Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2.0-dev3/Process.yml @ 0:4f3585e2f14b draft default tip
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author | shellac |
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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 $graph: |
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10 |
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11 - name: "Common Workflow Language, v1.2.0-dev3" |
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12 type: documentation |
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13 doc: {$include: concepts.md} |
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14 |
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15 - $import: "salad/schema_salad/metaschema/metaschema_base.yml" |
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16 |
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17 - name: BaseTypesDoc |
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18 type: documentation |
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19 doc: | |
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20 ## Base types |
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21 docChild: |
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22 - "#CWLType" |
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23 - "#Process" |
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24 |
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25 - type: enum |
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26 name: CWLVersion |
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27 doc: "Version symbols for published CWL document versions." |
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28 symbols: |
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29 - cwl:draft-2 |
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30 - cwl:draft-3.dev1 |
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31 - cwl:draft-3.dev2 |
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32 - cwl:draft-3.dev3 |
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33 - cwl:draft-3.dev4 |
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34 - cwl:draft-3.dev5 |
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35 - cwl:draft-3 |
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36 - cwl:draft-4.dev1 |
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37 - cwl:draft-4.dev2 |
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38 - cwl:draft-4.dev3 |
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39 - cwl:v1.0.dev4 |
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40 - cwl:v1.0 |
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41 - cwl:v1.1.0-dev1 # a dash is required by the semver 2.0 rules |
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42 - cwl:v1.1 |
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43 - cwl:v1.2.0-dev1 |
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44 - cwl:v1.2.0-dev2 |
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45 - cwl:v1.2.0-dev3 |
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46 |
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47 - name: CWLType |
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48 type: enum |
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49 extends: "sld:PrimitiveType" |
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50 symbols: |
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51 - cwl:File |
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52 - cwl:Directory |
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53 doc: |
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54 - "Extends primitive types with the concept of a file and directory as a builtin type." |
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55 - "File: A File object" |
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56 - "Directory: A Directory object" |
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57 |
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58 - name: File |
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59 type: record |
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60 docParent: "#CWLType" |
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61 doc: | |
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62 Represents a file (or group of files when `secondaryFiles` is provided) that |
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63 will be accessible by tools using standard POSIX file system call API such as |
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64 open(2) and read(2). |
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65 |
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66 Files are represented as objects with `class` of `File`. File objects have |
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67 a number of properties that provide metadata about the file. |
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68 |
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69 The `location` property of a File is a URI that uniquely identifies the |
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70 file. Implementations must support the file:// URI scheme and may support |
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71 other schemes such as http://. The value of `location` may also be a |
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72 relative reference, in which case it must be resolved relative to the URI |
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73 of the document it appears in. Alternately to `location`, implementations |
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74 must also accept the `path` property on File, which must be a filesystem |
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75 path available on the same host as the CWL runner (for inputs) or the |
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76 runtime environment of a command line tool execution (for command line tool |
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77 outputs). |
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78 |
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79 If no `location` or `path` is specified, a file object must specify |
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80 `contents` with the UTF-8 text content of the file. This is a "file |
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81 literal". File literals do not correspond to external resources, but are |
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82 created on disk with `contents` with when needed for a executing a tool. |
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83 Where appropriate, expressions can return file literals to define new files |
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84 on a runtime. The maximum size of `contents` is 64 kilobytes. |
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85 |
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86 The `basename` property defines the filename on disk where the file is |
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87 staged. This may differ from the resource name. If not provided, |
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88 `basename` must be computed from the last path part of `location` and made |
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89 available to expressions. |
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90 |
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91 The `secondaryFiles` property is a list of File or Directory objects that |
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92 must be staged in the same directory as the primary file. It is an error |
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93 for file names to be duplicated in `secondaryFiles`. |
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94 |
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95 The `size` property is the size in bytes of the File. It must be computed |
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96 from the resource and made available to expressions. The `checksum` field |
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97 contains a cryptographic hash of the file content for use it verifying file |
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98 contents. Implementations may, at user option, enable or disable |
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99 computation of the `checksum` field for performance or other reasons. |
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100 However, the ability to compute output checksums is required to pass the |
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101 CWL conformance test suite. |
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102 |
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103 When executing a CommandLineTool, the files and secondary files may be |
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104 staged to an arbitrary directory, but must use the value of `basename` for |
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105 the filename. The `path` property must be file path in the context of the |
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106 tool execution runtime (local to the compute node, or within the executing |
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107 container). All computed properties should be available to expressions. |
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108 File literals also must be staged and `path` must be set. |
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109 |
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110 When collecting CommandLineTool outputs, `glob` matching returns file paths |
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111 (with the `path` property) and the derived properties. This can all be |
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112 modified by `outputEval`. Alternately, if the file `cwl.output.json` is |
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113 present in the output, `outputBinding` is ignored. |
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114 |
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115 File objects in the output must provide either a `location` URI or a `path` |
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116 property in the context of the tool execution runtime (local to the compute |
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117 node, or within the executing container). |
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118 |
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119 When evaluating an ExpressionTool, file objects must be referenced via |
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120 `location` (the expression tool does not have access to files on disk so |
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121 `path` is meaningless) or as file literals. It is legal to return a file |
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122 object with an existing `location` but a different `basename`. The |
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123 `loadContents` field of ExpressionTool inputs behaves the same as on |
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124 CommandLineTool inputs, however it is not meaningful on the outputs. |
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125 |
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126 An ExpressionTool may forward file references from input to output by using |
