Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/schemas/v1.1/Process.yml @ 2:6af9afd405e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
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1 saladVersion: v1.1
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2 $base: "https://w3id.org/cwl/cwl#"
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3
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4 $namespaces:
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5 cwl: "https://w3id.org/cwl/cwl#"
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6 sld: "https://w3id.org/cwl/salad#"
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7 rdfs: "http://www.w3.org/2000/01/rdf-schema#"
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8
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9 $graph:
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10
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11 - name: "Common Workflow Language, v1.1"
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12 type: documentation
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13 doc: {$include: concepts.md}
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14
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15 - $import: "salad/schema_salad/metaschema/metaschema_base.yml"
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16
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17 - name: BaseTypesDoc
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18 type: documentation
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19 doc: |
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20 ## Base types
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21 docChild:
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22 - "#CWLType"
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23 - "#Process"
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24
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25 - type: enum
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26 name: CWLVersion
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27 doc: "Version symbols for published CWL document versions."
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28 symbols:
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29 - cwl:draft-2
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30 - cwl:draft-3.dev1
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31 - cwl:draft-3.dev2
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32 - cwl:draft-3.dev3
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33 - cwl:draft-3.dev4
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34 - cwl:draft-3.dev5
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35 - cwl:draft-3
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36 - cwl:draft-4.dev1
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37 - cwl:draft-4.dev2
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38 - cwl:draft-4.dev3
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39 - cwl:v1.0.dev4
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40 - cwl:v1.0
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41 - cwl:v1.1.0-dev1 # a dash is required by the semver 2.0 rules
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42 - cwl:v1.1
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43
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44 - name: CWLType
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45 type: enum
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46 extends: "sld:PrimitiveType"
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47 symbols:
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48 - cwl:File
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49 - cwl:Directory
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50 doc:
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51 - "Extends primitive types with the concept of a file and directory as a builtin type."
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52 - "File: A File object"
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53 - "Directory: A Directory object"
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54
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55 - name: File
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56 type: record
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57 docParent: "#CWLType"
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58 doc: |
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59 Represents a file (or group of files when `secondaryFiles` is provided) that
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60 will be accessible by tools using standard POSIX file system call API such as
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61 open(2) and read(2).
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62
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63 Files are represented as objects with `class` of `File`. File objects have
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64 a number of properties that provide metadata about the file.
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65
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66 The `location` property of a File is a URI that uniquely identifies the
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67 file. Implementations must support the file:// URI scheme and may support
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68 other schemes such as http://. The value of `location` may also be a
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69 relative reference, in which case it must be resolved relative to the URI
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70 of the document it appears in. Alternately to `location`, implementations
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71 must also accept the `path` property on File, which must be a filesystem
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72 path available on the same host as the CWL runner (for inputs) or the
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73 runtime environment of a command line tool execution (for command line tool
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74 outputs).
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75
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76 If no `location` or `path` is specified, a file object must specify
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77 `contents` with the UTF-8 text content of the file. This is a "file
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78 literal". File literals do not correspond to external resources, but are
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79 created on disk with `contents` with when needed for a executing a tool.
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80 Where appropriate, expressions can return file literals to define new files
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81 on a runtime. The maximum size of `contents` is 64 kilobytes.
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82
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83 The `basename` property defines the filename on disk where the file is
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84 staged. This may differ from the resource name. If not provided,
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85 `basename` must be computed from the last path part of `location` and made
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86 available to expressions.
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87
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88 The `secondaryFiles` property is a list of File or Directory objects that
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89 must be staged in the same directory as the primary file. It is an error
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90 for file names to be duplicated in `secondaryFiles`.
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91
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92 The `size` property is the size in bytes of the File. It must be computed
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93 from the resource and made available to expressions. The `checksum` field
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94 contains a cryptographic hash of the file content for use it verifying file
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95 contents. Implementations may, at user option, enable or disable
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96 computation of the `checksum` field for performance or other reasons.
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97 However, the ability to compute output checksums is required to pass the
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98 CWL conformance test suite.
