guppy_basecaller: env/lib/python3.7/site-packages/cwltool/schemas/v1.0/Process.yml annotate

author	shellac
date	Sat, 02 May 2020 07:14:21 -0400
parents
children

rev	line source
0 26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1 $base: "https://w3id.org/cwl/cwl#"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	3 $namespaces:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	4 cwl: "https://w3id.org/cwl/cwl#"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	5 sld: "https://w3id.org/cwl/salad#"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	6 rdfs: "http://www.w3.org/2000/01/rdf-schema#"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	7
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	8 $graph:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	9
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	10 - name: "Common Workflow Language, v1.0"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	11 type: documentation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	12 doc: {$include: concepts.md}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	13
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	14 - $import: "salad/schema_salad/metaschema/metaschema_base.yml"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	15
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	16 - name: BaseTypesDoc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	17 type: documentation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	18 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	19 ## Base types
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	20 docChild:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	21 - "#CWLType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	22 - "#Process"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	23
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	24 - type: enum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	25 name: CWLVersion
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	26 doc: "Version symbols for published CWL document versions."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	27 symbols:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	28 - cwl:draft-2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	29 - cwl:draft-3.dev1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	30 - cwl:draft-3.dev2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	31 - cwl:draft-3.dev3
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	32 - cwl:draft-3.dev4
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	33 - cwl:draft-3.dev5
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	34 - cwl:draft-3
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	35 - cwl:draft-4.dev1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	36 - cwl:draft-4.dev2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	37 - cwl:draft-4.dev3
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	38 - cwl:v1.0.dev4
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	39 - cwl:v1.0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	40
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	41 - name: CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	42 type: enum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	43 extends: "sld:PrimitiveType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	44 symbols:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	45 - cwl:File
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	46 - cwl:Directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	47 doc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	48 - "Extends primitive types with the concept of a file and directory as a builtin type."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	49 - "File: A File object"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	50 - "Directory: A Directory object"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	51
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	52 - name: File
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	53 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	54 docParent: "#CWLType"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	55 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	56 Represents a file (or group of files when `secondaryFiles` is provided) that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	57 will be accessible by tools using standard POSIX file system call API such as
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	58 open(2) and read(2).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	59
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	60 Files are represented as objects with `class` of `File`. File objects have
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	61 a number of properties that provide metadata about the file.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	62
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	63 The `location` property of a File is a URI that uniquely identifies the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	64 file. Implementations must support the file:// URI scheme and may support
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	65 other schemes such as http://. The value of `location` may also be a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	66 relative reference, in which case it must be resolved relative to the URI
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	67 of the document it appears in. Alternately to `location`, implementations
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	68 must also accept the `path` property on File, which must be a filesystem
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	69 path available on the same host as the CWL runner (for inputs) or the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	70 runtime environment of a command line tool execution (for command line tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	71 outputs).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	72
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	73 If no `location` or `path` is specified, a file object must specify
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	74 `contents` with the UTF-8 text content of the file. This is a "file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	75 literal". File literals do not correspond to external resources, but are
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	76 created on disk with `contents` with when needed for a executing a tool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	77 Where appropriate, expressions can return file literals to define new files
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	78 on a runtime. The maximum size of `contents` is 64 kilobytes.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	79
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	80 The `basename` property defines the filename on disk where the file is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	81 staged. This may differ from the resource name. If not provided,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	82 `basename` must be computed from the last path part of `location` and made
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	83 available to expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	84
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	85 The `secondaryFiles` property is a list of File or Directory objects that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	86 must be staged in the same directory as the primary file. It is an error
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	87 for file names to be duplicated in `secondaryFiles`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	88
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	89 The `size` property is the size in bytes of the File. It must be computed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	90 from the resource and made available to expressions. The `checksum` field
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	91 contains a cryptographic hash of the file content for use it verifying file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	92 contents. Implementations may, at user option, enable or disable
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	93 computation of the `checksum` field for performance or other reasons.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	94 However, the ability to compute output checksums is required to pass the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	95 CWL conformance test suite.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	96
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	97 When executing a CommandLineTool, the files and secondary files may be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	98 staged to an arbitrary directory, but must use the value of `basename` for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	99 the filename. The `path` property must be file path in the context of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	100 tool execution runtime (local to the compute node, or within the executing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	101 container). All computed properties should be available to expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	102 File literals also must be staged and `path` must be set.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	103
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	104 When collecting CommandLineTool outputs, `glob` matching returns file paths
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	105 (with the `path` property) and the derived properties. This can all be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	106 modified by `outputEval`. Alternately, if the file `cwl.output.json` is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	107 present in the output, `outputBinding` is ignored.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	108
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	109 File objects in the output must provide either a `location` URI or a `path`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	110 property in the context of the tool execution runtime (local to the compute
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	111 node, or within the executing container).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	112
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	113 When evaluating an ExpressionTool, file objects must be referenced via
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	114 `location` (the expression tool does not have access to files on disk so
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	115 `path` is meaningless) or as file literals. It is legal to return a file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	116 object with an existing `location` but a different `basename`. The
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	117 `loadContents` field of ExpressionTool inputs behaves the same as on
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	118 CommandLineTool inputs, however it is not meaningful on the outputs.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	119
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	120 An ExpressionTool may forward file references from input to output by using
