Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2.0-dev2/Process.yml @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 saladVersion: v1.1 |
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2 $base: "https://w3id.org/cwl/cwl#" |
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3 |
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4 $namespaces: |
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5 cwl: "https://w3id.org/cwl/cwl#" |
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6 sld: "https://w3id.org/cwl/salad#" |
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7 rdfs: "http://www.w3.org/2000/01/rdf-schema#" |
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8 |
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9 $graph: |
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10 |
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11 - name: "Common Workflow Language, v1.2.0-dev2" |
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12 type: documentation |
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13 doc: {$include: concepts.md} |
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14 |
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15 - $import: "salad/schema_salad/metaschema/metaschema_base.yml" |
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16 |
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17 - name: BaseTypesDoc |
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18 type: documentation |
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19 doc: | |
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20 ## Base types |
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21 docChild: |
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22 - "#CWLType" |
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23 - "#Process" |
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24 |
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25 - type: enum |
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26 name: CWLVersion |
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27 doc: "Version symbols for published CWL document versions." |
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28 symbols: |
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29 - cwl:draft-2 |
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30 - cwl:draft-3.dev1 |
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31 - cwl:draft-3.dev2 |
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32 - cwl:draft-3.dev3 |
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33 - cwl:draft-3.dev4 |
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34 - cwl:draft-3.dev5 |
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35 - cwl:draft-3 |
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36 - cwl:draft-4.dev1 |
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37 - cwl:draft-4.dev2 |
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38 - cwl:draft-4.dev3 |
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39 - cwl:v1.0.dev4 |
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40 - cwl:v1.0 |
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41 - cwl:v1.1.0-dev1 # a dash is required by the semver 2.0 rules |
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42 - cwl:v1.1 |
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43 - cwl:v1.2.0-dev1 |
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44 - cwl:v1.2.0-dev2 |
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45 |
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46 - name: CWLType |
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47 type: enum |
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48 extends: "sld:PrimitiveType" |
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49 symbols: |
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50 - cwl:File |
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51 - cwl:Directory |
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52 doc: |
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53 - "Extends primitive types with the concept of a file and directory as a builtin type." |
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54 - "File: A File object" |
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55 - "Directory: A Directory object" |
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56 |
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57 - name: File |
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58 type: record |
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59 docParent: "#CWLType" |
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60 doc: | |
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61 Represents a file (or group of files when `secondaryFiles` is provided) that |
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62 will be accessible by tools using standard POSIX file system call API such as |
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63 open(2) and read(2). |
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64 |
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65 Files are represented as objects with `class` of `File`. File objects have |
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66 a number of properties that provide metadata about the file. |
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67 |
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68 The `location` property of a File is a URI that uniquely identifies the |
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69 file. Implementations must support the file:// URI scheme and may support |
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70 other schemes such as http://. The value of `location` may also be a |
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71 relative reference, in which case it must be resolved relative to the URI |
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72 of the document it appears in. Alternately to `location`, implementations |
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73 must also accept the `path` property on File, which must be a filesystem |
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74 path available on the same host as the CWL runner (for inputs) or the |
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75 runtime environment of a command line tool execution (for command line tool |
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76 outputs). |
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77 |
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78 If no `location` or `path` is specified, a file object must specify |
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79 `contents` with the UTF-8 text content of the file. This is a "file |
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80 literal". File literals do not correspond to external resources, but are |
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81 created on disk with `contents` with when needed for a executing a tool. |
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82 Where appropriate, expressions can return file literals to define new files |
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83 on a runtime. The maximum size of `contents` is 64 kilobytes. |
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84 |
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85 The `basename` property defines the filename on disk where the file is |
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86 staged. This may differ from the resource name. If not provided, |
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87 `basename` must be computed from the last path part of `location` and made |
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88 available to expressions. |
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89 |
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90 The `secondaryFiles` property is a list of File or Directory objects that |
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91 must be staged in the same directory as the primary file. It is an error |
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92 for file names to be duplicated in `secondaryFiles`. |
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93 |
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94 The `size` property is the size in bytes of the File. It must be computed |
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95 from the resource and made available to expressions. The `checksum` field |
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96 contains a cryptographic hash of the file content for use it verifying file |
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97 contents. Implementations may, at user option, enable or disable |
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98 computation of the `checksum` field for performance or other reasons. |
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99 However, the ability to compute output checksums is required to pass the |
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100 CWL conformance test suite. |
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101 |
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102 When executing a CommandLineTool, the files and secondary files may be |
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103 staged to an arbitrary directory, but must use the value of `basename` for |
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104 the filename. The `path` property must be file path in the context of the |
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105 tool execution runtime (local to the compute node, or within the executing |
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106 container). All computed properties should be available to expressions. |
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107 File literals also must be staged and `path` must be set. |
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108 |
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109 When collecting CommandLineTool outputs, `glob` matching returns file paths |
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110 (with the `path` property) and the derived properties. This can all be |
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111 modified by `outputEval`. Alternately, if the file `cwl.output.json` is |
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112 present in the output, `outputBinding` is ignored. |
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113 |
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114 File objects in the output must provide either a `location` URI or a `path` |
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115 property in the context of the tool execution runtime (local to the compute |
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116 node, or within the executing container). |
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117 |
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118 When evaluating an ExpressionTool, file objects must be referenced via |
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119 `location` (the expression tool does not have access to files on disk so |
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120 `path` is meaningless) or as file literals. It is legal to return a file |
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121 object with an existing `location` but a different `basename`. The |