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127 the same value for `location`. |
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128 |
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129 fields: |
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130 - name: class |
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131 type: |
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132 type: enum |
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133 name: File_class |
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134 symbols: |
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135 - cwl:File |
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136 jsonldPredicate: |
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137 _id: "@type" |
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138 _type: "@vocab" |
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139 doc: Must be `File` to indicate this object describes a file. |
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140 - name: location |
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141 type: string? |
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142 doc: | |
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143 An IRI that identifies the file resource. This may be a relative |
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144 reference, in which case it must be resolved using the base IRI of the |
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145 document. The location may refer to a local or remote resource; the |
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146 implementation must use the IRI to retrieve file content. If an |
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147 implementation is unable to retrieve the file content stored at a |
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148 remote resource (due to unsupported protocol, access denied, or other |
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149 issue) it must signal an error. |
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150 |
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151 If the `location` field is not provided, the `contents` field must be |
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152 provided. The implementation must assign a unique identifier for |
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153 the `location` field. |
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154 |
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155 If the `path` field is provided but the `location` field is not, an |
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156 implementation may assign the value of the `path` field to `location`, |
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157 then follow the rules above. |
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158 jsonldPredicate: |
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159 _id: "@id" |
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160 _type: "@id" |
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161 - name: path |
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162 type: string? |
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163 doc: | |
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164 The local host path where the File is available when a CommandLineTool is |
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165 executed. This field must be set by the implementation. The final |
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166 path component must match the value of `basename`. This field |
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167 must not be used in any other context. The command line tool being |
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168 executed must be able to to access the file at `path` using the POSIX |
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169 `open(2)` syscall. |
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170 |
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171 As a special case, if the `path` field is provided but the `location` |
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172 field is not, an implementation may assign the value of the `path` |
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173 field to `location`, and remove the `path` field. |
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174 |
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175 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) |
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176 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, |
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177 `<space>`, `<tab>`, and `<newline>`) or characters |
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178 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) |
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179 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) |
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180 then implementations may terminate the process with a |
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181 `permanentFailure`. |
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182 jsonldPredicate: |
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183 "_id": "cwl:path" |
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184 "_type": "@id" |
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185 - name: basename |
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186 type: string? |
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187 doc: | |
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188 The base name of the file, that is, the name of the file without any |
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189 leading directory path. The base name must not contain a slash `/`. |
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190 |
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191 If not provided, the implementation must set this field based on the |
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192 `location` field by taking the final path component after parsing |
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193 `location` as an IRI. If `basename` is provided, it is not required to |
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194 match the value from `location`. |
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195 |
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196 When this file is made available to a CommandLineTool, it must be named |
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197 with `basename`, i.e. the final component of the `path` field must match |
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198 `basename`. |
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199 jsonldPredicate: "cwl:basename" |
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200 - name: dirname |
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201 type: string? |
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202 doc: | |
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203 The name of the directory containing file, that is, the path leading up |
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204 to the final slash in the path such that `dirname + '/' + basename == |
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205 path`. |
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206 |
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207 The implementation must set this field based on the value of `path` |
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208 prior to evaluating parameter references or expressions in a |
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209 CommandLineTool document. This field must not be used in any other |
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210 context. |
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211 - name: nameroot |
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212 type: string? |
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213 doc: | |
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214 The basename root such that `nameroot + nameext == basename`, and |
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215 `nameext` is empty or begins with a period and contains at most one |
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216 period. For the purposess of path splitting leading periods on the |
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217 basename are ignored; a basename of `.cshrc` will have a nameroot of |
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218 `.cshrc`. |
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219 |
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220 The implementation must set this field automatically based on the value |
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221 of `basename` prior to evaluating parameter references or expressions. |
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222 - name: nameext |
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223 type: string? |
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224 doc: | |
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225 The basename extension such that `nameroot + nameext == basename`, and |
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226 `nameext` is empty or begins with a period and contains at most one |
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227 period. Leading periods on the basename are ignored; a basename of |
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228 `.cshrc` will have an empty `nameext`. |
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229 |
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230 The implementation must set this field automatically based on the value |
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231 of `basename` prior to evaluating parameter references or expressions. |
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232 - name: checksum |
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233 type: string? |
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234 doc: | |
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235 Optional hash code for validating file integrity. Currently must be in the form |
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236 "sha1$ + hexadecimal string" using the SHA-1 algorithm. |
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237 - name: size |
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238 type: long? |
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239 doc: Optional file size |
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240 - name: "secondaryFiles" |
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241 type: |
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242 - "null" |
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243 - type: array |
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244 items: [File, Directory] |
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245 jsonldPredicate: |
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246 _id: "cwl:secondaryFiles" |
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247 secondaryFilesDSL: true |
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248 doc: | |
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249 A list of additional files or directories that are associated with the |