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	121 the same value for `location`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	122
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	123 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	124 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	125 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	126 type: enum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	127 name: File_class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	128 symbols:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	129 - cwl:File
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	130 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	131 _id: "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	132 _type: "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	133 doc: Must be `File` to indicate this object describes a file.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	134 - name: location
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	135 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	136 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	137 An IRI that identifies the file resource. This may be a relative
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	138 reference, in which case it must be resolved using the base IRI of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	139 document. The location may refer to a local or remote resource; the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	140 implementation must use the IRI to retrieve file content. If an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	141 implementation is unable to retrieve the file content stored at a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	142 remote resource (due to unsupported protocol, access denied, or other
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	143 issue) it must signal an error.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	144
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	145 If the `location` field is not provided, the `contents` field must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	146 provided. The implementation must assign a unique identifier for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	147 the `location` field.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	148
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	149 If the `path` field is provided but the `location` field is not, an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	150 implementation may assign the value of the `path` field to `location`,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	151 then follow the rules above.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	152 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	153 _id: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	154 _type: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	155 - name: path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	156 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	157 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	158 The local host path where the File is available when a CommandLineTool is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	159 executed. This field must be set by the implementation. The final
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	160 path component must match the value of `basename`. This field
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	161 must not be used in any other context. The command line tool being
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	162 executed must be able to to access the file at `path` using the POSIX
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	163 `open(2)` syscall.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	164
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	165 As a special case, if the `path` field is provided but the `location`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	166 field is not, an implementation may assign the value of the `path`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	167 field to `location`, and remove the `path` field.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	168
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	169 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	170 (`\|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	171 `<space>`, `<tab>`, and `<newline>`) or characters
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	172 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	173 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	174 then implementations may terminate the process with a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	175 `permanentFailure`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	176 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	177 "_id": "cwl:path"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	178 "_type": "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	179 - name: basename
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	180 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	181 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	182 The base name of the file, that is, the name of the file without any
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	183 leading directory path. The base name must not contain a slash `/`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	184
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	185 If not provided, the implementation must set this field based on the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	186 `location` field by taking the final path component after parsing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	187 `location` as an IRI. If `basename` is provided, it is not required to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	188 match the value from `location`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	189
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	190 When this file is made available to a CommandLineTool, it must be named
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	191 with `basename`, i.e. the final component of the `path` field must match
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	192 `basename`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	193 jsonldPredicate: "cwl:basename"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	194 - name: dirname
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	195 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	196 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	197 The name of the directory containing file, that is, the path leading up
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	198 to the final slash in the path such that `dirname + '/' + basename ==
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	199 path`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	200
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	201 The implementation must set this field based on the value of `path`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	202 prior to evaluating parameter references or expressions in a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	203 CommandLineTool document. This field must not be used in any other
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	204 context.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	205 - name: nameroot
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	206 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	207 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	208 The basename root such that `nameroot + nameext == basename`, and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	209 `nameext` is empty or begins with a period and contains at most one
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	210 period. For the purposess of path splitting leading periods on the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	211 basename are ignored; a basename of `.cshrc` will have a nameroot of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	212 `.cshrc`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	213
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	214 The implementation must set this field automatically based on the value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	215 of `basename` prior to evaluating parameter references or expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	216 - name: nameext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	217 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	218 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	219 The basename extension such that `nameroot + nameext == basename`, and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	220 `nameext` is empty or begins with a period and contains at most one
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	221 period. Leading periods on the basename are ignored; a basename of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	222 `.cshrc` will have an empty `nameext`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	223
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	224 The implementation must set this field automatically based on the value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	225 of `basename` prior to evaluating parameter references or expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	226 - name: checksum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	227 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	228 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	229 Optional hash code for validating file integrity. Currently must be in the form
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	230 "sha1$ + hexadecimal string" using the SHA-1 algorithm.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	231 - name: size
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	232 type: long?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	233 doc: Optional file size
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	234 - name: "secondaryFiles"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	235 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	236 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	237 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	238 items: [File, Directory]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	239 jsonldPredicate: "cwl:secondaryFiles"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	240 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	241 A list of additional files or directories that are associated with the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	242 primary file and must be transferred alongside the primary file.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	243 Examples include indexes of the primary file, or external references
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	244 which must be included when loading primary document. A file object
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	245 listed in `secondaryFiles` may itself include `secondaryFiles` for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	246 which the same rules apply.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	247 - name: format