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122 `loadContents` field of ExpressionTool inputs behaves the same as on |
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123 CommandLineTool inputs, however it is not meaningful on the outputs. |
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124 |
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125 An ExpressionTool may forward file references from input to output by using |
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126 the same value for `location`. |
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127 |
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128 fields: |
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129 - name: class |
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130 type: |
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131 type: enum |
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132 name: File_class |
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133 symbols: |
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134 - cwl:File |
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135 jsonldPredicate: |
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136 _id: "@type" |
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137 _type: "@vocab" |
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138 doc: Must be `File` to indicate this object describes a file. |
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139 - name: location |
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140 type: string? |
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141 doc: | |
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142 An IRI that identifies the file resource. This may be a relative |
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143 reference, in which case it must be resolved using the base IRI of the |
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144 document. The location may refer to a local or remote resource; the |
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145 implementation must use the IRI to retrieve file content. If an |
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146 implementation is unable to retrieve the file content stored at a |
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147 remote resource (due to unsupported protocol, access denied, or other |
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148 issue) it must signal an error. |
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149 |
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150 If the `location` field is not provided, the `contents` field must be |
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151 provided. The implementation must assign a unique identifier for |
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152 the `location` field. |
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153 |
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154 If the `path` field is provided but the `location` field is not, an |
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155 implementation may assign the value of the `path` field to `location`, |
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156 then follow the rules above. |
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157 jsonldPredicate: |
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158 _id: "@id" |
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159 _type: "@id" |
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160 - name: path |
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161 type: string? |
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162 doc: | |
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163 The local host path where the File is available when a CommandLineTool is |
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164 executed. This field must be set by the implementation. The final |
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165 path component must match the value of `basename`. This field |
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166 must not be used in any other context. The command line tool being |
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167 executed must be able to to access the file at `path` using the POSIX |
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168 `open(2)` syscall. |
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169 |
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170 As a special case, if the `path` field is provided but the `location` |
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171 field is not, an implementation may assign the value of the `path` |
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172 field to `location`, and remove the `path` field. |
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173 |
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174 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) |
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175 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, |
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176 `<space>`, `<tab>`, and `<newline>`) or characters |
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177 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) |
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178 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) |
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179 then implementations may terminate the process with a |
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180 `permanentFailure`. |
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181 jsonldPredicate: |
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182 "_id": "cwl:path" |
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183 "_type": "@id" |
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184 - name: basename |
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185 type: string? |
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186 doc: | |
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187 The base name of the file, that is, the name of the file without any |
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188 leading directory path. The base name must not contain a slash `/`. |
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189 |
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190 If not provided, the implementation must set this field based on the |
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191 `location` field by taking the final path component after parsing |
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192 `location` as an IRI. If `basename` is provided, it is not required to |
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193 match the value from `location`. |
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194 |
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195 When this file is made available to a CommandLineTool, it must be named |
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196 with `basename`, i.e. the final component of the `path` field must match |
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197 `basename`. |
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198 jsonldPredicate: "cwl:basename" |
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199 - name: dirname |
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200 type: string? |
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201 doc: | |
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202 The name of the directory containing file, that is, the path leading up |
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203 to the final slash in the path such that `dirname + '/' + basename == |
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204 path`. |
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205 |
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206 The implementation must set this field based on the value of `path` |
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207 prior to evaluating parameter references or expressions in a |
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208 CommandLineTool document. This field must not be used in any other |
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209 context. |
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210 - name: nameroot |
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211 type: string? |
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212 doc: | |
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213 The basename root such that `nameroot + nameext == basename`, and |
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214 `nameext` is empty or begins with a period and contains at most one |
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215 period. For the purposess of path splitting leading periods on the |
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216 basename are ignored; a basename of `.cshrc` will have a nameroot of |
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217 `.cshrc`. |
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218 |
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219 The implementation must set this field automatically based on the value |
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220 of `basename` prior to evaluating parameter references or expressions. |
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221 - name: nameext |
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222 type: string? |
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223 doc: | |
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224 The basename extension such that `nameroot + nameext == basename`, and |
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225 `nameext` is empty or begins with a period and contains at most one |
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226 period. Leading periods on the basename are ignored; a basename of |
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227 `.cshrc` will have an empty `nameext`. |
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228 |
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229 The implementation must set this field automatically based on the value |
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230 of `basename` prior to evaluating parameter references or expressions. |
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231 - name: checksum |
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232 type: string? |
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233 doc: | |
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234 Optional hash code for validating file integrity. Currently must be in the form |
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235 "sha1$ + hexadecimal string" using the SHA-1 algorithm. |
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236 - name: size |
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237 type: long? |
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238 doc: Optional file size |
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239 - name: "secondaryFiles" |
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240 type: |
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241 - "null" |
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242 - type: array |