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250 primary file and must be transferred alongside the primary file. |
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251 Examples include indexes of the primary file, or external references |
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252 which must be included when loading primary document. A file object |
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253 listed in `secondaryFiles` may itself include `secondaryFiles` for |
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254 which the same rules apply. |
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255 - name: format |
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256 type: string? |
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257 jsonldPredicate: |
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258 _id: cwl:format |
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259 _type: "@id" |
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260 identity: true |
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261 doc: | |
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262 The format of the file: this must be an IRI of a concept node that |
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263 represents the file format, preferrably defined within an ontology. |
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264 If no ontology is available, file formats may be tested by exact match. |
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265 |
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266 Reasoning about format compatability must be done by checking that an |
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267 input file format is the same, `owl:equivalentClass` or |
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268 `rdfs:subClassOf` the format required by the input parameter. |
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269 `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if |
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270 `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer |
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271 `<C> owl:subclassOf <A>`. |
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272 |
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273 File format ontologies may be provided in the "$schema" metadata at the |
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274 root of the document. If no ontologies are specified in `$schema`, the |
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275 runtime may perform exact file format matches. |
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276 - name: contents |
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277 type: string? |
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278 doc: | |
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279 File contents literal. Maximum of 64 KiB. |
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280 |
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281 If neither `location` nor `path` is provided, `contents` must be |
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282 non-null. The implementation must assign a unique identifier for the |
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283 `location` field. When the file is staged as input to CommandLineTool, |
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284 the value of `contents` must be written to a file. |
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285 |
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286 If `loadContents` of `inputBinding` or `outputBinding` is true and |
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287 `location` is valid, the implementation must read up to the first 64 |
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288 KiB of text from the file and place it in the "contents" field. |
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289 |
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290 |
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291 - name: Directory |
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292 type: record |
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293 docAfter: "#File" |
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294 doc: | |
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295 Represents a directory to present to a command line tool. |
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296 |
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297 Directories are represented as objects with `class` of `Directory`. Directory objects have |
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298 a number of properties that provide metadata about the directory. |
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299 |
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300 The `location` property of a Directory is a URI that uniquely identifies |
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301 the directory. Implementations must support the file:// URI scheme and may |
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302 support other schemes such as http://. Alternately to `location`, |
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303 implementations must also accept the `path` property on Directory, which |
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304 must be a filesystem path available on the same host as the CWL runner (for |
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305 inputs) or the runtime environment of a command line tool execution (for |
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306 command line tool outputs). |
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307 |
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308 A Directory object may have a `listing` field. This is a list of File and |
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309 Directory objects that are contained in the Directory. For each entry in |
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310 `listing`, the `basename` property defines the name of the File or |
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311 Subdirectory when staged to disk. If `listing` is not provided, the |
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312 implementation must have some way of fetching the Directory listing at |
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313 runtime based on the `location` field. |
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314 |
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315 If a Directory does not have `location`, it is a Directory literal. A |
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316 Directory literal must provide `listing`. Directory literals must be |
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317 created on disk at runtime as needed. |
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318 |
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319 The resources in a Directory literal do not need to have any implied |
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320 relationship in their `location`. For example, a Directory listing may |
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321 contain two files located on different hosts. It is the responsibility of |
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322 the runtime to ensure that those files are staged to disk appropriately. |
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323 Secondary files associated with files in `listing` must also be staged to |
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324 the same Directory. |
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325 |
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326 When executing a CommandLineTool, Directories must be recursively staged |
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327 first and have local values of `path` assigend. |
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328 |
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329 Directory objects in CommandLineTool output must provide either a |
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330 `location` URI or a `path` property in the context of the tool execution |
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331 runtime (local to the compute node, or within the executing container). |
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332 |
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333 An ExpressionTool may forward file references from input to output by using |
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334 the same value for `location`. |
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335 |
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336 Name conflicts (the same `basename` appearing multiple times in `listing` |
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337 or in any entry in `secondaryFiles` in the listing) is a fatal error. |
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338 |
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339 fields: |
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340 - name: class |
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341 type: |
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342 type: enum |
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343 name: Directory_class |
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344 symbols: |
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345 - cwl:Directory |
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346 jsonldPredicate: |
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347 _id: "@type" |
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348 _type: "@vocab" |
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349 doc: Must be `Directory` to indicate this object describes a Directory. |
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350 - name: location |
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351 type: string? |
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352 doc: | |
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353 An IRI that identifies the directory resource. This may be a relative |
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354 reference, in which case it must be resolved using the base IRI of the |
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355 document. The location may refer to a local or remote resource. If |
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356 the `listing` field is not set, the implementation must use the |
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357 location IRI to retrieve directory listing. If an implementation is |
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358 unable to retrieve the directory listing stored at a remote resource (due to |
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359 unsupported protocol, access denied, or other issue) it must signal an |
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360 error. |
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361 |
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362 If the `location` field is not provided, the `listing` field must be |
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363 provided. The implementation must assign a unique identifier for |
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364 the `location` field. |
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365 |
