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743 lines
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743 lines
25 KiB
$base: "https://w3id.org/cwl/cwl#"
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$namespaces:
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cwl: "https://w3id.org/cwl/cwl#"
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sld: "https://w3id.org/cwl/salad#"
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$graph:
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- name: "Common Workflow Language, v1.0"
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type: documentation
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doc: {$include: concepts.md}
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- $import: "metaschema_base.yml"
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- name: BaseTypesDoc
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type: documentation
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doc: |
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## Base types
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docChild:
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- "#CWLType"
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- "#Process"
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- type: enum
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name: CWLVersion
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doc: "Version symbols for published CWL document versions."
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symbols:
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- cwl:draft-2
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- cwl:draft-3.dev1
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- cwl:draft-3.dev2
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- cwl:draft-3.dev3
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- cwl:draft-3.dev4
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- cwl:draft-3.dev5
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- cwl:draft-3
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- cwl:draft-4.dev1
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- cwl:draft-4.dev2
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- cwl:draft-4.dev3
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- cwl:v1.0.dev4
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- cwl:v1.0
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- name: CWLType
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type: enum
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extends: "sld:PrimitiveType"
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symbols:
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- cwl:File
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- cwl:Directory
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doc:
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- "Extends primitive types with the concept of a file and directory as a builtin type."
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- "File: A File object"
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- "Directory: A Directory object"
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- name: File
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type: record
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docParent: "#CWLType"
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doc: |
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Represents a file (or group of files if `secondaryFiles` is specified) that
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must be accessible by tools using standard POSIX file system call API such as
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open(2) and read(2).
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fields:
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- name: class
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type:
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type: enum
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name: File_class
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symbols:
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- cwl:File
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jsonldPredicate:
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_id: "@type"
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_type: "@vocab"
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doc: Must be `File` to indicate this object describes a file.
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- name: location
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type: string?
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doc: |
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An IRI that identifies the file resource. This may be a relative
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reference, in which case it must be resolved using the base IRI of the
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document. The location may refer to a local or remote resource; the
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implementation must use the IRI to retrieve file content. If an
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implementation is unable to retrieve the file content stored at a
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remote resource (due to unsupported protocol, access denied, or other
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issue) it must signal an error.
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If the `location` field is not provided, the `contents` field must be
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provided. The implementation must assign a unique identifier for
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the `location` field.
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If the `path` field is provided but the `location` field is not, an
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implementation may assign the value of the `path` field to `location`,
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then follow the rules above.
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jsonldPredicate:
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_id: "@id"
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_type: "@id"
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- name: path
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type: string?
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doc: |
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The local host path where the File is available when a CommandLineTool is
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executed. This field must be set by the implementation. The final
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path component must match the value of `basename`. This field
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must not be used in any other context. The command line tool being
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executed must be able to to access the file at `path` using the POSIX
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`open(2)` syscall.
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As a special case, if the `path` field is provided but the `location`
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field is not, an implementation may assign the value of the `path`
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field to `location`, and remove the `path` field.
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If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
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(`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
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`<space>`, `<tab>`, and `<newline>`) or characters
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[not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
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for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
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then implementations may terminate the process with a
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`permanentFailure`.
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jsonldPredicate:
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"_id": "cwl:path"
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"_type": "@id"
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- name: basename
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type: string?
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doc: |
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The base name of the file, that is, the name of the file without any
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leading directory path. The base name must not contain a slash `/`.
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If not provided, the implementation must set this field based on the
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`location` field by taking the final path component after parsing
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`location` as an IRI. If `basename` is provided, it is not required to
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match the value from `location`.
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When this file is made available to a CommandLineTool, it must be named
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with `basename`, i.e. the final component of the `path` field must match
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`basename`.
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jsonldPredicate: "cwl:basename"
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- name: dirname
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type: string?
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doc: |
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The name of the directory containing file, that is, the path leading up
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to the final slash in the path such that `dirname + '/' + basename ==
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path`.
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The implementation must set this field based on the value of `path`
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prior to evaluating parameter references or expressions in a
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CommandLineTool document. This field must not be used in any other
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context.
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- name: nameroot
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type: string?
