineTool,
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276 the value of `contents` must be written to a file.
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277
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278 If `loadContents` of `inputBinding` or `outputBinding` is true and
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279 `location` is valid, the implementation must read up to the first 64
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280 KiB of text from the file and place it in the "contents" field.
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281
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282
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283 - name: Directory
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284 type: record
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285 docAfter: "#File"
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286 doc: |
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287 Represents a directory to present to a command line tool.
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288
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289 Directories are represented as objects with `class` of `Directory`. Directory objects have
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290 a number of properties that provide metadata about the directory.
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291
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292 The `location` property of a Directory is a URI that uniquely identifies
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293 the directory. Implementations must support the file:// URI scheme and may
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294 support other schemes such as http://. Alternately to `location`,
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295 implementations must also accept the `path` property on Direcotry, which
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296 must be a filesystem path available on the same host as the CWL runner (for
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297 inputs) or the runtime environment of a command line tool execution (for
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298 command line tool outputs).
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299
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300 A Directory object may have a `listing` field. This is a list of File and
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301 Directory objects that are contained in the Directory. For each entry in
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302 `listing`, the `basename` property defines the name of the File or
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303 Subdirectory when staged to disk. If `listing` is not provided, the
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304 implementation must have some way of fetching the Directory listing at
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305 runtime based on the `location` field.
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306
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307 If a Directory does not have `location`, it is a Directory literal. A
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308 Directory literal must provide `listing`. Directory literals must be
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309 created on disk at runtime as needed.
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310
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311 The resources in a Directory literal do not need to have any implied
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312 relationship in their `location`. For example, a Directory listing may
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313 contain two files located on different hosts. It is the responsibility of
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314 the runtime to ensure that those files are staged to disk appropriately.
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315 Secondary files associated with files in `listing` must also be staged to
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316 the same Directory.
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317
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318 When executing a CommandLineTool, Directories must be recursively staged
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319 first and have local values of `path` assigend.
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320
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321 Directory objects in CommandLineTool output must provide either a
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322 `location` URI or a `path` property in the context of the tool execution
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323 runtime (local to the compute node, or within the executing container).
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324
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325 An ExpressionTool may forward file references from input to output by using
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326 the same value for `location`.
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327
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328 Name conflicts (the same `basename` appearing multiple times in `listing`
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329 or in any entry in `secondaryFiles` in the listing) is a fatal error.
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330
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331 fields:
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332 - name: class
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333 type:
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334 type: enum
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335 name: Directory_class
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336 symbols:
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337 - cwl:Directory
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338 jsonldPredicate:
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339 _id: "@type"
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340 _type: "@vocab"
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341 doc: Must be `Directory` to indicate this object describes a Directory.
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342 - name: location
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343 type: string?
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344 doc: |
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345 An IRI that identifies the directory resource. This may be a relative
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346 reference, in which case it must be resolved using the base IRI of the
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347 document. The location may refer to a local or remote resource. If
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348 the `listing` field is not set, the implementation must use the
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349 location IRI to retrieve directory listing. If an implementation is
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350 unable to retrieve the directory listing stored at a remote resource (due to
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351 unsupported protocol, access denied, or other issue) it must signal an
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352 error.
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353
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354 If the `location` field is not provided, the `listing` field must be
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355 provided. The implementation must assign a unique identifier for
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356 the `location` field.
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357
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358 If the `path` field is provided but the `location` field is not, an
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359 implementation may assign the value of the `path` field to `location`,
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360 then follow the rules above.
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361 jsonldPredicate:
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362 _id: "@id"
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363 _type: "@id"
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364 - name: path
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365 type: string?
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366 doc: |
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367 The local path where the Directory is made available prior to executing a
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368 CommandLineTool. This must be set by the implementation. This field
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369 must not be used in any other context. The command line tool being
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370 executed must be able to to access the directory at `path` using the POSIX
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371 `opendir(2)` syscall.
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372
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373 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
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374 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
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375 `<space>`, `<tab>`, and `<newline>`) or characters
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376 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
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parents:
diff changeset
377 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
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parents:
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378 then implementations may terminate the process with a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
379 `permanentFailure`.
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parents:
diff changeset
380 jsonldPredicate:
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parents:
diff changeset
381 _id: "cwl:path"
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parents:
diff changeset
382 _type: "@id"
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parents:
diff changeset
383 - name: basename
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parents:
diff changeset
384 type: string?