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243 items: [File, Directory] |
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244 jsonldPredicate: |
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245 _id: "cwl:secondaryFiles" |
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246 secondaryFilesDSL: true |
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247 doc: | |
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248 A list of additional files or directories that are associated with the |
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249 primary file and must be transferred alongside the primary file. |
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250 Examples include indexes of the primary file, or external references |
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251 which must be included when loading primary document. A file object |
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252 listed in `secondaryFiles` may itself include `secondaryFiles` for |
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253 which the same rules apply. |
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254 - name: format |
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255 type: string? |
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256 jsonldPredicate: |
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257 _id: cwl:format |
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258 _type: "@id" |
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259 identity: true |
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260 doc: | |
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261 The format of the file: this must be an IRI of a concept node that |
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262 represents the file format, preferrably defined within an ontology. |
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263 If no ontology is available, file formats may be tested by exact match. |
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264 |
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265 Reasoning about format compatability must be done by checking that an |
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266 input file format is the same, `owl:equivalentClass` or |
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267 `rdfs:subClassOf` the format required by the input parameter. |
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268 `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if |
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269 `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer |
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270 `<C> owl:subclassOf <A>`. |
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271 |
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272 File format ontologies may be provided in the "$schema" metadata at the |
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273 root of the document. If no ontologies are specified in `$schema`, the |
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274 runtime may perform exact file format matches. |
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275 - name: contents |
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276 type: string? |
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277 doc: | |
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278 File contents literal. Maximum of 64 KiB. |
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279 |
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280 If neither `location` nor `path` is provided, `contents` must be |
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281 non-null. The implementation must assign a unique identifier for the |
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282 `location` field. When the file is staged as input to CommandLineTool, |
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283 the value of `contents` must be written to a file. |
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284 |
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285 If `loadContents` of `inputBinding` or `outputBinding` is true and |
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286 `location` is valid, the implementation must read up to the first 64 |
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287 KiB of text from the file and place it in the "contents" field. |
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288 |
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289 |
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290 - name: Directory |
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291 type: record |
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292 docAfter: "#File" |
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293 doc: | |
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294 Represents a directory to present to a command line tool. |
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295 |
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296 Directories are represented as objects with `class` of `Directory`. Directory objects have |
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297 a number of properties that provide metadata about the directory. |
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298 |
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299 The `location` property of a Directory is a URI that uniquely identifies |
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300 the directory. Implementations must support the file:// URI scheme and may |
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301 support other schemes such as http://. Alternately to `location`, |
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302 implementations must also accept the `path` property on Directory, which |
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303 must be a filesystem path available on the same host as the CWL runner (for |
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304 inputs) or the runtime environment of a command line tool execution (for |
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305 command line tool outputs). |
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306 |
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307 A Directory object may have a `listing` field. This is a list of File and |
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308 Directory objects that are contained in the Directory. For each entry in |
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309 `listing`, the `basename` property defines the name of the File or |
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310 Subdirectory when staged to disk. If `listing` is not provided, the |
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311 implementation must have some way of fetching the Directory listing at |
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312 runtime based on the `location` field. |
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313 |
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314 If a Directory does not have `location`, it is a Directory literal. A |
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315 Directory literal must provide `listing`. Directory literals must be |
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316 created on disk at runtime as needed. |
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317 |
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318 The resources in a Directory literal do not need to have any implied |
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319 relationship in their `location`. For example, a Directory listing may |
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320 contain two files located on different hosts. It is the responsibility of |
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321 the runtime to ensure that those files are staged to disk appropriately. |
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322 Secondary files associated with files in `listing` must also be staged to |
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323 the same Directory. |
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324 |
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325 When executing a CommandLineTool, Directories must be recursively staged |
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326 first and have local values of `path` assigend. |
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327 |
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328 Directory objects in CommandLineTool output must provide either a |
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329 `location` URI or a `path` property in the context of the tool execution |
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330 runtime (local to the compute node, or within the executing container). |
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331 |
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332 An ExpressionTool may forward file references from input to output by using |
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333 the same value for `location`. |
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334 |
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335 Name conflicts (the same `basename` appearing multiple times in `listing` |
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336 or in any entry in `secondaryFiles` in the listing) is a fatal error. |
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337 |
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338 fields: |
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339 - name: class |
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340 type: |
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341 type: enum |
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342 name: Directory_class |
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343 symbols: |
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344 - cwl:Directory |
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345 jsonldPredicate: |
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346 _id: "@type" |
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347 _type: "@vocab" |
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348 doc: Must be `Directory` to indicate this object describes a Directory. |
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349 - name: location |
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350 type: string? |
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351 doc: | |
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352 An IRI that identifies the directory resource. This may be a relative |
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353 reference, in which case it must be resolved using the base IRI of the |
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354 document. The location may refer to a local or remote resource. If |
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355 the `listing` field is not set, the implementation must use the |
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356 location IRI to retrieve directory listing. If an implementation is |
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357 unable to retrieve the directory listing stored at a remote resource (due to |