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doc: |
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The basename root such that `nameroot + nameext == basename`, and
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`nameext` is empty or begins with a period and contains at most one
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period. For the purposess of path splitting leading periods on the
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basename are ignored; a basename of `.cshrc` will have a nameroot of
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`.cshrc`.
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The implementation must set this field automatically based on the value
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of `basename` prior to evaluating parameter references or expressions.
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- name: nameext
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type: string?
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doc: |
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The basename extension such that `nameroot + nameext == basename`, and
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`nameext` is empty or begins with a period and contains at most one
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period. Leading periods on the basename are ignored; a basename of
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`.cshrc` will have an empty `nameext`.
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The implementation must set this field automatically based on the value
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of `basename` prior to evaluating parameter references or expressions.
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- name: checksum
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type: string?
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doc: |
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Optional hash code for validating file integrity. Currently must be in the form
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"sha1$ + hexadecimal string" using the SHA-1 algorithm.
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- name: size
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type: long?
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doc: Optional file size
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- name: "secondaryFiles"
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type:
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- "null"
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- type: array
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items: [File, Directory]
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jsonldPredicate: "cwl:secondaryFiles"
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doc: |
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A list of additional files that are associated with the primary file
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and must be transferred alongside the primary file. Examples include
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indexes of the primary file, or external references which must be
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included when loading primary document. A file object listed in
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`secondaryFiles` may itself include `secondaryFiles` for which the same
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rules apply.
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- name: format
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type: string?
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jsonldPredicate:
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_id: cwl:format
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_type: "@id"
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identity: true
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doc: |
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The format of the file: this must be an IRI of a concept node that
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represents the file format, preferably defined within an ontology.
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If no ontology is available, file formats may be tested by exact match.
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Reasoning about format compatibility must be done by checking that an
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input file format is the same, `owl:equivalentClass` or
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`rdfs:subClassOf` the format required by the input parameter.
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`owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if
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`<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer
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`<C> owl:subclassOf <A>`.
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File format ontologies may be provided in the "$schema" metadata at the
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root of the document. If no ontologies are specified in `$schema`, the
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runtime may perform exact file format matches.
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- name: contents
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type: string?
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doc: |
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File contents literal. Maximum of 64 KiB.
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If neither `location` nor `path` is provided, `contents` must be
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non-null. The implementation must assign a unique identifier for the
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`location` field. When the file is staged as input to CommandLineTool,
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the value of `contents` must be written to a file.
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If `loadContents` of `inputBinding` or `outputBinding` is true and
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`location` is valid, the implementation must read up to the first 64
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KiB of text from the file and place it in the "contents" field.
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- name: Directory
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type: record
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docAfter: "#File"
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doc: |
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Represents a directory to present to a command line tool.
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fields:
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- name: class
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type:
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type: enum
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name: Directory_class
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symbols:
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- cwl:Directory
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jsonldPredicate:
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_id: "@type"
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_type: "@vocab"
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|
doc: Must be `Directory` to indicate this object describes a Directory.
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- name: location
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type: string?
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|
doc: |
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|
An IRI that identifies the directory resource. This may be a relative
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|
reference, in which case it must be resolved using the base IRI of the
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|
document. The location may refer to a local or remote resource. If
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|
the `listing` field is not set, the implementation must use the
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|
location IRI to retrieve directory listing. If an implementation is
|
|
unable to retrieve the directory listing stored at a remote resource (due to
|
|
unsupported protocol, access denied, or other issue) it must signal an
|
|
error.
|
|
|
|
If the `location` field is not provided, the `listing` field must be
|
|
provided. The implementation must assign a unique identifier for
|
|
the `location` field.
|
|
|
|
If the `path` field is provided but the `location` field is not, an
|
|
implementation may assign the value of the `path` field to `location`,
|
|
then follow the rules above.
|
|
jsonldPredicate:
|
|
_id: "@id"
|
|
_type: "@id"
|
|
- name: path
|
|
type: string?
|
|
doc: |
|
|
The local path where the Directory is made available prior to executing a
|
|
CommandLineTool. This must be set by the implementation. This field
|
|
must not be used in any other context. The command line tool being
|
|
executed must be able to to access the directory at `path` using the POSIX
|
|
`opendir(2)` syscall.