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parents:
diff changeset
385 doc: |
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diff changeset
386 The base name of the directory, that is, the name of the file without any
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parents:
diff changeset
387 leading directory path. The base name must not contain a slash `/`.
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parents:
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388
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389 If not provided, the implementation must set this field based on the
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parents:
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390 `location` field by taking the final path component after parsing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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391 `location` as an IRI. If `basename` is provided, it is not required to
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parents:
diff changeset
392 match the value from `location`.
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parents:
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393
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394 When this file is made available to a CommandLineTool, it must be named
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parents:
diff changeset
395 with `basename`, i.e. the final component of the `path` field must match
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parents:
diff changeset
396 `basename`.
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parents:
diff changeset
397 jsonldPredicate: "cwl:basename"
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parents:
diff changeset
398 - name: listing
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parents:
diff changeset
399 type:
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parents:
diff changeset
400 - "null"
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parents:
diff changeset
401 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
402 items: [File, Directory]
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parents:
diff changeset
403 doc: |
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parents:
diff changeset
404 List of files or subdirectories contained in this directory. The name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
405 of each file or subdirectory is determined by the `basename` field of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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406 each `File` or `Directory` object. It is an error if a `File` shares a
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parents:
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407 `basename` with any other entry in `listing`. If two or more
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408 `Directory` object share the same `basename`, this must be treated as
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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409 equivalent to a single subdirectory with the listings recursively
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parents:
diff changeset
410 merged.
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parents:
diff changeset
411 jsonldPredicate:
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parents:
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412 _id: "cwl:listing"
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parents:
diff changeset
413
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parents:
diff changeset
414 - name: SchemaBase
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
415 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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416 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
417 fields:
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parents:
diff changeset
418 - name: label
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
419 type:
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parents:
diff changeset
420 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
421 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
422 jsonldPredicate: "rdfs:label"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
423 doc: "A short, human-readable label of this object."
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parents:
diff changeset
424
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
425
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
426 - name: Parameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
427 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
428 extends: SchemaBase
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
429 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
430 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
431 Define an input or output parameter to a process.
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432
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diff changeset
433 fields:
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parents:
diff changeset
434 - name: secondaryFiles
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
435 type:
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parents:
diff changeset
436 - "null"
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parents:
diff changeset
437 - string
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parents:
diff changeset
438 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
439 - type: array
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parents:
diff changeset
440 items: [string, Expression]
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diff changeset
441 jsonldPredicate: "cwl:secondaryFiles"
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diff changeset
442 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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443 Only valid when `type: File` or is an array of `items: File`.
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444
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445 Provides a pattern or expression specifying files or directories that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
446 must be included alongside the primary file. All listed secondary
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
447 files must be present. An implementation may fail workflow execution
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
448 if an expected secondary file does not exist.
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diff changeset
449
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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450 If the value is an expression, the value of `self` in the expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
451 must be the primary input or output File object to which this binding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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452 applies. The `basename`, `nameroot` and `nameext` fields must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
453 present in `self`. For `CommandLineTool` outputs the `path` field must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
454 also be present. The expression must return a filename string relative
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
455 to the path to the primary File, a File or Directory object with either
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
456 `path` or `location` and `basename` fields set, or an array consisting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
457 of strings or File or Directory objects. It is legal to reference an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
458 unchanged File or Directory object taken from input as a secondaryFile.