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358 unsupported protocol, access denied, or other issue) it must signal an |
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359 error. |
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360 |
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361 If the `location` field is not provided, the `listing` field must be |
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362 provided. The implementation must assign a unique identifier for |
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363 the `location` field. |
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364 |
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365 If the `path` field is provided but the `location` field is not, an |
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366 implementation may assign the value of the `path` field to `location`, |
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367 then follow the rules above. |
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368 jsonldPredicate: |
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369 _id: "@id" |
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370 _type: "@id" |
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371 - name: path |
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372 type: string? |
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373 doc: | |
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374 The local path where the Directory is made available prior to executing a |
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375 CommandLineTool. This must be set by the implementation. This field |
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376 must not be used in any other context. The command line tool being |
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377 executed must be able to to access the directory at `path` using the POSIX |
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378 `opendir(2)` syscall. |
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379 |
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380 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) |
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381 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, |
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382 `<space>`, `<tab>`, and `<newline>`) or characters |
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383 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) |
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384 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) |
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385 then implementations may terminate the process with a |
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386 `permanentFailure`. |
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387 jsonldPredicate: |
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388 _id: "cwl:path" |
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389 _type: "@id" |
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390 - name: basename |
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391 type: string? |
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392 doc: | |
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393 The base name of the directory, that is, the name of the file without any |
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394 leading directory path. The base name must not contain a slash `/`. |
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395 |
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396 If not provided, the implementation must set this field based on the |
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397 `location` field by taking the final path component after parsing |
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398 `location` as an IRI. If `basename` is provided, it is not required to |
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399 match the value from `location`. |
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400 |
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401 When this file is made available to a CommandLineTool, it must be named |
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402 with `basename`, i.e. the final component of the `path` field must match |
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403 `basename`. |
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404 jsonldPredicate: "cwl:basename" |
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405 - name: listing |
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406 type: |
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407 - "null" |
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408 - type: array |
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409 items: [File, Directory] |
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410 doc: | |
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411 List of files or subdirectories contained in this directory. The name |
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412 of each file or subdirectory is determined by the `basename` field of |
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413 each `File` or `Directory` object. It is an error if a `File` shares a |
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414 `basename` with any other entry in `listing`. If two or more |
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415 `Directory` object share the same `basename`, this must be treated as |
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416 equivalent to a single subdirectory with the listings recursively |
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417 merged. |
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418 jsonldPredicate: |
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419 _id: "cwl:listing" |
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420 |
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421 - name: Labeled |
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422 type: record |
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423 abstract: true |
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424 fields: |
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425 - name: label |
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426 type: |
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427 - "null" |
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428 - string |
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429 jsonldPredicate: "rdfs:label" |
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430 doc: "A short, human-readable label of this object." |
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431 |
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432 |
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433 - name: Identified |
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434 type: record |
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435 abstract: true |
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436 fields: |
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437 - name: id |
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438 type: string? |
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439 jsonldPredicate: "@id" |
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440 doc: "The unique identifier for this object." |
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441 |
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442 |
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443 - name: LoadListingEnum |
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444 type: enum |
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445 symbols: [no_listing, shallow_listing, deep_listing] |
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446 doc: |
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447 - | |
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448 Specify the desired behavior for loading the `listing` field of |
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449 a Directory object for use by expressions. |
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450 - "no_listing: Do not load the directory listing." |
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451 - "shallow_listing: Only load the top level listing, do not recurse into subdirectories." |
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452 - "deep_listing: Load the directory listing and recursively load all subdirectories as well." |
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453 |
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454 |
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455 - name: LoadContents |
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456 type: record |
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457 abstract: true |
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458 fields: |
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459 - name: loadContents |
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460 type: boolean? |
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461 jsonldPredicate: "cwl:loadContents" |
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462 doc: | |
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463 Only valid when `type: File` or is an array of `items: File`. |
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464 |
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465 Read up to the first 64 KiB of text from the file and place it in the |
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466 "contents" field of the file object for use by expressions. |
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467 - name: loadListing |
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468 type: LoadListingEnum? |
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469 jsonldPredicate: "cwl:loadListing" |
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470 doc: | |
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471 Only valid when `type: Directory` or is an array of `items: Directory`. |
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472 |
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473 Specify the desired behavior for loading the `listing` field of |
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474 a Directory object for use by expressions. |
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475 |
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476 The order of precedence for loadListing is: |
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477 |
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478 1. `loadListing` on an individual parameter |
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479 2. Inherited from `LoadListingRequirement` |
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480 3. By default: `no_listing` |
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481 |
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482 - name: FieldBase |
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483 type: record |
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484 extends: Labeled |
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485 abstract: true |
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486 fields: |
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487 secondaryFiles: |
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488 type: |