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99
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100 When executing a CommandLineTool, the files and secondary files may be
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101 staged to an arbitrary directory, but must use the value of `basename` for
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102 the filename. The `path` property must be file path in the context of the
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103 tool execution runtime (local to the compute node, or within the executing
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104 container). All computed properties should be available to expressions.
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105 File literals also must be staged and `path` must be set.
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106
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107 When collecting CommandLineTool outputs, `glob` matching returns file paths
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108 (with the `path` property) and the derived properties. This can all be
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109 modified by `outputEval`. Alternately, if the file `cwl.output.json` is
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110 present in the output, `outputBinding` is ignored.
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111
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112 File objects in the output must provide either a `location` URI or a `path`
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113 property in the context of the tool execution runtime (local to the compute
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114 node, or within the executing container).
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115
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116 When evaluating an ExpressionTool, file objects must be referenced via
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117 `location` (the expression tool does not have access to files on disk so
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118 `path` is meaningless) or as file literals. It is legal to return a file
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119 object with an existing `location` but a different `basename`. The
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120 `loadContents` field of ExpressionTool inputs behaves the same as on
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121 CommandLineTool inputs, however it is not meaningful on the outputs.
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122
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123 An ExpressionTool may forward file references from input to output by using
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124 the same value for `location`.
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125
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126 fields:
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127 - name: class
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128 type:
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129 type: enum
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130 name: File_class
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131 symbols:
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132 - cwl:File
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133 jsonldPredicate:
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134 _id: "@type"
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135 _type: "@vocab"
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136 doc: Must be `File` to indicate this object describes a file.
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137 - name: location
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138 type: string?
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139 doc: |
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140 An IRI that identifies the file resource. This may be a relative
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141 reference, in which case it must be resolved using the base IRI of the
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142 document. The location may refer to a local or remote resource; the
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143 implementation must use the IRI to retrieve file content. If an
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144 implementation is unable to retrieve the file content stored at a
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145 remote resource (due to unsupported protocol, access denied, or other
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146 issue) it must signal an error.
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147
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148 If the `location` field is not provided, the `contents` field must be
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149 provided. The implementation must assign a unique identifier for
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150 the `location` field.
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151
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152 If the `path` field is provided but the `location` field is not, an
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153 implementation may assign the value of the `path` field to `location`,
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154 then follow the rules above.
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155 jsonldPredicate:
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156 _id: "@id"
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157 _type: "@id"
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158 - name: path
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159 type: string?
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160 doc: |
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161 The local host path where the File is available when a CommandLineTool is
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162 executed. This field must be set by the implementation. The final
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163 path component must match the value of `basename`. This field
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164 must not be used in any other context. The command line tool being
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165 executed must be able to to access the file at `path` using the POSIX
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166 `open(2)` syscall.
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167
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168 As a special case, if the `path` field is provided but the `location`
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169 field is not, an implementation may assign the value of the `path`
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170 field to `location`, and remove the `path` field.
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171
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172 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
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173 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
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174 `<space>`, `<tab>`, and `<newline>`) or characters
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175 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
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176 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
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177 then implementations may terminate the process with a
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178 `permanentFailure`.
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179 jsonldPredicate:
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180 "_id": "cwl:path"
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181 "_type": "@id"
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182 - name: basename
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183 type: string?
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184 doc: |
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185 The base name of the file, that is, the name of the file without any
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186 leading directory path. The base name must not contain a slash `/`.
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187
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188 If not provided, the implementation must set this field based on the
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189 `location` field by taking the final path component after parsing
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190 `location` as an IRI. If `basename` is provided, it is not required to
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191 match the value from `location`.
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192
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193 When this file is made available to a CommandLineTool, it must be named
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194 with `basename`, i.e. the final component of the `path` field must match
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195 `basename`.
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196 jsonldPredicate: "cwl:basename"
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197 - name: dirname
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198 type: string?
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199 doc: |
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200 The name of the directory containing file, that is, the path leading up
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201 to the final slash in the path such that `dirname + '/' + basename ==
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202 path`.
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203
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204 The implementation must set this field based on the value of `path`
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205 prior to evaluating parameter references or expressions in a
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206 CommandLineTool document. This field must not be used in any other
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207 context.