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diff changeset
459
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
460 To work on non-filename-preserving storage systems, portable tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
461 descriptions should avoid constructing new values from `location`, but
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
462 should construct relative references using `basename` or `nameroot`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
463 instead.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
464
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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465 If a value in `secondaryFiles` is a string that is not an expression,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
466 it specifies that the following pattern should be applied to the path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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467 of the primary file to yield a filename relative to the primary File:
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468
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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469 1. If string begins with one or more caret `^` characters, for each
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
470 caret, remove the last file extension from the path (the last
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
471 period `.` and all following characters). If there are no file
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parents:
diff changeset
472 extensions, the path is unchanged.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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473 2. Append the remainder of the string to the end of the file path.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
474
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
475 - name: streamable
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
476 type: boolean?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
477 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
478 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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479
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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480 A value of `true` indicates that the file is read or written
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
481 sequentially without seeking. An implementation may use this flag to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
482 indicate whether it is valid to stream file contents using a named
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
483 pipe. Default: `false`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
484
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
485 - name: doc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
486 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
487 - string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
488 - string[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
489 doc: "A documentation string for this type, or an array of strings which should be concatenated."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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490 jsonldPredicate: "rdfs:comment"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
491
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
492
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
493 - type: enum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
494 name: Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
495 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
496 'Expression' is not a real type. It indicates that a field must allow
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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497 runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement)
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parents:
diff changeset
498 is declared and supported by the platform, the field must also allow
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
499 Javascript expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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500 symbols:
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parents:
diff changeset
501 - cwl:ExpressionPlaceholder
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parents:
diff changeset
502
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parents:
diff changeset
503
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
504 - name: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
505 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
506 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
507 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
508 - name: loadContents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
509 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
510 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
511 - boolean
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
512 jsonldPredicate: "cwl:loadContents"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
513 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
514 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
515
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
516 Read up to the first 64 KiB of text from the file and place it in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
517 "contents" field of the file object for use by expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
518
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
519
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
520 - name: OutputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
521 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
522 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
523
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
524
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
525 - name: InputSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
526 extends: SchemaBase
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
527 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
528 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
529
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
530
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
531 - name: OutputSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
532 extends: SchemaBase
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
533 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
534 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
535
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
536
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
537 - name: InputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
538 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
539 extends: "sld:RecordField"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
540 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
541 - specializeFrom: "sld:RecordSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
542 specializeTo: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
543 - specializeFrom: "sld:EnumSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
544 specializeTo: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
545 - specializeFrom: "sld:ArraySchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
546 specializeTo: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
547 - specializeFrom: "sld:PrimitiveType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
548 specializeTo: CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
549 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
550 - name: inputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
551 type: InputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
552 jsonldPredicate: "cwl:inputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
553 - name: label
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
554 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
555 jsonldPredicate: "rdfs:label"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
556 doc: "A short, human-readable label of this process object."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
557
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
558
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
559 - name: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
560 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
561 extends: ["sld:RecordSchema", InputSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
562 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
563 - specializeFrom: "sld:RecordField"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
564 specializeTo: InputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
565
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
566
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
567 - name: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
568 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
569 extends: ["sld:EnumSchema", InputSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
570 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
571 - name: inputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
572 type: InputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
573 jsonldPredicate: "cwl:inputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
574
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
575
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
576 - name: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
577 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
578 extends: ["sld:ArraySchema", InputSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
579 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
580 - specializeFrom: "sld:RecordSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
581 specializeTo: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
582 - specializeFrom: "sld:EnumSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
583 specializeTo: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
584 - specializeFrom: "sld:ArraySchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
585 specializeTo: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
586 - specializeFrom: "sld:PrimitiveType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
587 specializeTo: CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
588 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
589 - name: inputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
590 type: InputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
591 jsonldPredicate: "cwl:inputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
592
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
593
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
594 - name: OutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
595 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
596 extends: "sld:RecordField"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
597 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
598 - specializeFrom: "sld:RecordSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
599 specializeTo: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
600 - specializeFrom: "sld:EnumSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
601 specializeTo: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
602 - specializeFrom: "sld:ArraySchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
603 specializeTo: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
604 - specializeFrom: "sld:PrimitiveType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
605 specializeTo: CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
606 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
607 - name: outputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
608 type: OutputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
609 jsonldPredicate: "cwl:outputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
610
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
611
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
612 - name: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
613 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
614 extends: ["sld:RecordSchema", "#OutputSchema"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
615 docParent: "#OutputParameter"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
616 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
617 - specializeFrom: "sld:RecordField"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
618 specializeTo: OutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
619
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
620
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
621 - name: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
622 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
623 extends: ["sld:EnumSchema", OutputSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
624 docParent: "#OutputParameter"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
625 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
626 - name: outputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
627 type: OutputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
628 jsonldPredicate: "cwl:outputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
629
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
630 - name: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
631 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
632 extends: ["sld:ArraySchema", OutputSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