|
|
|
|
If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
|
|
(`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
|
|
`<space>`, `<tab>`, and `<newline>`) or characters
|
|
[not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
|
|
for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
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then implementations may terminate the process with a
|
|
`permanentFailure`.
|
|
jsonldPredicate:
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|
_id: "cwl:path"
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|
_type: "@id"
|
|
- name: basename
|
|
type: string?
|
|
doc: |
|
|
The base name of the directory, that is, the name of the file without any
|
|
leading directory path. The base name must not contain a slash `/`.
|
|
|
|
If not provided, the implementation must set this field based on the
|
|
`location` field by taking the final path component after parsing
|
|
`location` as an IRI. If `basename` is provided, it is not required to
|
|
match the value from `location`.
|
|
|
|
When this file is made available to a CommandLineTool, it must be named
|
|
with `basename`, i.e. the final component of the `path` field must match
|
|
`basename`.
|
|
jsonldPredicate: "cwl:basename"
|
|
- name: listing
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|
type:
|
|
- "null"
|
|
- type: array
|
|
items: [File, Directory]
|
|
doc: |
|
|
List of files or subdirectories contained in this directory. The name
|
|
of each file or subdirectory is determined by the `basename` field of
|
|
each `File` or `Directory` object. It is an error if a `File` shares a
|
|
`basename` with any other entry in `listing`. If two or more
|
|
`Directory` object share the same `basename`, this must be treated as
|
|
equivalent to a single subdirectory with the listings recursively
|
|
merged.
|
|
jsonldPredicate:
|
|
_id: "cwl:listing"
|
|
|
|
- name: SchemaBase
|
|
type: record
|
|
abstract: true
|
|
fields:
|
|
- name: label
|
|
type:
|
|
- "null"
|
|
- string
|
|
jsonldPredicate: "rdfs:label"
|
|
doc: "A short, human-readable label of this object."
|
|
|
|
|
|
- name: Parameter
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|
type: record
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|
extends: SchemaBase
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|
abstract: true
|
|
doc: |
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Define an input or output parameter to a process.
|
|
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fields:
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|
- name: secondaryFiles
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type:
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|
- "null"
|
|
- string
|
|
- Expression
|
|
- type: array
|
|
items: [string, Expression]
|
|
jsonldPredicate: "cwl:secondaryFiles"
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|
doc: |
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|
Only valid when `type: File` or is an array of `items: File`.
|
|
|
|
Describes files that must be included alongside the primary file(s).
|
|
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If the value is an expression, the value of `self` in the expression
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|
must be the primary input or output File to which this binding applies.
|
|
|
|
If the value is a string, it specifies that the following pattern
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|
should be applied to the primary file:
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|
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|
1. If string begins with one or more caret `^` characters, for each
|
|
caret, remove the last file extension from the path (the last
|
|
period `.` and all following characters). If there are no file
|
|
extensions, the path is unchanged.
|
|
2. Append the remainder of the string to the end of the file path.
|
|
|
|
- name: format
|
|
type:
|
|
- "null"
|
|
- string
|
|
- type: array
|
|
items: string
|
|
- Expression
|
|
jsonldPredicate:
|
|
_id: cwl:format
|
|
_type: "@id"
|
|
identity: true
|
|
doc: |
|
|
Only valid when `type: File` or is an array of `items: File`.
|
|
|
|
For input parameters, this must be one or more IRIs of concept nodes
|
|
that represents file formats which are allowed as input to this
|
|
parameter, preferably defined within an ontology. If no ontology is
|
|
available, file formats may be tested by exact match.
|
|
|
|
For output parameters, this is the file format that will be assigned to
|
|
the output parameter.
|
|
|
|
- name: streamable
|
|
type: boolean?
|
|
doc: |
|
|
Only valid when `type: File` or is an array of `items: File`.
|
|
|
|
A value of `true` indicates that the file is read or written
|
|
sequentially without seeking. An implementation may use this flag to
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|
indicate whether it is valid to stream file contents using a named
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|
pipe. Default: `false`.
|
|
|
|
- name: doc
|
|
type:
|
|
- string?
|
|
- string[]?
|
|
doc: "A documentation string for this type, or an array of strings which should be concatenated."