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	248 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	249 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	250 _id: cwl:format
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	251 _type: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	252 identity: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	253 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	254 The format of the file: this must be an IRI of a concept node that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	255 represents the file format, preferrably defined within an ontology.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	256 If no ontology is available, file formats may be tested by exact match.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	257
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	258 Reasoning about format compatability must be done by checking that an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	259 input file format is the same, `owl:equivalentClass` or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	260 `rdfs:subClassOf` the format required by the input parameter.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	261 `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	262 `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	263 `<C> owl:subclassOf <A>`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	264
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	265 File format ontologies may be provided in the "$schema" metadata at the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	266 root of the document. If no ontologies are specified in `$schema`, the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	267 runtime may perform exact file format matches.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	268 - name: contents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	269 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	270 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	271 File contents literal. Maximum of 64 KiB.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	272
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	273 If neither `location` nor `path` is provided, `contents` must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	274 non-null. The implementation must assign a unique identifier for the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	275 `location` field. When the file is staged as input to CommandLineTool,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	276 the value of `contents` must be written to a file.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	277
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	278 If `loadContents` of `inputBinding` or `outputBinding` is true and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	279 `location` is valid, the implementation must read up to the first 64
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	280 KiB of text from the file and place it in the "contents" field.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	281
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	282
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	283 - name: Directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	284 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	285 docAfter: "#File"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	286 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	287 Represents a directory to present to a command line tool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	288
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	289 Directories are represented as objects with `class` of `Directory`. Directory objects have
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	290 a number of properties that provide metadata about the directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	291
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	292 The `location` property of a Directory is a URI that uniquely identifies
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	293 the directory. Implementations must support the file:// URI scheme and may
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	294 support other schemes such as http://. Alternately to `location`,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	295 implementations must also accept the `path` property on Direcotry, which
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	296 must be a filesystem path available on the same host as the CWL runner (for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	297 inputs) or the runtime environment of a command line tool execution (for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	298 command line tool outputs).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	299
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	300 A Directory object may have a `listing` field. This is a list of File and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	301 Directory objects that are contained in the Directory. For each entry in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	302 `listing`, the `basename` property defines the name of the File or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	303 Subdirectory when staged to disk. If `listing` is not provided, the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	304 implementation must have some way of fetching the Directory listing at
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	305 runtime based on the `location` field.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	306
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	307 If a Directory does not have `location`, it is a Directory literal. A
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	308 Directory literal must provide `listing`. Directory literals must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	309 created on disk at runtime as needed.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	310
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	311 The resources in a Directory literal do not need to have any implied
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	312 relationship in their `location`. For example, a Directory listing may
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	313 contain two files located on different hosts. It is the responsibility of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	314 the runtime to ensure that those files are staged to disk appropriately.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	315 Secondary files associated with files in `listing` must also be staged to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	316 the same Directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	317
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	318 When executing a CommandLineTool, Directories must be recursively staged
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	319 first and have local values of `path` assigend.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	320
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	321 Directory objects in CommandLineTool output must provide either a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	322 `location` URI or a `path` property in the context of the tool execution
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	323 runtime (local to the compute node, or within the executing container).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	324
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	325 An ExpressionTool may forward file references from input to output by using
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	326 the same value for `location`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	327
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	328 Name conflicts (the same `basename` appearing multiple times in `listing`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	329 or in any entry in `secondaryFiles` in the listing) is a fatal error.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	330
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	331 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	332 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	333 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	334 type: enum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	335 name: Directory_class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	336 symbols:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	337 - cwl:Directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	338 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	339 _id: "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	340 _type: "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	341 doc: Must be `Directory` to indicate this object describes a Directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	342 - name: location
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	343 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	344 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	345 An IRI that identifies the directory resource. This may be a relative
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	346 reference, in which case it must be resolved using the base IRI of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	347 document. The location may refer to a local or remote resource. If
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	348 the `listing` field is not set, the implementation must use the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	349 location IRI to retrieve directory listing. If an implementation is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	350 unable to retrieve the directory listing stored at a remote resource (due to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	351 unsupported protocol, access denied, or other issue) it must signal an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	352 error.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	353
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	354 If the `location` field is not provided, the `listing` field must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	355 provided. The implementation must assign a unique identifier for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	356 the `location` field.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	357
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	358 If the `path` field is provided but the `location` field is not, an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	359 implementation may assign the value of the `path` field to `location`,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	360 then follow the rules above.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	361 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	362 _id: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	363 _type: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	364 - name: path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	365 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	366 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	367 The local path where the Directory is made available prior to executing a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	368 CommandLineTool. This must be set by the implementation. This field