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208 - name: nameroot
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209 type: string?
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210 doc: |
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211 The basename root such that `nameroot + nameext == basename`, and
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212 `nameext` is empty or begins with a period and contains at most one
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213 period. For the purposess of path splitting leading periods on the
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214 basename are ignored; a basename of `.cshrc` will have a nameroot of
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215 `.cshrc`.
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216
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217 The implementation must set this field automatically based on the value
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218 of `basename` prior to evaluating parameter references or expressions.
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219 - name: nameext
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220 type: string?
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221 doc: |
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222 The basename extension such that `nameroot + nameext == basename`, and
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223 `nameext` is empty or begins with a period and contains at most one
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224 period. Leading periods on the basename are ignored; a basename of
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225 `.cshrc` will have an empty `nameext`.
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226
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227 The implementation must set this field automatically based on the value
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228 of `basename` prior to evaluating parameter references or expressions.
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229 - name: checksum
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230 type: string?
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231 doc: |
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232 Optional hash code for validating file integrity. Currently must be in the form
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233 "sha1$ + hexadecimal string" using the SHA-1 algorithm.
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234 - name: size
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235 type: long?
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236 doc: Optional file size
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237 - name: "secondaryFiles"
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238 type:
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239 - "null"
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240 - type: array
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241 items: [File, Directory]
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242 jsonldPredicate:
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243 _id: "cwl:secondaryFiles"
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244 secondaryFilesDSL: true
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245 doc: |
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246 A list of additional files or directories that are associated with the
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247 primary file and must be transferred alongside the primary file.
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248 Examples include indexes of the primary file, or external references
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249 which must be included when loading primary document. A file object
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250 listed in `secondaryFiles` may itself include `secondaryFiles` for
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251 which the same rules apply.
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252 - name: format
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253 type: string?
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254 jsonldPredicate:
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255 _id: cwl:format
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256 _type: "@id"
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257 identity: true
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258 doc: |
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259 The format of the file: this must be an IRI of a concept node that
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260 represents the file format, preferrably defined within an ontology.
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261 If no ontology is available, file formats may be tested by exact match.
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262
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263 Reasoning about format compatability must be done by checking that an
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264 input file format is the same, `owl:equivalentClass` or
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265 `rdfs:subClassOf` the format required by the input parameter.
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266 `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if
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267 `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer
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268 `<C> owl:subclassOf <A>`.
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269
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270 File format ontologies may be provided in the "$schema" metadata at the
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271 root of the document. If no ontologies are specified in `$schema`, the
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272 runtime may perform exact file format matches.
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273 - name: contents
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274 type: string?
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275 doc: |
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276 File contents literal. Maximum of 64 KiB.
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277
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278 If neither `location` nor `path` is provided, `contents` must be
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279 non-null. The implementation must assign a unique identifier for the
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280 `location` field. When the file is staged as input to CommandLineTool,
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281 the value of `contents` must be written to a file.
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282
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283 If `loadContents` of `inputBinding` or `outputBinding` is true and
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284 `location` is valid, the implementation must read up to the first 64
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285 KiB of text from the file and place it in the "contents" field.
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286
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287
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288 - name: Directory
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289 type: record
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290 docAfter: "#File"
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291 doc: |
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292 Represents a directory to present to a command line tool.
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293
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294 Directories are represented as objects with `class` of `Directory`. Directory objects have
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295 a number of properties that provide metadata about the directory.
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296
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297 The `location` property of a Directory is a URI that uniquely identifies
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298 the directory. Implementations must support the file:// URI scheme and may
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299 support other schemes such as http://. Alternately to `location`,
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300 implementations must also accept the `path` property on Directory, which
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301 must be a filesystem path available on the same host as the CWL runner (for
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302 inputs) or the runtime environment of a command line tool execution (for
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303 command line tool outputs).
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304
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305 A Directory object may have a `listing` field. This is a list of File and
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306 Directory objects that are contained in the Directory. For each entry in
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307 `listing`, the `basename` property defines the name of the File or
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308 Subdirectory when staged to disk. If `listing` is not provided, the
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309 implementation must have some way of fetching the Directory listing at
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310 runtime based on the `location` field.