|
|
jsonldPredicate: "rdfs:comment"
|
|
|
|
|
|
- type: enum
|
|
name: Expression
|
|
doc: |
|
|
'Expression' is not a real type. It indicates that a field must allow
|
|
runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement)
|
|
is declared and supported by the platform, the field must also allow
|
|
Javascript expressions.
|
|
symbols:
|
|
- cwl:ExpressionPlaceholder
|
|
|
|
|
|
- name: InputBinding
|
|
type: record
|
|
abstract: true
|
|
fields:
|
|
- name: loadContents
|
|
type:
|
|
- "null"
|
|
- boolean
|
|
jsonldPredicate: "cwl:loadContents"
|
|
doc: |
|
|
Only valid when `type: File` or is an array of `items: File`.
|
|
|
|
Read up to the first 64 KiB of text from the file and place it in the
|
|
"contents" field of the file object for use by expressions.
|
|
|
|
|
|
- name: OutputBinding
|
|
type: record
|
|
abstract: true
|
|
|
|
|
|
- name: InputSchema
|
|
extends: SchemaBase
|
|
type: record
|
|
abstract: true
|
|
|
|
|
|
- name: OutputSchema
|
|
extends: SchemaBase
|
|
type: record
|
|
abstract: true
|
|
|
|
|
|
- name: InputRecordField
|
|
type: record
|
|
extends: "sld:RecordField"
|
|
specialize:
|
|
- specializeFrom: "sld:RecordSchema"
|
|
specializeTo: InputRecordSchema
|
|
- specializeFrom: "sld:EnumSchema"
|
|
specializeTo: InputEnumSchema
|
|
- specializeFrom: "sld:ArraySchema"
|
|
specializeTo: InputArraySchema
|
|
- specializeFrom: "sld:PrimitiveType"
|
|
specializeTo: CWLType
|
|
fields:
|
|
- name: inputBinding
|
|
type: InputBinding?
|
|
jsonldPredicate: "cwl:inputBinding"
|
|
- name: label
|
|
type: string?
|
|
jsonldPredicate: "rdfs:label"
|
|
doc: "A short, human-readable label of this process object."
|
|
|
|
|
|
- name: InputRecordSchema
|
|
type: record
|
|
extends: ["sld:RecordSchema", InputSchema]
|
|
specialize:
|
|
- specializeFrom: "sld:RecordField"
|
|
specializeTo: InputRecordField
|
|
|
|
|
|
- name: InputEnumSchema
|
|
type: record
|
|
extends: ["sld:EnumSchema", InputSchema]
|
|
fields:
|
|
- name: inputBinding
|
|
type: InputBinding?
|
|
jsonldPredicate: "cwl:inputBinding"
|
|
|
|
|
|
- name: InputArraySchema
|
|
type: record
|
|
extends: ["sld:ArraySchema", InputSchema]
|
|
specialize:
|
|
- specializeFrom: "sld:RecordSchema"
|
|
specializeTo: InputRecordSchema
|
|
- specializeFrom: "sld:EnumSchema"
|
|
specializeTo: InputEnumSchema
|
|
- specializeFrom: "sld:ArraySchema"
|
|
specializeTo: InputArraySchema
|
|
- specializeFrom: "sld:PrimitiveType"
|
|
specializeTo: CWLType
|
|
fields:
|
|
- name: inputBinding
|
|
type: InputBinding?
|
|
jsonldPredicate: "cwl:inputBinding"
|
|
|
|
|
|
- name: OutputRecordField
|
|
type: record
|
|
extends: "sld:RecordField"
|
|
specialize:
|
|
- specializeFrom: "sld:RecordSchema"
|
|
specializeTo: OutputRecordSchema
|
|
- specializeFrom: "sld:EnumSchema"
|
|
specializeTo: OutputEnumSchema
|
|
- specializeFrom: "sld:ArraySchema"
|
|
specializeTo: OutputArraySchema
|
|
- specializeFrom: "sld:PrimitiveType"
|
|
specializeTo: CWLType
|
|
fields:
|
|
- name: outputBinding
|
|
type: OutputBinding?