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366 If the `path` field is provided but the `location` field is not, an |
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367 implementation may assign the value of the `path` field to `location`, |
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368 then follow the rules above. |
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369 jsonldPredicate: |
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370 _id: "@id" |
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371 _type: "@id" |
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372 - name: path |
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373 type: string? |
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374 doc: | |
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375 The local path where the Directory is made available prior to executing a |
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376 CommandLineTool. This must be set by the implementation. This field |
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377 must not be used in any other context. The command line tool being |
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378 executed must be able to to access the directory at `path` using the POSIX |
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379 `opendir(2)` syscall. |
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380 |
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381 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02) |
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382 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`, |
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383 `<space>`, `<tab>`, and `<newline>`) or characters |
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384 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml) |
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385 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452) |
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386 then implementations may terminate the process with a |
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387 `permanentFailure`. |
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388 jsonldPredicate: |
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389 _id: "cwl:path" |
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390 _type: "@id" |
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391 - name: basename |
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392 type: string? |
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393 doc: | |
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394 The base name of the directory, that is, the name of the file without any |
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395 leading directory path. The base name must not contain a slash `/`. |
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396 |
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397 If not provided, the implementation must set this field based on the |
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398 `location` field by taking the final path component after parsing |
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399 `location` as an IRI. If `basename` is provided, it is not required to |
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400 match the value from `location`. |
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401 |
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402 When this file is made available to a CommandLineTool, it must be named |
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403 with `basename`, i.e. the final component of the `path` field must match |
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404 `basename`. |
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405 jsonldPredicate: "cwl:basename" |
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406 - name: listing |
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407 type: |
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408 - "null" |
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409 - type: array |
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410 items: [File, Directory] |
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411 doc: | |
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412 List of files or subdirectories contained in this directory. The name |
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413 of each file or subdirectory is determined by the `basename` field of |
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414 each `File` or `Directory` object. It is an error if a `File` shares a |
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415 `basename` with any other entry in `listing`. If two or more |
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416 `Directory` object share the same `basename`, this must be treated as |
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417 equivalent to a single subdirectory with the listings recursively |
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418 merged. |
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419 jsonldPredicate: |
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420 _id: "cwl:listing" |
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421 |
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422 - name: Labeled |
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423 type: record |
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424 abstract: true |
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425 fields: |
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426 - name: label |
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427 type: |
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428 - "null" |
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429 - string |
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430 jsonldPredicate: "rdfs:label" |
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431 doc: "A short, human-readable label of this object." |
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432 |
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433 |
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434 - name: Identified |
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435 type: record |
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436 abstract: true |
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437 fields: |
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438 - name: id |
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439 type: string? |
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440 jsonldPredicate: "@id" |
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441 doc: "The unique identifier for this object." |
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442 |
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443 |
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444 - name: LoadListingEnum |
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445 type: enum |
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446 symbols: [no_listing, shallow_listing, deep_listing] |
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447 doc: |
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448 - | |
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449 Specify the desired behavior for loading the `listing` field of |
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450 a Directory object for use by expressions. |
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451 - "no_listing: Do not load the directory listing." |
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452 - "shallow_listing: Only load the top level listing, do not recurse into subdirectories." |
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453 - "deep_listing: Load the directory listing and recursively load all subdirectories as well." |
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454 |
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455 |
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456 - name: LoadContents |
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457 type: record |
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458 abstract: true |
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459 fields: |
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460 - name: loadContents |
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461 type: boolean? |
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462 jsonldPredicate: "cwl:loadContents" |
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463 doc: | |
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464 Only valid when `type: File` or is an array of `items: File`. |
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465 |
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466 Read up to the first 64 KiB of text from the file and place it in the |
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467 "contents" field of the file object for use by expressions. |
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468 - name: loadListing |
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469 type: LoadListingEnum? |
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470 jsonldPredicate: "cwl:loadListing" |
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471 doc: | |
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472 Only valid when `type: Directory` or is an array of `items: Directory`. |
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473 |
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474 Specify the desired behavior for loading the `listing` field of |
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475 a Directory object for use by expressions. |
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476 |
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477 The order of precedence for loadListing is: |
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478 |
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479 1. `loadListing` on an individual parameter |
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480 2. Inherited from `LoadListingRequirement` |
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481 3. By default: `no_listing` |
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482 |
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483 - name: FieldBase |
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484 type: record |
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485 extends: Labeled |
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486 abstract: true |
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487 fields: |
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488 secondaryFiles: |
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489 type: |
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490 - "null" |
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491 - SecondaryFileSchema |
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492 - type: array |
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493 items: SecondaryFileSchema |
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494 jsonldPredicate: |
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495 _id: "cwl:secondaryFiles" |
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496 secondaryFilesDSL: true |
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497 doc: | |