633 docParent: "#OutputParameter"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
634 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
635 - specializeFrom: "sld:RecordSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
636 specializeTo: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
637 - specializeFrom: "sld:EnumSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
638 specializeTo: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
639 - specializeFrom: "sld:ArraySchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
640 specializeTo: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
641 - specializeFrom: "sld:PrimitiveType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
642 specializeTo: CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
643 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
644 - name: outputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
645 type: OutputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
646 jsonldPredicate: "cwl:outputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
647
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
648
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
649 - name: InputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
650 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
651 extends: Parameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
652 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
653 - name: id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
654 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
655 jsonldPredicate: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
656 doc: "The unique identifier for this parameter object."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
657
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
658 - name: format
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
659 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
660 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
661 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
662 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
663 items: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
664 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
665 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
666 _id: cwl:format
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
667 _type: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
668 identity: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
669 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
670 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
671
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
672 This must be one or more IRIs of concept nodes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
673 that represents file formats which are allowed as input to this
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
674 parameter, preferrably defined within an ontology. If no ontology is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
675 available, file formats may be tested by exact match.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
676
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
677
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
678 - name: inputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
679 type: InputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
680 jsonldPredicate: "cwl:inputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
681 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
682 Describes how to handle the inputs of a process and convert them
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
683 into a concrete form for execution, such as command line parameters.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
684
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
685 - name: default
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
686 type: Any?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
687 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
688 _id: cwl:default
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
689 noLinkCheck: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
690 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
691 The default value to use for this parameter if the parameter is missing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
692 from the input object, or if the value of the parameter in the input
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
693 object is `null`. Default values are applied before evaluating expressions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
694 (e.g. dependent `valueFrom` fields).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
695
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
696 - name: type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
697 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
698 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
699 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
700 - InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
701 - InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
702 - InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
703 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
704 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
705 items:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
706 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
707 - InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
708 - InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
709 - InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
710 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
711 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
712 "_id": "sld:type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
713 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
714 refScope: 2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
715 typeDSL: True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
716 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
717 Specify valid types of data that may be assigned to this parameter.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
718
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
719 - name: OutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
720 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
721 extends: Parameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
722 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
723 - name: id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
724 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
725 jsonldPredicate: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
726 doc: "The unique identifier for this parameter object."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
727 - name: outputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
728 type: OutputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
729 jsonldPredicate: "cwl:outputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
730 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
731 Describes how to handle the outputs of a process.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
732 - name: format
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
733 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
734 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
735 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
736 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
737 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
738 _id: cwl:format
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
739 _type: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
740 identity: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
741 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
742 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
743
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
744 This is the file format that will be assigned to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
745 the output parameter.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
746
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
747
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
748
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
749 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
750 name: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
751 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
752 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
753 A process requirement declares a prerequisite that may or must be fulfilled
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
754 before executing a process. See [`Process.hints`](#process) and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
755 [`Process.requirements`](#process).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
756
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
757 Process requirements are the primary mechanism for specifying extensions to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
758 the CWL core specification.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
759
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
760
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
761 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
762 name: Process
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
763 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
764 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
765
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
766 The base executable type in CWL is the `Process` object defined by the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
767 document. Note that the `Process` object is abstract and cannot be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
768 directly executed.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
769
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
770 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
771 - name: id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
772 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
773 jsonldPredicate: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
774 doc: "The unique identifier for this process object."
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diff changeset
775 - name: inputs
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parents:
diff changeset
776 type:
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diff changeset
777 type: array
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parents:
diff changeset
778 items: InputParameter
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parents:
diff changeset
779 jsonldPredicate:
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780 _id: "cwl:inputs"
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parents:
diff changeset
781 mapSubject: id
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parents:
diff changeset
782 mapPredicate: type
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diff changeset
783 doc: |
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diff changeset
784 Defines the input parameters of the process. The process is ready to
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parents:
diff changeset
785 run when all required input parameters are associated with concrete
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parents:
diff changeset
786 values. Input parameters include a schema for each parameter which is
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parents:
diff changeset
787 used to validate the input object. It may also be used to build a user
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parents:
diff changeset
788 interface for constructing the input object.
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parents:
diff changeset
789
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parents:
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790 When accepting an input object, all input parameters must have a value.
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parents:
diff changeset
791 If an input parameter is missing from the input object, it must be
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parents:
diff changeset
792 assigned a value of `null` (or the value of `default` for that
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parents:
diff changeset
793 parameter, if provided) for the purposes of validation and evaluation
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parents:
diff changeset
794 of expressions.
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parents:
diff changeset
795
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parents:
diff changeset
796 - name: outputs
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parents:
diff changeset
797 type:
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parents:
diff changeset
798 type: array
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parents:
diff changeset
799 items: OutputParameter
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parents:
diff changeset
800 jsonldPredicate:
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parents:
diff changeset
801 _id: "cwl:outputs"
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parents:
diff changeset
802 mapSubject: id
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parents:
diff changeset
803 mapPredicate: type
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parents:
diff changeset
804 doc: |
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diff changeset
805 Defines the parameters representing the output of the process. May be
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parents:
diff changeset
806 used to generate and/or validate the output object.