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311
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312 If a Directory does not have `location`, it is a Directory literal. A
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313 Directory literal must provide `listing`. Directory literals must be
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314 created on disk at runtime as needed.
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315
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316 The resources in a Directory literal do not need to have any implied
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317 relationship in their `location`. For example, a Directory listing may
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318 contain two files located on different hosts. It is the responsibility of
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319 the runtime to ensure that those files are staged to disk appropriately.
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320 Secondary files associated with files in `listing` must also be staged to
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321 the same Directory.
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322
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323 When executing a CommandLineTool, Directories must be recursively staged
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324 first and have local values of `path` assigend.
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325
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326 Directory objects in CommandLineTool output must provide either a
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327 `location` URI or a `path` property in the context of the tool execution
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328 runtime (local to the compute node, or within the executing container).
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329
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330 An ExpressionTool may forward file references from input to output by using
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331 the same value for `location`.
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332
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333 Name conflicts (the same `basename` appearing multiple times in `listing`
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334 or in any entry in `secondaryFiles` in the listing) is a fatal error.
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335
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336 fields:
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337 - name: class
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338 type:
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339 type: enum
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340 name: Directory_class
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341 symbols:
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342 - cwl:Directory
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343 jsonldPredicate:
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344 _id: "@type"
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345 _type: "@vocab"
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346 doc: Must be `Directory` to indicate this object describes a Directory.
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347 - name: location
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348 type: string?
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349 doc: |
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350 An IRI that identifies the directory resource. This may be a relative
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351 reference, in which case it must be resolved using the base IRI of the
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352 document. The location may refer to a local or remote resource. If
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353 the `listing` field is not set, the implementation must use the
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354 location IRI to retrieve directory listing. If an implementation is
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355 unable to retrieve the directory listing stored at a remote resource (due to
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356 unsupported protocol, access denied, or other issue) it must signal an
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357 error.
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358
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359 If the `location` field is not provided, the `listing` field must be
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360 provided. The implementation must assign a unique identifier for
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361 the `location` field.
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362
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363 If the `path` field is provided but the `location` field is not, an
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364 implementation may assign the value of the `path` field to `location`,
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365 then follow the rules above.
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366 jsonldPredicate:
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367 _id: "@id"
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368 _type: "@id"
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369 - name: path
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370 type: string?
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371 doc: |
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372 The local path where the Directory is made available prior to executing a
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373 CommandLineTool. This must be set by the implementation. This field
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374 must not be used in any other context. The command line tool being
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375 executed must be able to to access the directory at `path` using the POSIX
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376 `opendir(2)` syscall.
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377
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parents:
diff changeset
378 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
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parents:
diff changeset
379 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
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parents:
diff changeset
380 `<space>`, `<tab>`, and `<newline>`) or characters
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parents:
diff changeset
381 [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
382 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
383 then implementations may terminate the process with a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
384 `permanentFailure`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
385 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
386 _id: "cwl:path"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
387 _type: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
388 - name: basename
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
389 type: string?
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parents:
diff changeset
390 doc: |
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391 The base name of the directory, that is, the name of the file without any
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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392 leading directory path. The base name must not contain a slash `/`.
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parents:
diff changeset
393
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394 If not provided, the implementation must set this field based on the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
395 `location` field by taking the final path component after parsing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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396 `location` as an IRI. If `basename` is provided, it is not required to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
397 match the value from `location`.