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498 Only valid when `type: File` or is an array of `items: File`. |
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499 |
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500 Provides a pattern or expression specifying files or |
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501 directories that should be included alongside the primary |
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502 file. Secondary files may be required or optional. When not |
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503 explicitly specified, secondary files specified for `inputs` |
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504 are required and `outputs` are optional. An implementation |
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505 must include matching Files and Directories in the |
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506 `secondaryFiles` property of the primary file. These Files |
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507 and Directories must be transferred and staged alongside the |
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508 primary file. An implementation may fail workflow execution |
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509 if a required secondary file does not exist. |
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510 |
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511 If the value is an expression, the value of `self` in the expression |
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512 must be the primary input or output File object to which this binding |
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513 applies. The `basename`, `nameroot` and `nameext` fields must be |
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514 present in `self`. For `CommandLineTool` outputs the `path` field must |
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515 also be present. The expression must return a filename string relative |
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516 to the path to the primary File, a File or Directory object with either |
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517 `path` or `location` and `basename` fields set, or an array consisting |
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518 of strings or File or Directory objects. It is legal to reference an |
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519 unchanged File or Directory object taken from input as a secondaryFile. |
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520 The expression may return "null" in which case there is no secondaryFile |
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521 from that expression. |
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522 |
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523 To work on non-filename-preserving storage systems, portable tool |
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524 descriptions should avoid constructing new values from `location`, but |
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525 should construct relative references using `basename` or `nameroot` |
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526 instead. |
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527 |
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528 If a value in `secondaryFiles` is a string that is not an expression, |
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529 it specifies that the following pattern should be applied to the path |
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530 of the primary file to yield a filename relative to the primary File: |
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531 |
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532 1. If string ends with `?` character, remove the last `?` and mark |
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533 the resulting secondary file as optional. |
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534 2. If string begins with one or more caret `^` characters, for each |
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535 caret, remove the last file extension from the path (the last |
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536 period `.` and all following characters). If there are no file |
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537 extensions, the path is unchanged. |
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538 3. Append the remainder of the string to the end of the file path. |
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539 |
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540 streamable: |
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541 type: boolean? |
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542 doc: | |
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543 Only valid when `type: File` or is an array of `items: File`. |
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544 |
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545 A value of `true` indicates that the file is read or written |
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546 sequentially without seeking. An implementation may use this flag to |
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547 indicate whether it is valid to stream file contents using a named |
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548 pipe. Default: `false`. |
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549 |
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550 |
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551 - name: InputFormat |
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552 type: record |
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553 abstract: true |
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554 fields: |
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555 format: |
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|
556 type: |
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changeset
|
557 - "null" |
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|
558 - string |
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|
559 - type: array |
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|
560 items: string |
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|
561 - Expression |
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562 jsonldPredicate: |
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563 _id: cwl:format |
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564 _type: "@id" |
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565 identity: true |
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|
566 doc: | |
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|
567 Only valid when `type: File` or is an array of `items: File`. |
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|
568 |
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569 This must be one or more IRIs of concept nodes |
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|
570 that represents file formats which are allowed as input to this |
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571 parameter, preferrably defined within an ontology. If no ontology is |
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572 available, file formats may be tested by exact match. |
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|
573 |
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|
574 |
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|
575 - name: OutputFormat |
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576 type: record |
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|
577 abstract: true |
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|
578 fields: |
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|
579 format: |
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|
580 type: |
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|
581 - "null" |
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|
582 - string |
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583 - Expression |
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584 jsonldPredicate: |
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585 _id: cwl:format |
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586 _type: "@id" |
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587 identity: true |
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588 doc: | |
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589 Only valid when `type: File` or is an array of `items: File`. |
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590 |
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591 This is the file format that will be assigned to the output |
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592 File object. |
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593 |
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|
594 |
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595 - name: Parameter |
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596 type: record |
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597 extends: [FieldBase, sld:Documented, Identified] |
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598 abstract: true |
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599 doc: | |
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600 Define an input or output parameter to a process. |
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601 |
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|
602 |
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603 - type: enum |
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604 name: Expression |
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605 doc: | |
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606 'Expression' is not a real type. It indicates that a field must allow |
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607 runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement) |
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608 is declared and supported by the platform, the field must also allow |
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609 Javascript expressions. |
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610 symbols: |
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|
611 - cwl:ExpressionPlaceholder |
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612 |
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|
613 |
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614 - name: InputBinding |
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615 type: record |
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616 fields: |
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617 - name: loadContents |
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618 type: |
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619 - "null" |
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620 - boolean |
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621 jsonldPredicate: "cwl:loadContents" |
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622 doc: | |
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623 Use of `loadContents` in `InputBinding` is deprecated. |
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624 Preserved for v1.0 backwards compatability. Will be removed in |
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625 CWL v2.0. Use `InputParameter.loadContents` instead. |