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parents:
diff changeset
807 - name: requirements
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parents:
diff changeset
808 type: ProcessRequirement[]?
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parents:
diff changeset
809 jsonldPredicate:
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parents:
diff changeset
810 _id: "cwl:requirements"
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parents:
diff changeset
811 mapSubject: class
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diff changeset
812 doc: |
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parents:
diff changeset
813 Declares requirements that apply to either the runtime environment or the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
814 workflow engine that must be met in order to execute this process. If
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parents:
diff changeset
815 an implementation cannot satisfy all requirements, or a requirement is
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parents:
diff changeset
816 listed which is not recognized by the implementation, it is a fatal
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
817 error and the implementation must not attempt to run the process,
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parents:
diff changeset
818 unless overridden at user option.
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parents:
diff changeset
819 - name: hints
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parents:
diff changeset
820 type: Any[]?
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diff changeset
821 doc: |
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parents:
diff changeset
822 Declares hints applying to either the runtime environment or the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
823 workflow engine that may be helpful in executing this process. It is
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parents:
diff changeset
824 not an error if an implementation cannot satisfy all hints, however
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parents:
diff changeset
825 the implementation may report a warning.
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parents:
diff changeset
826 jsonldPredicate:
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parents:
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827 _id: cwl:hints
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parents:
diff changeset
828 noLinkCheck: true
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parents:
diff changeset
829 mapSubject: class
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parents:
diff changeset
830 - name: label
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parents:
diff changeset
831 type: string?
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parents:
diff changeset
832 jsonldPredicate: "rdfs:label"
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parents:
diff changeset
833 doc: "A short, human-readable label of this process object."
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parents:
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834 - name: doc
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parents:
diff changeset
835 type: string?
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parents:
diff changeset
836 jsonldPredicate: "rdfs:comment"
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parents:
diff changeset
837 doc: "A long, human-readable description of this process object."
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parents:
diff changeset
838 - name: cwlVersion
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parents:
diff changeset
839 type: CWLVersion?
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parents:
diff changeset
840 doc: |
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diff changeset
841 CWL document version. Always required at the document root. Not
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parents:
diff changeset
842 required for a Process embedded inside another Process.
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parents:
diff changeset
843 jsonldPredicate:
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parents:
diff changeset
844 "_id": "cwl:cwlVersion"
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parents:
diff changeset
845 "_type": "@vocab"
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parents:
diff changeset
846
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parents:
diff changeset
847 - name: InlineJavascriptRequirement
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parents:
diff changeset
848 type: record
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parents:
diff changeset
849 extends: ProcessRequirement
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parents:
diff changeset
850 doc: |
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parents:
diff changeset
851 Indicates that the workflow platform must support inline Javascript expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
852 If this requirement is not present, the workflow platform must not perform expression
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parents:
diff changeset
853 interpolatation.
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parents:
diff changeset
854 fields:
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parents:
diff changeset
855 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
856 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
857 doc: "Always 'InlineJavascriptRequirement'"
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parents:
diff changeset
858 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
859 "_id": "@type"
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parents:
diff changeset
860 "_type": "@vocab"
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parents:
diff changeset
861 - name: expressionLib
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
862 type: string[]?
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diff changeset
863 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
864 Additional code fragments that will also be inserted
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
865 before executing the expression code. Allows for function definitions that may
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
866 be called from CWL expressions.
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diff changeset
867
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diff changeset
868
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869 - name: SchemaDefRequirement
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parents:
diff changeset
870 type: record
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diff changeset
871 extends: ProcessRequirement
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872 doc: |
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873 This field consists of an array of type definitions which must be used when
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
874 interpreting the `inputs` and `outputs` fields. When a `type` field
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
875 contain a IRI, the implementation must check if the type is defined in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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876 `schemaDefs` and use that definition. If the type is not found in
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parents:
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877 `schemaDefs`, it is an error. The entries in `schemaDefs` must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
878 processed in the order listed such that later schema definitions may refer
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parents:
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879 to earlier schema definitions.
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880 fields:
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881 - name: class
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882 type: string
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883 doc: "Always 'SchemaDefRequirement'"
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884 jsonldPredicate:
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885 "_id": "@type"
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886 "_type": "@vocab"
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887 - name: types
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888 type:
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889 type: array
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890 items: InputSchema
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891 doc: The list of type definitions.