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diff changeset
398
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399 When this file is made available to a CommandLineTool, it must be named
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parents:
diff changeset
400 with `basename`, i.e. the final component of the `path` field must match
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
401 `basename`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
402 jsonldPredicate: "cwl:basename"
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parents:
diff changeset
403 - name: listing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
404 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
405 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
406 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
407 items: [File, Directory]
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parents:
diff changeset
408 doc: |
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409 List of files or subdirectories contained in this directory. The name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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410 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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411 each `File` or `Directory` object. It is an error if a `File` shares a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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412 `basename` with any other entry in `listing`. If two or more
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
413 `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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414 equivalent to a single subdirectory with the listings recursively
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
415 merged.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
416 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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417 _id: "cwl:listing"
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diff changeset
418
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
419 - name: Labeled
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
420 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
421 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
422 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
423 - name: label
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
424 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
425 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
426 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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427 jsonldPredicate: "rdfs:label"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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428 doc: "A short, human-readable label of this object."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
429
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
430
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
431 - name: Identified
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
432 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
433 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
434 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
435 - name: id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
436 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
437 jsonldPredicate: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
438 doc: "The unique identifier for this object."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
439
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
440
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
441 - name: LoadListingEnum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
442 type: enum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
443 symbols: [no_listing, shallow_listing, deep_listing]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
444 doc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
445 - |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
446 Specify the desired behavior for loading the `listing` field of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
447 a Directory object for use by expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
448 - "no_listing: Do not load the directory listing."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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449 - "shallow_listing: Only load the top level listing, do not recurse into subdirectories."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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450 - "deep_listing: Load the directory listing and recursively load all subdirectories as well."
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451
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
452
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
453 - name: LoadContents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
454 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
455 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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456 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
457 - name: loadContents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
458 type: boolean?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
459 jsonldPredicate: "cwl:loadContents"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
460 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
461 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
462
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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463 Read up to the first 64 KiB of text from the file and place it in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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464 "contents" field of the file object for use by expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
465 - name: loadListing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
466 type: LoadListingEnum?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
467 jsonldPredicate: "cwl:loadListing"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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468 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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469 Only valid when `type: Directory` or is an array of `items: Directory`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
470
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
471 Specify the desired behavior for loading the `listing` field of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
472 a Directory object for use by expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
473
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
474 The order of precedence for loadListing is:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
475
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
476 1. `loadListing` on an individual parameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
477 2. Inherited from `LoadListingRequirement`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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478 3. By default: `no_listing`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
479
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
480 - name: FieldBase
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
481 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
482 extends: Labeled
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
483 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
484 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
485 secondaryFiles:
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 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
488 - SecondaryFileSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
489 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
490 items: SecondaryFileSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
491 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
492 _id: "cwl:secondaryFiles"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
493 secondaryFilesDSL: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
494 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
495 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
496
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
497 Provides a pattern or expression specifying files or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
498 directories that should be included alongside the primary
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
499 file. Secondary files may be required or optional. When not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
500 explicitly specified, secondary files specified for `inputs`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
501 are required and `outputs` are optional. An implementation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
502 must include matching Files and Directories in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
503 `secondaryFiles` property of the primary file. These Files
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
504 and Directories must be transferred and staged alongside the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
505 primary file. An implementation may fail workflow execution
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
506 if a required secondary file does not exist.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
507
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
508 If the value is an expression, the value of `self` in the expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
509 must be the primary input or output File object to which this binding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
510 applies. The `basename`, `nameroot` and `nameext` fields must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
511 present in `self`. For `CommandLineTool` outputs the `path` field must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
512 also be present. The expression must return a filename string relative
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
513 to the path to the primary File, a File or Directory object with either
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
514 `path` or `location` and `basename` fields set, or an array consisting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
515 of strings or File or Directory objects. It is legal to reference an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
516 unchanged File or Directory object taken from input as a secondaryFile.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
517 The expression may return "null" in which case there is no secondaryFile
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
518 from that expression.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
519
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
520 To work on non-filename-preserving storage systems, portable tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
521 descriptions should avoid constructing new values from `location`, but
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
522 should construct relative references using `basename` or `nameroot`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
523 instead.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
524
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
525 If a value in `secondaryFiles` is a string that is not an expression,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
526 it specifies that the following pattern should be applied to the path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
527 of the primary file to yield a filename relative to the primary File:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
528