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	369 must not be used in any other context. The command line tool being
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	370 executed must be able to to access the directory at `path` using the POSIX
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	371 `opendir(2)` syscall.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	372
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	373 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	374 (`\|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	375 `<space>`, `<tab>`, and `<newline>`) or characters
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	376 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	377 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	378 then implementations may terminate the process with a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	379 `permanentFailure`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	380 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	381 _id: "cwl:path"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	382 _type: "@id"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	383 - name: basename
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	384 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	385 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	386 The base name of the directory, that is, the name of the file without any
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	387 leading directory path. The base name must not contain a slash `/`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	388
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	389 If not provided, the implementation must set this field based on the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	390 `location` field by taking the final path component after parsing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	391 `location` as an IRI. If `basename` is provided, it is not required to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	392 match the value from `location`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	393
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	394 When this file is made available to a CommandLineTool, it must be named
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	395 with `basename`, i.e. the final component of the `path` field must match
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	396 `basename`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	397 jsonldPredicate: "cwl:basename"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	398 - name: listing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	399 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	400 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	401 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	402 items: [File, Directory]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	403 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	404 List of files or subdirectories contained in this directory. The name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	405 of each file or subdirectory is determined by the `basename` field of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	406 each `File` or `Directory` object. It is an error if a `File` shares a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	407 `basename` with any other entry in `listing`. If two or more
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	408 `Directory` object share the same `basename`, this must be treated as
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	409 equivalent to a single subdirectory with the listings recursively
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	410 merged.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	411 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	412 _id: "cwl:listing"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	413
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	414 - name: SchemaBase
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	415 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	416 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	417 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	418 - name: label
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	419 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	420 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	421 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	422 jsonldPredicate: "rdfs:label"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	423 doc: "A short, human-readable label of this object."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	424
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	425
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	426 - name: Parameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	427 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	428 extends: SchemaBase
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	429 abstract: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	430 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	431 Define an input or output parameter to a process.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	432
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	433 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	434 - name: secondaryFiles
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	435 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	436 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	437 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	438 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	439 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	440 items: [string, Expression]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	441 jsonldPredicate: "cwl:secondaryFiles"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	442 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	443 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	444
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	445 Provides a pattern or expression specifying files or directories that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	446 must be included alongside the primary file. All listed secondary
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	447 files must be present. An implementation may fail workflow execution
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	448 if an expected secondary file does not exist.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	449
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	450 If the value is an expression, the value of `self` in the expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	451 must be the primary input or output File object to which this binding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	452 applies. The `basename`, `nameroot` and `nameext` fields must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	453 present in `self`. For `CommandLineTool` outputs the `path` field must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	454 also be present. The expression must return a filename string relative
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	455 to the path to the primary File, a File or Directory object with either
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	456 `path` or `location` and `basename` fields set, or an array consisting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	457 of strings or File or Directory objects. It is legal to reference an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	458 unchanged File or Directory object taken from input as a secondaryFile.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	459
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	460 To work on non-filename-preserving storage systems, portable tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	461 descriptions should avoid constructing new values from `location`, but
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	462 should construct relative references using `basename` or `nameroot`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	463 instead.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	464
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	465 If a value in `secondaryFiles` is a string that is not an expression,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	466 it specifies that the following pattern should be applied to the path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	467 of the primary file to yield a filename relative to the primary File:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	468
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	469 1. If string begins with one or more caret `^` characters, for each
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	470 caret, remove the last file extension from the path (the last
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	471 period `.` and all following characters). If there are no file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	472 extensions, the path is unchanged.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	473 2. Append the remainder of the string to the end of the file path.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	474
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	475 - name: streamable
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	476 type: boolean?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	477 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	478 Only valid when `type: File` or is an array of `items: File`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	479
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	480 A value of `true` indicates that the file is read or written
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	481 sequentially without seeking. An implementation may use this flag to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	482 indicate whether it is valid to stream file contents using a named
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	483 pipe. Default: `false`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	484
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	485 - name: doc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	486 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	487 - string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	488 - string[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	489 doc: "A documentation string for this type, or an array of strings which should be concatenated."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	490 jsonldPredicate: "rdfs:comment"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	491
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	492
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	493 - type: enum
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	494 name: Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	495 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	496 'Expression' is not a real type. It indicates that a field must allow
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	497 runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	498 is declared and supported by the platform, the field must also allow
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	499 Javascript expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	500 symbols:

0

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1 $base: "https://w3id.org/cwl/cwl#"

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2

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3 $namespaces:

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4 cwl: "https://w3id.org/cwl/cwl#"

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5 sld: "https://w3id.org/cwl/salad#"

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6 rdfs: "http://www.w3.org/2000/01/rdf-schema#"

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7

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8 $graph:

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9

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10 - name: "Common Workflow Language, v1.0"

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11 type: documentation

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12 doc: {$include: concepts.md}

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13

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14 - $import: "salad/schema_salad/metaschema/metaschema_base.yml"

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15

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16 - name: BaseTypesDoc

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17 type: documentation

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18 doc: |

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19 ## Base types

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20 docChild:

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21 - "#CWLType"

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22 - "#Process"

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23

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24 - type: enum

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25 name: CWLVersion

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26 doc: "Version symbols for published CWL document versions."

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27 symbols:

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28 - cwl:draft-2

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29 - cwl:draft-3.dev1

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30 - cwl:draft-3.dev2

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31 - cwl:draft-3.dev3

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32 - cwl:draft-3.dev4

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33 - cwl:draft-3.dev5

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34 - cwl:draft-3

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35 - cwl:draft-4.dev1

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36 - cwl:draft-4.dev2

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37 - cwl:draft-4.dev3

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38 - cwl:v1.0.dev4

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39 - cwl:v1.0

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40

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41 - name: CWLType

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42 type: enum

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43 extends: "sld:PrimitiveType"

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44 symbols:

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45 - cwl:File

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46 - cwl:Directory

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47 doc:

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48 - "Extends primitive types with the concept of a file and directory as a builtin type."

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49 - "File: A File object"

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50 - "Directory: A Directory object"

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51

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52 - name: File

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53 type: record

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54 docParent: "#CWLType"

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55 doc: |

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56 Represents a file (or group of files when `secondaryFiles` is provided) that

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57 will be accessible by tools using standard POSIX file system call API such as

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58 open(2) and read(2).

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59

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60 Files are represented as objects with `class` of `File`. File objects have

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61 a number of properties that provide metadata about the file.

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62

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63 The `location` property of a File is a URI that uniquely identifies the

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64 file. Implementations must support the file:// URI scheme and may support

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65 other schemes such as http://. The value of `location` may also be a

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66 relative reference, in which case it must be resolved relative to the URI

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67 of the document it appears in. Alternately to `location`, implementations

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68 must also accept the `path` property on File, which must be a filesystem

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69 path available on the same host as the CWL runner (for inputs) or the

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70 runtime environment of a command line tool execution (for command line tool

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71 outputs).