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489 - "null" |
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490 - SecondaryFileSchema |
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491 - type: array |
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492 items: SecondaryFileSchema |
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493 jsonldPredicate: |
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494 _id: "cwl:secondaryFiles" |
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495 secondaryFilesDSL: true |
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496 doc: | |
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497 Only valid when `type: File` or is an array of `items: File`. |
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498 |
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499 Provides a pattern or expression specifying files or |
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500 directories that should be included alongside the primary |
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501 file. Secondary files may be required or optional. When not |
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502 explicitly specified, secondary files specified for `inputs` |
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503 are required and `outputs` are optional. An implementation |
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504 must include matching Files and Directories in the |
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505 `secondaryFiles` property of the primary file. These Files |
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506 and Directories must be transferred and staged alongside the |
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507 primary file. An implementation may fail workflow execution |
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508 if a required secondary file does not exist. |
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509 |
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510 If the value is an expression, the value of `self` in the expression |
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511 must be the primary input or output File object to which this binding |
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512 applies. The `basename`, `nameroot` and `nameext` fields must be |
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513 present in `self`. For `CommandLineTool` outputs the `path` field must |
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514 also be present. The expression must return a filename string relative |
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515 to the path to the primary File, a File or Directory object with either |
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516 `path` or `location` and `basename` fields set, or an array consisting |
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517 of strings or File or Directory objects. It is legal to reference an |
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518 unchanged File or Directory object taken from input as a secondaryFile. |
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519 The expression may return "null" in which case there is no secondaryFile |
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520 from that expression. |
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521 |
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522 To work on non-filename-preserving storage systems, portable tool |
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523 descriptions should avoid constructing new values from `location`, but |
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524 should construct relative references using `basename` or `nameroot` |
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525 instead. |
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526 |
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527 If a value in `secondaryFiles` is a string that is not an expression, |
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528 it specifies that the following pattern should be applied to the path |
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529 of the primary file to yield a filename relative to the primary File: |
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530 |
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531 1. If string ends with `?` character, remove the last `?` and mark |
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532 the resulting secondary file as optional. |
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533 2. If string begins with one or more caret `^` characters, for each |
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534 caret, remove the last file extension from the path (the last |
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535 period `.` and all following characters). If there are no file |
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536 extensions, the path is unchanged. |
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537 3. Append the remainder of the string to the end of the file path. |
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538 |
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539 streamable: |
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540 type: boolean? |
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541 doc: | |
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542 Only valid when `type: File` or is an array of `items: File`. |
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543 |
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544 A value of `true` indicates that the file is read or written |
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545 sequentially without seeking. An implementation may use this flag to |
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546 indicate whether it is valid to stream file contents using a named |
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547 pipe. Default: `false`. |
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548 |
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549 |
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550 - name: InputFormat |
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551 type: record |
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552 abstract: true |
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553 fields: |
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554 format: |
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555 type: |
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|
556 - "null" |
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diff
changeset
|
557 - string |
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|
558 - type: array |
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|
559 items: string |
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|
560 - Expression |
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561 jsonldPredicate: |
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|
562 _id: cwl:format |
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|
563 _type: "@id" |
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|
564 identity: true |
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|
565 doc: | |
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|
566 Only valid when `type: File` or is an array of `items: File`. |
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|
567 |
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|
568 This must be one or more IRIs of concept nodes |
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|
569 that represents file formats which are allowed as input to this |
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570 parameter, preferrably defined within an ontology. If no ontology is |
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|
571 available, file formats may be tested by exact match. |
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|
572 |
4f3585e2f14b
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changeset
|
573 |
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|
574 - name: OutputFormat |
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|
575 type: record |
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|
576 abstract: true |
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|
577 fields: |
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|
578 format: |
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|
579 type: |
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|
580 - "null" |
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|
581 - string |
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|
582 - Expression |
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583 jsonldPredicate: |
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584 _id: cwl:format |
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585 _type: "@id" |
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586 identity: true |
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|
587 doc: | |
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588 Only valid when `type: File` or is an array of `items: File`. |
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589 |
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|
590 This is the file format that will be assigned to the output |
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591 File object. |
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|
592 |
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|
593 |
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594 - name: Parameter |
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595 type: record |
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596 extends: [FieldBase, sld:Documented, Identified] |
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|
597 abstract: true |
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|
598 doc: | |
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599 Define an input or output parameter to a process. |
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|
600 |
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|
601 |
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602 - type: enum |
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603 name: Expression |
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604 doc: | |
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605 'Expression' is not a real type. It indicates that a field must allow |
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606 runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement) |
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|
607 is declared and supported by the platform, the field must also allow |
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|
608 Javascript expressions. |
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|
609 symbols: |
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|
610 - cwl:ExpressionPlaceholder |
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|
611 |
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|
612 |
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|
613 - name: InputBinding |
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614 type: record |
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|
615 fields: |
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|