|
|
jsonldPredicate: "cwl:outputBinding"
|
|
|
|
|
|
- name: OutputRecordSchema
|
|
type: record
|
|
extends: ["sld:RecordSchema", "#OutputSchema"]
|
|
docParent: "#OutputParameter"
|
|
specialize:
|
|
- specializeFrom: "sld:RecordField"
|
|
specializeTo: OutputRecordField
|
|
|
|
|
|
- name: OutputEnumSchema
|
|
type: record
|
|
extends: ["sld:EnumSchema", OutputSchema]
|
|
docParent: "#OutputParameter"
|
|
fields:
|
|
- name: outputBinding
|
|
type: OutputBinding?
|
|
jsonldPredicate: "cwl:outputBinding"
|
|
|
|
- name: OutputArraySchema
|
|
type: record
|
|
extends: ["sld:ArraySchema", OutputSchema]
|
|
docParent: "#OutputParameter"
|
|
specialize:
|
|
- specializeFrom: "sld:RecordSchema"
|
|
specializeTo: OutputRecordSchema
|
|
- specializeFrom: "sld:EnumSchema"
|
|
specializeTo: OutputEnumSchema
|
|
- specializeFrom: "sld:ArraySchema"
|
|
specializeTo: OutputArraySchema
|
|
- specializeFrom: "sld:PrimitiveType"
|
|
specializeTo: CWLType
|
|
fields:
|
|
- name: outputBinding
|
|
type: OutputBinding?
|
|
jsonldPredicate: "cwl:outputBinding"
|
|
|
|
|
|
- name: InputParameter
|
|
type: record
|
|
extends: Parameter
|
|
fields:
|
|
- name: id
|
|
type: string
|
|
jsonldPredicate: "@id"
|
|
doc: "The unique identifier for this parameter object."
|
|
|
|
- name: inputBinding
|
|
type: InputBinding?
|
|
jsonldPredicate: "cwl:inputBinding"
|
|
doc: |
|
|
Describes how to handle the inputs of a process and convert them
|
|
into a concrete form for execution, such as command line parameters.
|
|
|
|
- name: default
|
|
type: Any?
|
|
jsonldPredicate: "cwl:default"
|
|
doc: |
|
|
The default value for this parameter if not provided in the input
|
|
object.
|
|
|
|
- name: type
|
|
type:
|
|
- "null"
|
|
- CWLType
|
|
- InputRecordSchema
|
|
- InputEnumSchema
|
|
- InputArraySchema
|
|
- string
|
|
- type: array
|
|
items:
|
|
- CWLType
|
|
- InputRecordSchema
|
|
- InputEnumSchema
|
|
- InputArraySchema
|
|
- string
|
|
jsonldPredicate:
|
|
"_id": "sld:type"
|
|
"_type": "@vocab"
|
|
refScope: 2
|
|
typeDSL: True
|
|
doc: |
|
|
Specify valid types of data that may be assigned to this parameter.
|
|
|
|
- name: OutputParameter
|
|
type: record
|
|
extends: Parameter
|
|
fields:
|
|
- name: id
|
|
type: string
|
|
jsonldPredicate: "@id"
|
|
doc: "The unique identifier for this parameter object."
|
|
- name: outputBinding
|
|
type: OutputBinding?
|
|
jsonldPredicate: "cwl:outputBinding"
|
|
doc: |
|
|
Describes how to handle the outputs of a process.
|
|
|
|
|
|
- type: record
|
|
name: ProcessRequirement
|
|
abstract: true
|
|
doc: |
|
|
A process requirement declares a prerequisite that may or must be fulfilled
|
|
before executing a process. See [`Process.hints`](#process) and
|
|
[`Process.requirements`](#process).
|
|
|
|
Process requirements are the primary mechanism for specifying extensions to
|
|
the CWL core specification.
|
|
|
|
|
|
- type: record
|
|
name: Process
|
|
abstract: true
|
|
doc: |
|
|
|
|
The base executable type in CWL is the `Process` object defined by the
|
|
document. Note that the `Process` object is abstract and cannot be
|
|
directly executed.
|
|
|
|
fields:
|
|
- name: id
|
|
type: string?
|
|
jsonldPredicate: "@id"
|
|
doc: "The unique identifier for this process object."