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72

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73 If no `location` or `path` is specified, a file object must specify

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74 `contents` with the UTF-8 text content of the file. This is a "file

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75 literal". File literals do not correspond to external resources, but are

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76 created on disk with `contents` with when needed for a executing a tool.

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77 Where appropriate, expressions can return file literals to define new files

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78 on a runtime. The maximum size of `contents` is 64 kilobytes.

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79

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80 The `basename` property defines the filename on disk where the file is

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81 staged. This may differ from the resource name. If not provided,

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82 `basename` must be computed from the last path part of `location` and made

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83 available to expressions.

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84

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85 The `secondaryFiles` property is a list of File or Directory objects that

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86 must be staged in the same directory as the primary file. It is an error

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87 for file names to be duplicated in `secondaryFiles`.

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88

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89 The `size` property is the size in bytes of the File. It must be computed

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90 from the resource and made available to expressions. The `checksum` field

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91 contains a cryptographic hash of the file content for use it verifying file

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92 contents. Implementations may, at user option, enable or disable

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93 computation of the `checksum` field for performance or other reasons.

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94 However, the ability to compute output checksums is required to pass the

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95 CWL conformance test suite.

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96

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97 When executing a CommandLineTool, the files and secondary files may be

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98 staged to an arbitrary directory, but must use the value of `basename` for

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99 the filename. The `path` property must be file path in the context of the

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100 tool execution runtime (local to the compute node, or within the executing

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101 container). All computed properties should be available to expressions.

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102 File literals also must be staged and `path` must be set.

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103

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104 When collecting CommandLineTool outputs, `glob` matching returns file paths

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105 (with the `path` property) and the derived properties. This can all be

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106 modified by `outputEval`. Alternately, if the file `cwl.output.json` is

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107 present in the output, `outputBinding` is ignored.

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108

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109 File objects in the output must provide either a `location` URI or a `path`

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110 property in the context of the tool execution runtime (local to the compute

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111 node, or within the executing container).

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112

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113 When evaluating an ExpressionTool, file objects must be referenced via

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114 `location` (the expression tool does not have access to files on disk so

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115 `path` is meaningless) or as file literals. It is legal to return a file

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116 object with an existing `location` but a different `basename`. The

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117 `loadContents` field of ExpressionTool inputs behaves the same as on

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118 CommandLineTool inputs, however it is not meaningful on the outputs.

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119

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120 An ExpressionTool may forward file references from input to output by using

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121 the same value for `location`.

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122

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123 fields:

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124 - name: class

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125 type:

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126 type: enum

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127 name: File_class

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128 symbols:

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129 - cwl:File

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130 jsonldPredicate:

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131 _id: "@type"

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132 _type: "@vocab"

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133 doc: Must be `File` to indicate this object describes a file.

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134 - name: location

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135 type: string?

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136 doc: |

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137 An IRI that identifies the file resource. This may be a relative

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138 reference, in which case it must be resolved using the base IRI of the

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139 document. The location may refer to a local or remote resource; the

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140 implementation must use the IRI to retrieve file content. If an

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141 implementation is unable to retrieve the file content stored at a

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142 remote resource (due to unsupported protocol, access denied, or other

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143 issue) it must signal an error.

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144

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145 If the `location` field is not provided, the `contents` field must be

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146 provided. The implementation must assign a unique identifier for

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147 the `location` field.

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148

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149 If the `path` field is provided but the `location` field is not, an

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150 implementation may assign the value of the `path` field to `location`,

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151 then follow the rules above.

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152 jsonldPredicate:

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153 _id: "@id"

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154 _type: "@id"

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155 - name: path

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156 type: string?

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157 doc: |

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158 The local host path where the File is available when a CommandLineTool is

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159 executed. This field must be set by the implementation. The final

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160 path component must match the value of `basename`. This field

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161 must not be used in any other context. The command line tool being

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162 executed must be able to to access the file at `path` using the POSIX

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163 `open(2)` syscall.