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|
626 |
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|
627 Only valid when `type: File` or is an array of `items: File`. |
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|
628 |
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629 Read up to the first 64 KiB of text from the file and place it in the |
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630 "contents" field of the file object for use by expressions. |
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|
631 |
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|
632 |
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|
633 - name: IOSchema |
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|
634 extends: [Labeled, sld:Documented] |
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|
635 type: record |
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|
636 abstract: true |
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|
637 fields: |
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|
638 - name: name |
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|
639 type: string? |
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|
640 jsonldPredicate: "@id" |
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641 doc: "The identifier for this type" |
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642 |
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643 - name: InputSchema |
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644 extends: [IOSchema] |
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645 type: record |
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|
646 abstract: true |
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|
647 |
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648 - name: OutputSchema |
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649 extends: [IOSchema] |
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650 type: record |
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|
651 abstract: true |
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|
652 |
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|
653 |
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654 - name: InputRecordField |
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655 type: record |
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656 extends: [sld:RecordField, FieldBase, InputFormat, LoadContents] |
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657 specialize: |
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658 - specializeFrom: "sld:RecordSchema" |
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659 specializeTo: InputRecordSchema |
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660 - specializeFrom: "sld:EnumSchema" |
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661 specializeTo: InputEnumSchema |
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662 - specializeFrom: "sld:ArraySchema" |
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663 specializeTo: InputArraySchema |
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664 - specializeFrom: "sld:PrimitiveType" |
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665 specializeTo: CWLType |
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|
666 |
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|
667 |
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668 - name: InputRecordSchema |
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669 type: record |
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670 extends: ["sld:RecordSchema", InputSchema] |
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671 specialize: |
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|
672 - specializeFrom: "sld:RecordField" |
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673 specializeTo: InputRecordField |
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|
674 |
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|
675 |
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|
676 - name: InputEnumSchema |
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677 type: record |
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|
678 extends: ["sld:EnumSchema", InputSchema] |
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|
679 |
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|
680 |
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|
681 - name: InputArraySchema |
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|
682 type: record |
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|
683 extends: ["sld:ArraySchema", InputSchema] |
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|
684 specialize: |
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|
685 - specializeFrom: "sld:RecordSchema" |
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|
686 specializeTo: InputRecordSchema |
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|
687 - specializeFrom: "sld:EnumSchema" |
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|
688 specializeTo: InputEnumSchema |
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|
689 - specializeFrom: "sld:ArraySchema" |
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|
690 specializeTo: InputArraySchema |
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|
691 - specializeFrom: "sld:PrimitiveType" |
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|
692 specializeTo: CWLType |
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|
693 |
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|
694 |
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|
695 - name: OutputRecordField |
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|
696 type: record |
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|
697 extends: [sld:RecordField, FieldBase, OutputFormat] |
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|
698 specialize: |
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|
699 - specializeFrom: "sld:RecordSchema" |
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|
700 specializeTo: OutputRecordSchema |
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|
701 - specializeFrom: "sld:EnumSchema" |
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702 specializeTo: OutputEnumSchema |
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703 - specializeFrom: "sld:ArraySchema" |
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704 specializeTo: OutputArraySchema |
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705 - specializeFrom: "sld:PrimitiveType" |
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706 specializeTo: CWLType |
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|
707 |
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|
708 |
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|
709 - name: OutputRecordSchema |
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|
710 type: record |
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|
711 extends: ["sld:RecordSchema", "#OutputSchema"] |
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|
712 docParent: "#OutputParameter" |
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|
713 specialize: |
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|
714 - specializeFrom: "sld:RecordField" |
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|
715 specializeTo: OutputRecordField |
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|
716 |
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|
717 |
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|
718 - name: OutputEnumSchema |
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|
719 type: record |
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|
720 extends: ["sld:EnumSchema", OutputSchema] |
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|
721 docParent: "#OutputParameter" |
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|
722 |
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|
723 |
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|
724 - name: OutputArraySchema |
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|
725 type: record |
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|
726 extends: ["sld:ArraySchema", OutputSchema] |
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|
727 docParent: "#OutputParameter" |
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|
728 specialize: |
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|
729 - specializeFrom: "sld:RecordSchema" |
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|
730 specializeTo: OutputRecordSchema |
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|
731 - specializeFrom: "sld:EnumSchema" |
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|
732 specializeTo: OutputEnumSchema |
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|
733 - specializeFrom: "sld:ArraySchema" |
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|
734 specializeTo: OutputArraySchema |
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|
735 - specializeFrom: "sld:PrimitiveType" |
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|
736 specializeTo: CWLType |
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|
737 |
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|
738 |
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739 - name: InputParameter |
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|
740 type: record |
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|
741 abstract: true |
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|
742 extends: [Parameter, InputFormat, LoadContents] |
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|
743 fields: |
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|
744 - name: default |
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|
745 type: Any? |
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|
746 jsonldPredicate: |
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|
747 _id: sld:default |
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|
748 noLinkCheck: true |
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|
749 doc: | |
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|
750 The default value to use for this parameter if the parameter is missing |
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|
751 from the input object, or if the value of the parameter in the input |
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|
752 object is `null`. Default values are applied before evaluating expressions |
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|
753 (e.g. dependent `valueFrom` fields). |
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|
754 |
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|
755 |
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|
756 - name: OutputParameter |
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|
757 type: record |
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|
758 extends: [Parameter, OutputFormat] |
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|
759 abstract: true |
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|
760 |
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|
761 |
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|
762 - type: record |
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|
763 name: ProcessRequirement |
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764 abstract: true |
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|
765 doc: | |