616 - name: loadContents |
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|
617 type: |
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|
618 - "null" |
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|
619 - boolean |
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620 jsonldPredicate: "cwl:loadContents" |
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|
621 doc: | |
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622 Use of `loadContents` in `InputBinding` is deprecated. |
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623 Preserved for v1.0 backwards compatability. Will be removed in |
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624 CWL v2.0. Use `InputParameter.loadContents` instead. |
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|
625 |
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|
626 Only valid when `type: File` or is an array of `items: File`. |
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|
627 |
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|
628 Read up to the first 64 KiB of text from the file and place it in the |
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|
629 "contents" field of the file object for use by expressions. |
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|
630 |
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|
631 |
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|
632 - name: IOSchema |
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|
633 extends: [Labeled, sld:Documented] |
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|
634 type: record |
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|
635 abstract: true |
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|
636 fields: |
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|
637 - name: name |
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|
638 type: string? |
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|
639 jsonldPredicate: "@id" |
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|
640 doc: "The identifier for this type" |
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|
641 |
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|
642 - name: InputSchema |
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|
643 extends: [IOSchema] |
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|
644 type: record |
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|
645 abstract: true |
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|
646 |
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|
647 - name: OutputSchema |
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|
648 extends: [IOSchema] |
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649 type: record |
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|
650 abstract: true |
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|
651 |
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|
652 |
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|
653 - name: InputRecordField |
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654 type: record |
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|
655 extends: [sld:RecordField, FieldBase, InputFormat, LoadContents] |
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|
656 specialize: |
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657 - specializeFrom: "sld:RecordSchema" |
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658 specializeTo: InputRecordSchema |
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659 - specializeFrom: "sld:EnumSchema" |
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|
660 specializeTo: InputEnumSchema |
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|
661 - specializeFrom: "sld:ArraySchema" |
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662 specializeTo: InputArraySchema |
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663 - specializeFrom: "sld:PrimitiveType" |
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664 specializeTo: CWLType |
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|
665 |
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changeset
|
666 |
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|
667 - name: InputRecordSchema |
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|
668 type: record |
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|
669 extends: ["sld:RecordSchema", InputSchema] |
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|
670 specialize: |
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|
671 - specializeFrom: "sld:RecordField" |
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|
672 specializeTo: InputRecordField |
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|
673 |
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changeset
|
674 |
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|
675 - name: InputEnumSchema |
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|
676 type: record |
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|
677 extends: ["sld:EnumSchema", InputSchema] |
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|
678 |
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changeset
|
679 |
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|
680 - name: InputArraySchema |
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|
681 type: record |
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|
682 extends: ["sld:ArraySchema", InputSchema] |
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|
683 specialize: |
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|
684 - specializeFrom: "sld:RecordSchema" |
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|
685 specializeTo: InputRecordSchema |
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|
686 - specializeFrom: "sld:EnumSchema" |
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|
687 specializeTo: InputEnumSchema |
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|
688 - specializeFrom: "sld:ArraySchema" |
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|
689 specializeTo: InputArraySchema |
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|
690 - specializeFrom: "sld:PrimitiveType" |
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|
691 specializeTo: CWLType |
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|
692 |
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|
693 |
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|
694 - name: OutputRecordField |
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|
695 type: record |
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|
696 extends: [sld:RecordField, FieldBase, OutputFormat] |
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|
697 specialize: |
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|
698 - specializeFrom: "sld:RecordSchema" |
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699 specializeTo: OutputRecordSchema |
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|
700 - specializeFrom: "sld:EnumSchema" |
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|
701 specializeTo: OutputEnumSchema |
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|
702 - specializeFrom: "sld:ArraySchema" |
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703 specializeTo: OutputArraySchema |
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|
704 - specializeFrom: "sld:PrimitiveType" |
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705 specializeTo: CWLType |
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|
706 |
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|
707 |
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|
708 - name: OutputRecordSchema |
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|
709 type: record |
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|
710 extends: ["sld:RecordSchema", "#OutputSchema"] |
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|
711 docParent: "#OutputParameter" |
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|
712 specialize: |
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|
713 - specializeFrom: "sld:RecordField" |
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|
714 specializeTo: OutputRecordField |
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|
715 |
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|
716 |
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|
717 - name: OutputEnumSchema |
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|
718 type: record |
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|
719 extends: ["sld:EnumSchema", OutputSchema] |
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|
720 docParent: "#OutputParameter" |
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|
721 |
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|
722 |
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|
723 - name: OutputArraySchema |
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|
724 type: record |
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|
725 extends: ["sld:ArraySchema", OutputSchema] |
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|
726 docParent: "#OutputParameter" |
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|
727 specialize: |
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|
728 - specializeFrom: "sld:RecordSchema" |
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|
729 specializeTo: OutputRecordSchema |
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|
730 - specializeFrom: "sld:EnumSchema" |
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|
731 specializeTo: OutputEnumSchema |
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|
732 - specializeFrom: "sld:ArraySchema" |
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|
733 specializeTo: OutputArraySchema |
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|
734 - specializeFrom: "sld:PrimitiveType" |
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|
735 specializeTo: CWLType |
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parents:
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|
736 |
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|
737 |
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|
738 - name: InputParameter |
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|
739 type: record |
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|
740 abstract: true |
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|
741 extends: [Parameter, InputFormat, LoadContents] |
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|
742 fields: |
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|
743 - name: default |
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|
744 type: Any? |
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|
745 jsonldPredicate: |
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|
746 _id: sld:default |
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|
747 noLinkCheck: true |
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|
748 doc: | |
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|
749 The default value to use for this parameter if the parameter is missing |
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|
750 from the input object, or if the value of the parameter in the input |
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|
751 object is `null`. Default values are applied before evaluating expressions |
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|
752 (e.g. dependent `valueFrom` fields). |