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
529 1. If string ends with `?` character, remove the last `?` and mark
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
530 the resulting secondary file as optional.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
531 2. If string begins with one or more caret `^` characters, for each
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
532 caret, remove the last file extension from the path (the last
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
533 period `.` and all following characters). If there are no file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
534 extensions, the path is unchanged.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
535 3. Append the remainder of the string to the end of the file path.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
536
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
537 streamable:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
538 type: boolean?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
539 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
540 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
541
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
542 A value of `true` indicates that the file is read or written
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
543 sequentially without seeking. An implementation may use this flag to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
544 indicate whether it is valid to stream file contents using a named
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
545 pipe. Default: `false`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
546
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
547
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
548 - name: InputFormat
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
549 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
550 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
551 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
552 format:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
553 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
554 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
555 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
556 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
557 items: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
558 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
559 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
560 _id: cwl:format
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
561 _type: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
562 identity: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
563 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
564 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
565
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
566 This must be one or more IRIs of concept nodes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
567 that represents file formats which are allowed as input to this
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
568 parameter, preferrably defined within an ontology. If no ontology is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
569 available, file formats may be tested by exact match.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
570
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
571
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
572 - name: OutputFormat
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
573 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
574 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
575 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
576 format:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
577 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
578 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
579 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
580 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
581 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
582 _id: cwl:format
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
583 _type: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
584 identity: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
585 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
586 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
587
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
588 This is the file format that will be assigned to the output
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
589 File object.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
590
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
591
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
592 - name: Parameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
593 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
594 extends: [FieldBase, sld:Documented, Identified]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
595 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
596 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
597 Define an input or output parameter to a process.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
598
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
599
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
600 - type: enum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
601 name: Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
602 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
603 'Expression' is not a real type. It indicates that a field must allow
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
604 runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
605 is declared and supported by the platform, the field must also allow
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
606 Javascript expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
607 symbols:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
608 - cwl:ExpressionPlaceholder
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
609
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
610
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
611 - name: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
612 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
613 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
614 - name: loadContents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
615 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
616 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
617 - boolean
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
618 jsonldPredicate: "cwl:loadContents"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
619 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
620 Use of `loadContents` in `InputBinding` is deprecated.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
621 Preserved for v1.0 backwards compatability. Will be removed in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
622 CWL v2.0. Use `InputParameter.loadContents` instead.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
623
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
624 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
625
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
626 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
627 "contents" field of the file object for use by expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
628
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
629
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
630 - name: IOSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
631 extends: [Labeled, sld:Documented]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
632 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
633 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
634 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
635 - name: name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
636 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
637 jsonldPredicate: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
638 doc: "The identifier for this type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
639
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
640 - name: InputSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
641 extends: [IOSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
642 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
643 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
644
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
645 - name: OutputSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
646 extends: [IOSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
647 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
648 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
649
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
650
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
651 - name: InputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
652 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
653 extends: [sld:RecordField, FieldBase, InputFormat, LoadContents]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
654 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
655 - specializeFrom: "sld:RecordSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
656 specializeTo: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
657 - specializeFrom: "sld:EnumSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
658 specializeTo: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
659 - specializeFrom: "sld:ArraySchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
660 specializeTo: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
661 - specializeFrom: "sld:PrimitiveType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
662 specializeTo: CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
663
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
664
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
665 - name: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
666 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
667 extends: ["sld:RecordSchema", InputSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
668 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
669 - specializeFrom: "sld:RecordField"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
670 specializeTo: InputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
671
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
672
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
673 - name: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
674 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
675 extends: ["sld:EnumSchema", InputSchema]
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: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
679 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
680 extends: ["sld:ArraySchema", InputSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
681 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
682 - specializeFrom: "sld:RecordSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
683 specializeTo: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
684 - specializeFrom: "sld:EnumSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
685 specializeTo: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
686 - specializeFrom: "sld:ArraySchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
687 specializeTo: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
688 - specializeFrom: "sld:PrimitiveType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
689 specializeTo: CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
690
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
691
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
692 - name: OutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
693 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