|
|
- name: inputs
|
|
type:
|
|
type: array
|
|
items: InputParameter
|
|
jsonldPredicate:
|
|
_id: "cwl:inputs"
|
|
mapSubject: id
|
|
mapPredicate: type
|
|
doc: |
|
|
Defines the input parameters of the process. The process is ready to
|
|
run when all required input parameters are associated with concrete
|
|
values. Input parameters include a schema for each parameter which is
|
|
used to validate the input object. It may also be used to build a user
|
|
interface for constructing the input object.
|
|
- name: outputs
|
|
type:
|
|
type: array
|
|
items: OutputParameter
|
|
jsonldPredicate:
|
|
_id: "cwl:outputs"
|
|
mapSubject: id
|
|
mapPredicate: type
|
|
doc: |
|
|
Defines the parameters representing the output of the process. May be
|
|
used to generate and/or validate the output object.
|
|
- name: requirements
|
|
type: ProcessRequirement[]?
|
|
jsonldPredicate:
|
|
_id: "cwl:requirements"
|
|
mapSubject: class
|
|
doc: |
|
|
Declares requirements that apply to either the runtime environment or the
|
|
workflow engine that must be met in order to execute this process. If
|
|
an implementation cannot satisfy all requirements, or a requirement is
|
|
listed which is not recognized by the implementation, it is a fatal
|
|
error and the implementation must not attempt to run the process,
|
|
unless overridden at user option.
|
|
- name: hints
|
|
type: Any[]?
|
|
doc: |
|
|
Declares hints applying to either the runtime environment or the
|
|
workflow engine that may be helpful in executing this process. It is
|
|
not an error if an implementation cannot satisfy all hints, however
|
|
the implementation may report a warning.
|
|
jsonldPredicate:
|
|
_id: cwl:hints
|
|
noLinkCheck: true
|
|
mapSubject: class
|
|
- name: label
|
|
type: string?
|
|
jsonldPredicate: "rdfs:label"
|
|
doc: "A short, human-readable label of this process object."
|
|
- name: doc
|
|
type: string?
|
|
jsonldPredicate: "rdfs:comment"
|
|
doc: "A long, human-readable description of this process object."
|
|
- name: cwlVersion
|
|
type: CWLVersion?
|
|
doc: |
|
|
CWL document version. Always required at the document root. Not
|
|
required for a Process embedded inside another Process.
|
|
jsonldPredicate:
|
|
"_id": "cwl:cwlVersion"
|
|
"_type": "@vocab"
|
|
|
|
- name: InlineJavascriptRequirement
|
|
type: record
|
|
extends: ProcessRequirement
|
|
doc: |
|
|
Indicates that the workflow platform must support inline Javascript expressions.
|
|
If this requirement is not present, the workflow platform must not perform expression
|
|
interpolatation.
|
|
fields:
|
|
- name: class
|
|
type: string
|
|
doc: "Always 'InlineJavascriptRequirement'"
|
|
jsonldPredicate:
|
|
"_id": "@type"
|
|
"_type": "@vocab"
|
|
- name: expressionLib
|
|
type: string[]?
|
|
doc: |
|
|
Additional code fragments that will also be inserted
|
|
before executing the expression code. Allows for function definitions that may
|
|
be called from CWL expressions.
|
|
|
|
|
|
- name: SchemaDefRequirement
|
|
type: record
|
|
extends: ProcessRequirement
|
|
doc: |
|
|
This field consists of an array of type definitions which must be used when
|
|
interpreting the `inputs` and `outputs` fields. When a `type` field
|
|
contain a IRI, the implementation must check if the type is defined in
|
|
`schemaDefs` and use that definition. If the type is not found in
|
|
`schemaDefs`, it is an error. The entries in `schemaDefs` must be
|
|
processed in the order listed such that later schema definitions may refer
|
|
to earlier schema definitions.
|
|
fields:
|
|
- name: class
|
|
type: string
|
|
doc: "Always 'SchemaDefRequirement'"
|
|
jsonldPredicate:
|
|
"_id": "@type"
|
|
"_type": "@vocab"
|
|
- name: types
|
|
type:
|
|
type: array
|
|
items: InputSchema
|
|
doc: The list of type definitions.
|