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|
753 |
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|
754 |
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|
755 - name: OutputParameter |
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|
756 type: record |
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|
757 extends: [Parameter, OutputFormat] |
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|
758 abstract: true |
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|
759 |
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|
760 |
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|
761 - type: record |
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|
762 name: ProcessRequirement |
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|
763 abstract: true |
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|
764 doc: | |
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parents:
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|
765 A process requirement declares a prerequisite that may or must be fulfilled |
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|
766 before executing a process. See [`Process.hints`](#process) and |
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|
767 [`Process.requirements`](#process). |
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|
768 |
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|
769 Process requirements are the primary mechanism for specifying extensions to |
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parents:
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|
770 the CWL core specification. |
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parents:
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|
771 |
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parents:
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|
772 |
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parents:
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|
773 - type: record |
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|
774 name: Process |
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parents:
diff
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|
775 extends: [Identified, Labeled, sld:Documented] |
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parents:
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|
776 abstract: true |
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|
777 doc: | |
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|
778 |
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|
779 The base executable type in CWL is the `Process` object defined by the |
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|
780 document. Note that the `Process` object is abstract and cannot be |
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parents:
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|
781 directly executed. |
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parents:
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|
782 |
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parents:
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|
783 fields: |
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parents:
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|
784 - name: inputs |
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|
785 type: |
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parents:
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|
786 type: array |
4f3585e2f14b
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parents:
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|
787 items: InputParameter |
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parents:
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|
788 jsonldPredicate: |
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789 _id: "cwl:inputs" |
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790 mapSubject: id |
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791 mapPredicate: type |
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792 doc: | |
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793 Defines the input parameters of the process. The process is ready to |
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794 run when all required input parameters are associated with concrete |
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795 values. Input parameters include a schema for each parameter which is |
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796 used to validate the input object. It may also be used to build a user |
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797 interface for constructing the input object. |
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798 |
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799 When accepting an input object, all input parameters must have a value. |
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800 If an input parameter is missing from the input object, it must be |
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801 assigned a value of `null` (or the value of `default` for that |
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802 parameter, if provided) for the purposes of validation and evaluation |
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803 of expressions. |
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804 |
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805 - name: outputs |
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806 type: |
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807 type: array |
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808 items: OutputParameter |
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809 jsonldPredicate: |
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810 _id: "cwl:outputs" |
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811 mapSubject: id |
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812 mapPredicate: type |
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813 doc: | |
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814 Defines the parameters representing the output of the process. May be |
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815 used to generate and/or validate the output object. |
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816 - name: requirements |
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817 type: ProcessRequirement[]? |
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818 jsonldPredicate: |
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819 _id: "cwl:requirements" |
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820 mapSubject: class |
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821 doc: | |
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822 Declares requirements that apply to either the runtime environment or the |
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823 workflow engine that must be met in order to execute this process. If |
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824 an implementation cannot satisfy all requirements, or a requirement is |
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825 listed which is not recognized by the implementation, it is a fatal |
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826 error and the implementation must not attempt to run the process, |
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827 unless overridden at user option. |
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828 - name: hints |
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829 type: Any[]? |
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830 doc: | |
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831 Declares hints applying to either the runtime environment or the |
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832 workflow engine that may be helpful in executing this process. It is |
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833 not an error if an implementation cannot satisfy all hints, however |
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834 the implementation may report a warning. |
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835 jsonldPredicate: |
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836 _id: cwl:hints |
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837 noLinkCheck: true |
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838 mapSubject: class |
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839 - name: cwlVersion |
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840 type: CWLVersion? |
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841 doc: | |
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842 CWL document version. Always required at the document root. Not |
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843 required for a Process embedded inside another Process. |
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844 jsonldPredicate: |
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845 "_id": "cwl:cwlVersion" |
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846 "_type": "@vocab" |
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847 - name: intent |
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848 type: string[]? |
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849 jsonldPredicate: |
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850 _type: "@id" |
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851 identity: true |
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852 doc: | |
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853 An identifier for the type of computational operation, of this Process. |
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854 Especially useful for "class: Operation", but can also be used for |
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855 CommandLineTool, Workflow, or ExpressionTool. |
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856 |
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857 If provided, then this must be an IRI of a concept node that |
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858 represents the type of operation, preferrably defined within an ontology. |
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859 |
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860 For example, in the domain of bioinformatics, one can use an IRI from |
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861 the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), |
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862 like [Alignment](http://edamontology.org/operation_2928), |
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863 or [Clustering](http://edamontology.org/operation_3432); or a more |
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864 specific Operation concept like |
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865 [Split read mapping](http://edamontology.org/operation_3199). |
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866 |
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867 - name: InlineJavascriptRequirement |
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868 type: record |
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869 extends: ProcessRequirement |
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870 doc: | |
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871 Indicates that the workflow platform must support inline Javascript expressions. |