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766 A process requirement declares a prerequisite that may or must be fulfilled |
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767 before executing a process. See [`Process.hints`](#process) and |
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|
768 [`Process.requirements`](#process). |
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|
769 |
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|
770 Process requirements are the primary mechanism for specifying extensions to |
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|
771 the CWL core specification. |
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parents:
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|
772 |
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|
773 |
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|
774 - type: record |
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|
775 name: Process |
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|
776 extends: [Identified, Labeled, sld:Documented] |
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777 abstract: true |
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|
778 doc: | |
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|
779 |
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|
780 The base executable type in CWL is the `Process` object defined by the |
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|
781 document. Note that the `Process` object is abstract and cannot be |
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|
782 directly executed. |
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|
783 |
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|
784 fields: |
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|
785 - name: inputs |
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|
786 type: |
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|
787 type: array |
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788 items: InputParameter |
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789 jsonldPredicate: |
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790 _id: "cwl:inputs" |
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791 mapSubject: id |
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792 mapPredicate: type |
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793 doc: | |
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794 Defines the input parameters of the process. The process is ready to |
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795 run when all required input parameters are associated with concrete |
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796 values. Input parameters include a schema for each parameter which is |
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797 used to validate the input object. It may also be used to build a user |
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798 interface for constructing the input object. |
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799 |
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800 When accepting an input object, all input parameters must have a value. |
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801 If an input parameter is missing from the input object, it must be |
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802 assigned a value of `null` (or the value of `default` for that |
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803 parameter, if provided) for the purposes of validation and evaluation |
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804 of expressions. |
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805 |
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806 - name: outputs |
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807 type: |
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808 type: array |
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809 items: OutputParameter |
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810 jsonldPredicate: |
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811 _id: "cwl:outputs" |
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812 mapSubject: id |
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813 mapPredicate: type |
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814 doc: | |
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815 Defines the parameters representing the output of the process. May be |
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816 used to generate and/or validate the output object. |
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817 - name: requirements |
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818 type: ProcessRequirement[]? |
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819 jsonldPredicate: |
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820 _id: "cwl:requirements" |
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821 mapSubject: class |
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822 doc: | |
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823 Declares requirements that apply to either the runtime environment or the |
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824 workflow engine that must be met in order to execute this process. If |
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825 an implementation cannot satisfy all requirements, or a requirement is |
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826 listed which is not recognized by the implementation, it is a fatal |
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827 error and the implementation must not attempt to run the process, |
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828 unless overridden at user option. |
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829 - name: hints |
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830 type: Any[]? |
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831 doc: | |
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832 Declares hints applying to either the runtime environment or the |
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833 workflow engine that may be helpful in executing this process. It is |
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834 not an error if an implementation cannot satisfy all hints, however |
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835 the implementation may report a warning. |
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836 jsonldPredicate: |
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837 _id: cwl:hints |
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838 noLinkCheck: true |
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839 mapSubject: class |
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840 - name: cwlVersion |
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841 type: CWLVersion? |
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842 doc: | |
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843 CWL document version. Always required at the document root. Not |
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844 required for a Process embedded inside another Process. |
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845 jsonldPredicate: |
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846 "_id": "cwl:cwlVersion" |
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847 "_type": "@vocab" |
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848 - name: intent |
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849 type: string[]? |
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850 jsonldPredicate: |
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851 _type: "@id" |
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852 identity: true |
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853 doc: | |
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854 An identifier for the type of computational operation, of this Process. |
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855 Especially useful for "class: Operation", but can also be used for |
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856 CommandLineTool, Workflow, or ExpressionTool. |
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857 |
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858 If provided, then this must be an IRI of a concept node that |
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859 represents the type of operation, preferrably defined within an ontology. |
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860 |
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861 For example, in the domain of bioinformatics, one can use an IRI from |
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862 the EDAM Ontology's [Operation concept nodes](http://edamontology.org/operation_0004), |
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863 like [Alignment](http://edamontology.org/operation_2928), |
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864 or [Clustering](http://edamontology.org/operation_3432); or a more |
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865 specific Operation concept like |
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866 [Split read mapping](http://edamontology.org/operation_3199). |
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867 |
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868 - name: InlineJavascriptRequirement |
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869 type: record |
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870 extends: ProcessRequirement |
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871 doc: | |
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872 Indicates that the workflow platform must support inline Javascript expressions. |
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873 If this requirement is not present, the workflow platform must not perform expression |
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874 interpolatation. |
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875 fields: |
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876 - name: class |
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877 type: string |
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878 doc: "Always 'InlineJavascriptRequirement'" |
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879 jsonldPredicate: |
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880 "_id": "@type" |
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881 "_type": "@vocab" |
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882 - name: expressionLib |
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883 type: string[]? |
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884 doc: | |
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885 Additional code fragments that will also be inserted |
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886 before executing the expression code. Allows for function definitions that may |
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887 be called from CWL expressions. |
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888 |
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889 |
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890 - name: CommandInputSchema |
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891 type: record |
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892 abstract: true |
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893 |