694 extends: [sld:RecordField, FieldBase, OutputFormat]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
695 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
696 - specializeFrom: "sld:RecordSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
697 specializeTo: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
698 - specializeFrom: "sld:EnumSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
699 specializeTo: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
700 - specializeFrom: "sld:ArraySchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
701 specializeTo: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
702 - specializeFrom: "sld:PrimitiveType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
703 specializeTo: CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
704
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
705
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
706 - name: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
707 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
708 extends: ["sld:RecordSchema", "#OutputSchema"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
709 docParent: "#OutputParameter"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
710 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
711 - specializeFrom: "sld:RecordField"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
712 specializeTo: OutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
713
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
714
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
715 - name: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
716 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
717 extends: ["sld:EnumSchema", OutputSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
718 docParent: "#OutputParameter"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
719
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
720
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
721 - name: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
722 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
723 extends: ["sld:ArraySchema", OutputSchema]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
724 docParent: "#OutputParameter"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
725 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
726 - specializeFrom: "sld:RecordSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
727 specializeTo: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
728 - specializeFrom: "sld:EnumSchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
729 specializeTo: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
730 - specializeFrom: "sld:ArraySchema"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
731 specializeTo: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
732 - specializeFrom: "sld:PrimitiveType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
733 specializeTo: CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
734
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
735
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
736 - name: InputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
737 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
738 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
739 extends: [Parameter, InputFormat, LoadContents]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
740 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
741 - name: default
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
742 type: Any?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
743 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
744 _id: sld:default
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
745 noLinkCheck: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
746 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
747 The default value to use for this parameter if the parameter is missing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
748 from the input object, or if the value of the parameter in the input
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
749 object is `null`. Default values are applied before evaluating expressions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
750 (e.g. dependent `valueFrom` fields).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
751
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
752
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
753 - name: OutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
754 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
755 extends: [Parameter, OutputFormat]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
756 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
757
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
758
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
759 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
760 name: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
761 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
762 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
763 A process requirement declares a prerequisite that may or must be fulfilled
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
764 before executing a process. See [`Process.hints`](#process) and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
765 [`Process.requirements`](#process).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
766
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
767 Process requirements are the primary mechanism for specifying extensions to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
768 the CWL core specification.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
769
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
770
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
771 - type: record
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parents:
diff changeset
772 name: Process
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
773 extends: [Identified, Labeled, sld:Documented]
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parents:
diff changeset
774 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
775 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
776
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
777 The base executable type in CWL is the `Process` object defined by the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
778 document. Note that the `Process` object is abstract and cannot be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
779 directly executed.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
780
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
781 fields:
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parents:
diff changeset
782 - name: inputs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
783 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
784 type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
785 items: InputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
786 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
787 _id: "cwl:inputs"
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parents:
diff changeset
788 mapSubject: id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
789 mapPredicate: type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
790 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
791 Defines the input parameters of the process. The process is ready to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
792 run when all required input parameters are associated with concrete
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
793 values. Input parameters include a schema for each parameter which is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
794 used to validate the input object. It may also be used to build a user
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
795 interface for constructing the input object.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
796
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
797 When accepting an input object, all input parameters must have a value.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
798 If an input parameter is missing from the input object, it must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
799 assigned a value of `null` (or the value of `default` for that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
800 parameter, if provided) for the purposes of validation and evaluation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
801 of expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
802
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
803 - name: outputs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
804 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
805 type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
806 items: OutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
807 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
808 _id: "cwl:outputs"
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parents:
diff changeset
809 mapSubject: id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
810 mapPredicate: type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
811 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
812 Defines the parameters representing the output of the process. May be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
813 used to generate and/or validate the output object.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
814 - name: requirements
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
815 type: ProcessRequirement[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
816 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
817 _id: "cwl:requirements"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
818 mapSubject: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
819 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
820 Declares requirements that apply to either the runtime environment or the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
821 workflow engine that must be met in order to execute this process. If
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
822 an implementation cannot satisfy all requirements, or a requirement is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
823 listed which is not recognized by the implementation, it is a fatal
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
824 error and the implementation must not attempt to run the process,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
825 unless overridden at user option.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
826 - name: hints
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
827 type: Any[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
828 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
829 Declares hints applying to either the runtime environment or the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
830 workflow engine that may be helpful in executing this process. It is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
831 not an error if an implementation cannot satisfy all hints, however
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
832 the implementation may report a warning.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
833 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
834 _id: cwl:hints
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
835 noLinkCheck: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
836 mapSubject: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
837 - name: cwlVersion
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
838 type: CWLVersion?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
839 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
840 CWL document version. Always required at the document root. Not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