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872 If this requirement is not present, the workflow platform must not perform expression |
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873 interpolatation. |
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874 fields: |
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875 - name: class |
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876 type: string |
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877 doc: "Always 'InlineJavascriptRequirement'" |
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878 jsonldPredicate: |
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879 "_id": "@type" |
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880 "_type": "@vocab" |
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881 - name: expressionLib |
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882 type: string[]? |
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883 doc: | |
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884 Additional code fragments that will also be inserted |
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885 before executing the expression code. Allows for function definitions that may |
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886 be called from CWL expressions. |
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887 |
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888 |
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889 - name: CommandInputSchema |
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890 type: record |
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891 abstract: true |
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892 |
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893 - name: SchemaDefRequirement |
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894 type: record |
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895 extends: ProcessRequirement |
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896 doc: | |
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897 This field consists of an array of type definitions which must be used when |
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898 interpreting the `inputs` and `outputs` fields. When a `type` field |
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899 contain a IRI, the implementation must check if the type is defined in |
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900 `schemaDefs` and use that definition. If the type is not found in |
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901 `schemaDefs`, it is an error. The entries in `schemaDefs` must be |
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902 processed in the order listed such that later schema definitions may refer |
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|
903 to earlier schema definitions. |
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|
904 fields: |
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|
905 - name: class |
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906 type: string |
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|
907 doc: "Always 'SchemaDefRequirement'" |
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908 jsonldPredicate: |
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909 "_id": "@type" |
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910 "_type": "@vocab" |
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911 - name: types |
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912 type: |
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913 type: array |
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914 items: CommandInputSchema |
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915 doc: The list of type definitions. |
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916 |
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|
917 - name: SecondaryFileSchema |
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918 type: record |
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|
919 fields: |
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|
920 - name: pattern |
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921 type: |
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922 - string |
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923 - Expression |
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|
924 doc: | |
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925 Provides a pattern or expression specifying files or directories that |
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926 should be included alongside the primary file. |
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927 |
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928 If the value is an expression, the value of `self` in the expression |
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929 must be the primary input or output File object to which this binding |
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930 applies. The `basename`, `nameroot` and `nameext` fields must be |
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931 present in `self`. For `CommandLineTool` outputs the `path` field must |
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932 also be present. The expression must return a filename string relative |
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933 to the path to the primary File, a File or Directory object with either |
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934 `path` or `location` and `basename` fields set, or an array consisting |
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935 of strings or File or Directory objects. It is legal to reference an |
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936 unchanged File or Directory object taken from input as a secondaryFile. |
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937 The expression may return "null" in which case there is no secondaryFile |
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938 from that expression. |
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939 |
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940 To work on non-filename-preserving storage systems, portable tool |
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941 descriptions should avoid constructing new values from `location`, but |
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942 should construct relative references using `basename` or `nameroot` |
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943 instead. |
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944 |
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945 If a value in `secondaryFiles` is a string that is not an expression, |
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946 it specifies that the following pattern should be applied to the path |
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947 of the primary file to yield a filename relative to the primary File: |
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948 |
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949 1. If string ends with `?` character, remove the last `?` and mark |
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950 the resulting secondary file as optional. |
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951 2. If string begins with one or more caret `^` characters, for each |
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952 caret, remove the last file extension from the path (the last |
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953 period `.` and all following characters). If there are no file |
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954 extensions, the path is unchanged. |
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955 3. Append the remainder of the string to the end of the file path. |
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956 - name: required |
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957 type: ["null", boolean, Expression] |
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958 doc: | |
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959 An implementation must not fail workflow execution if `required` is |
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960 set to `false` and the expected secondary file does not exist. |
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961 Default value for `required` field is `true` for secondary files on |
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962 input and `false` for secondary files on output. |
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963 doc: | |
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964 Secondary files are specified using the following micro-DSL for secondary files: |
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965 |
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966 * If the value is a string, it is transformed to an object with two fields |
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967 `pattern` and `required` |
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968 * By default, the value of `required` is `null` |
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969 (this indicates default behavior, which may be based on the context) |
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970 * If the value ends with a question mark `?` the question mark is |
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971 stripped off and the value of the field `required` is set to `False` |
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972 * The remaining value is assigned to the field `pattern` |
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973 |
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974 For implementation details and examples, please see |
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975 [this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files) |
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976 in the Schema Salad specification. |
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977 |
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978 - name: LoadListingRequirement |
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979 type: record |
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980 extends: ProcessRequirement |
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981 doc: | |
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982 Specify the desired behavior for loading the `listing` field of |
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983 a Directory object for use by expressions. |
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984 fields: |
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985 class: |
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986 type: string |
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987 doc: "Always 'LoadListingRequirement'" |
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988 jsonldPredicate: |
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989 "_id": "@type" |
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990 "_type": "@vocab" |
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991 loadListing: |
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992 type: LoadListingEnum? |
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993 jsonldPredicate: "cwl:loadListing" |