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894 - name: SchemaDefRequirement |
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895 type: record |
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896 extends: ProcessRequirement |
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897 doc: | |
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898 This field consists of an array of type definitions which must be used when |
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899 interpreting the `inputs` and `outputs` fields. When a `type` field |
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900 contain a IRI, the implementation must check if the type is defined in |
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901 `schemaDefs` and use that definition. If the type is not found in |
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|
902 `schemaDefs`, it is an error. The entries in `schemaDefs` must be |
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|
903 processed in the order listed such that later schema definitions may refer |
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|
904 to earlier schema definitions. |
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|
905 fields: |
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|
906 - name: class |
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|
907 type: string |
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|
908 doc: "Always 'SchemaDefRequirement'" |
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909 jsonldPredicate: |
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910 "_id": "@type" |
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911 "_type": "@vocab" |
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912 - name: types |
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|
913 type: |
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914 type: array |
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915 items: CommandInputSchema |
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|
916 doc: The list of type definitions. |
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917 |
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918 - name: SecondaryFileSchema |
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|
919 type: record |
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|
920 fields: |
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921 - name: pattern |
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922 type: |
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923 - string |
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924 - Expression |
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|
925 doc: | |
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926 Provides a pattern or expression specifying files or directories that |
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927 should be included alongside the primary file. |
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928 |
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929 If the value is an expression, the value of `self` in the |
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930 expression must be the primary input or output File object to |
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|
931 which this binding applies. The `basename`, `nameroot` and |
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932 `nameext` fields must be present in `self`. For |
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933 `CommandLineTool` inputs the `location` field must also be |
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934 present. For `CommandLineTool` outputs the `path` field must |
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935 also be present. If secondary files were included on an input |
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936 File object as part of the Process invocation, they must also |
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937 be present in `secondaryFiles` on `self`. |
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938 |
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939 The expression must return either: a filename string relative |
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940 to the path to the primary File, a File or Directory object |
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941 (`class: File` or 'class: Directory`) with either `location` |
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942 (for inputs) or `path` (for outputs) and `basename` fields |
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943 set, or an array consisting of strings or File or Directory |
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944 objects as previously described. |
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945 |
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946 It is legal to use `location` from a File or Directory object |
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947 passed in as input, including `location` from secondary files |
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948 on `self`. If an expression returns a File object with the |
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949 same `location` but a different `basename` as a secondary file |
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950 that was passed in, the expression result takes precedence. |
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951 Setting the basename with an expression this way affects the |
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952 `path` where the secondary file will be staged to in the |
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953 CommandLineTool. |
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954 |
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955 The expression may return "null" in which case there is no |
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956 secondary file from that expression. |
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957 |
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958 To work on non-filename-preserving storage systems, portable |
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959 tool descriptions should treat `location` as an opaque |
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960 identifier and avoid constructing new values from `location`, |
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961 but should construct relative references using `basename` or |
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962 `nameroot` instead, or propagate `location` from defined inputs. |
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963 |
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964 If a value in `secondaryFiles` is a string that is not an expression, |
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965 it specifies that the following pattern should be applied to the path |
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966 of the primary file to yield a filename relative to the primary File: |
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967 |
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968 1. If string ends with `?` character, remove the last `?` and mark |
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969 the resulting secondary file as optional. |
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970 2. If string begins with one or more caret `^` characters, for each |
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971 caret, remove the last file extension from the path (the last |
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972 period `.` and all following characters). If there are no file |
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973 extensions, the path is unchanged. |
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974 3. Append the remainder of the string to the end of the file path. |
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975 - name: required |
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976 type: ["null", boolean, Expression] |
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977 doc: | |
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978 An implementation must not fail workflow execution if `required` is |
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979 set to `false` and the expected secondary file does not exist. |
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980 Default value for `required` field is `true` for secondary files on |
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981 input and `false` for secondary files on output. |
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982 doc: | |
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983 Secondary files are specified using the following micro-DSL for secondary files: |
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984 |
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985 * If the value is a string, it is transformed to an object with two fields |
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986 `pattern` and `required` |
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987 * By default, the value of `required` is `null` |
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988 (this indicates default behavior, which may be based on the context) |
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989 * If the value ends with a question mark `?` the question mark is |
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990 stripped off and the value of the field `required` is set to `False` |
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991 * The remaining value is assigned to the field `pattern` |
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992 |
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993 For implementation details and examples, please see |
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994 [this section](SchemaSalad.html#Domain_Specific_Language_for_secondary_files) |
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995 in the Schema Salad specification. |
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996 |
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997 - name: LoadListingRequirement |
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998 type: record |
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999 extends: ProcessRequirement |
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1000 doc: | |
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1001 Specify the desired behavior for loading the `listing` field of |
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1002 a Directory object for use by expressions. |
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1003 fields: |
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1004 class: |
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1005 type: string |
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1006 doc: "Always 'LoadListingRequirement'" |
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1007 jsonldPredicate: |
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1008 "_id": "@type" |
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1009 "_type": "@vocab" |
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1010 loadListing: |
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1011 type: LoadListingEnum? |
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1012 jsonldPredicate: "cwl:loadListing" |