841 required for a Process embedded inside another Process.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
842 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
843 "_id": "cwl:cwlVersion"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
844 "_type": "@vocab"
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parents:
diff changeset
845
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
846 - name: InlineJavascriptRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
847 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
848 extends: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
849 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
850 Indicates that the workflow platform must support inline Javascript expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
851 If this requirement is not present, the workflow platform must not perform expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
852 interpolatation.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
853 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
854 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
855 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
856 doc: "Always 'InlineJavascriptRequirement'"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
857 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
858 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
859 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
860 - name: expressionLib
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
861 type: string[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
862 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
863 Additional code fragments that will also be inserted
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
864 before executing the expression code. Allows for function definitions that may
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
865 be called from CWL expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
866
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
867
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
868 - name: CommandInputSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
869 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
870 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
871
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
872 - name: SchemaDefRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
873 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
874 extends: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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875 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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876 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
877 interpreting the `inputs` and `outputs` fields. When a `type` field
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
878 contain a IRI, the implementation must check if the type is defined in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
879 `schemaDefs` and use that definition. If the type is not found in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
880 `schemaDefs`, it is an error. The entries in `schemaDefs` must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
881 processed in the order listed such that later schema definitions may refer
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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882 to earlier schema definitions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
883 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
884 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
885 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
886 doc: "Always 'SchemaDefRequirement'"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
887 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
888 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
889 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
890 - name: types
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
891 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
892 type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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893 items: CommandInputSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
894 doc: The list of type definitions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
895
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
896 - name: SecondaryFileSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
897 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
898 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
899 - name: pattern
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
900 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
901 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
902 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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903 doc: |
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904 Provides a pattern or expression specifying files or directories that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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905 should be included alongside the primary file.
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906
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907 If the value is an expression, the value of `self` in the expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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908 must be the primary input or output File object to which this binding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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909 applies. The `basename`, `nameroot` and `nameext` fields must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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910 present in `self`. For `CommandLineTool` outputs the `path` field must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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911 also be present. The expression must return a filename string relative
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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912 to the path to the primary File, a File or Directory object with either
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913 `path` or `location` and `basename` fields set, or an array consisting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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914 of strings or File or Directory objects. It is legal to reference an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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915 unchanged File or Directory object taken from input as a secondaryFile.
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916 The expression may return "null" in which case there is no secondaryFile
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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917 from that expression.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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918
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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919 To work on non-filename-preserving storage systems, portable tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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920 descriptions should avoid constructing new values from `location`, but
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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921 should construct relative references using `basename` or `nameroot`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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922 instead.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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923
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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924 If a value in `secondaryFiles` is a string that is not an expression,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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925 it specifies that the following pattern should be applied to the path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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926 of the primary file to yield a filename relative to the primary File:
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927
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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928 1. If string ends with `?` character, remove the last `?` and mark
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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929 the resulting secondary file as optional.
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930 2. If string begins with one or more caret `^` characters, for each
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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931 caret, remove the last file extension from the path (the last
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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932 period `.` and all following characters). If there are no file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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933 extensions, the path is unchanged.
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934 3. Append the remainder of the string to the end of the file path.
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935 - name: required
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936 type: ["null", boolean, Expression]
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937 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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938 An implementation must not fail workflow execution if `required` is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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939 set to `false` and the expected secondary file does not exist.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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940 Default value for `required` field is `true` for secondary files on
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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941 input and `false` for secondary files on output.
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942
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943 - name: LoadListingRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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944 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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945 extends: ProcessRequirement
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
946 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
947 Specify the desired behavior for loading the `listing` field of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
948 a Directory object for use by expressions.
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949 fields:
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950 class:
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951 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
952 doc: "Always 'LoadListingRequirement'"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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953 jsonldPredicate:
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954 "_id": "@type"
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955 "_type": "@vocab"
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956 loadListing:
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957 type: LoadListingEnum?
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958 jsonldPredicate: "cwl:loadListing"