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164

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165 As a special case, if the `path` field is provided but the `location`

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166 field is not, an implementation may assign the value of the `path`

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167 field to `location`, and remove the `path` field.

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168

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169 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)

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170 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,

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171 `<space>`, `<tab>`, and `<newline>`) or characters

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172 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)

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173 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)

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174 then implementations may terminate the process with a

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175 `permanentFailure`.

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176 jsonldPredicate:

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177 "_id": "cwl:path"

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178 "_type": "@id"

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179 - name: basename

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180 type: string?

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181 doc: |

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182 The base name of the file, that is, the name of the file without any

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183 leading directory path. The base name must not contain a slash `/`.

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184

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185 If not provided, the implementation must set this field based on the

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186 `location` field by taking the final path component after parsing

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187 `location` as an IRI. If `basename` is provided, it is not required to

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188 match the value from `location`.

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189

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190 When this file is made available to a CommandLineTool, it must be named

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191 with `basename`, i.e. the final component of the `path` field must match

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192 `basename`.

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193 jsonldPredicate: "cwl:basename"

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194 - name: dirname

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195 type: string?

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196 doc: |

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197 The name of the directory containing file, that is, the path leading up

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198 to the final slash in the path such that `dirname + '/' + basename ==

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199 path`.

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200

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201 The implementation must set this field based on the value of `path`

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202 prior to evaluating parameter references or expressions in a

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203 CommandLineTool document. This field must not be used in any other

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204 context.

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205 - name: nameroot

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206 type: string?

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207 doc: |

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208 The basename root such that `nameroot + nameext == basename`, and

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209 `nameext` is empty or begins with a period and contains at most one

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210 period. For the purposess of path splitting leading periods on the

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211 basename are ignored; a basename of `.cshrc` will have a nameroot of

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212 `.cshrc`.

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213

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214 The implementation must set this field automatically based on the value

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215 of `basename` prior to evaluating parameter references or expressions.

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216 - name: nameext

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217 type: string?

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218 doc: |

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219 The basename extension such that `nameroot + nameext == basename`, and

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220 `nameext` is empty or begins with a period and contains at most one

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221 period. Leading periods on the basename are ignored; a basename of

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222 `.cshrc` will have an empty `nameext`.

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223

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224 The implementation must set this field automatically based on the value

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225 of `basename` prior to evaluating parameter references or expressions.

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226 - name: checksum

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227 type: string?

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228 doc: |

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229 Optional hash code for validating file integrity. Currently must be in the form

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230 "sha1$ + hexadecimal string" using the SHA-1 algorithm.

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231 - name: size

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232 type: long?

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233 doc: Optional file size

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234 - name: "secondaryFiles"

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235 type:

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236 - "null"

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237 - type: array

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238 items: [File, Directory]

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239 jsonldPredicate: "cwl:secondaryFiles"

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240 doc: |

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241 A list of additional files or directories that are associated with the

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242 primary file and must be transferred alongside the primary file.

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243 Examples include indexes of the primary file, or external references

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244 which must be included when loading primary document. A file object

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245 listed in `secondaryFiles` may itself include `secondaryFiles` for

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246 which the same rules apply.

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247 - name: format

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248 type: string?

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249 jsonldPredicate:

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250 _id: cwl:format

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251 _type: "@id"

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252 identity: true

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253 doc: |

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254 The format of the file: this must be an IRI of a concept node that

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255 represents the file format, preferrably defined within an ontology.

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256 If no ontology is available, file formats may be tested by exact match.

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257

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258 Reasoning about format compatability must be done by checking that an

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259 input file format is the same, `owl:equivalentClass` or

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260 `rdfs:subClassOf` the format required by the input parameter.

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261 `owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if

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262 `<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer

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263 `<C> owl:subclassOf <A>`.

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264

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265 File format ontologies may be provided in the "$schema" metadata at the

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266 root of the document. If no ontologies are specified in `$schema`, the

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267 runtime may perform exact file format matches.

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268 - name: contents

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269 type: string?

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270 doc: |

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271 File contents literal. Maximum of 64 KiB.

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272

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273 If neither `location` nor `path` is provided, `contents` must be

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274 non-null. The implementation must assign a unique identifier for the

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275 `location` field. When the file is staged as input to CommandLineTool,

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276 the value of `contents` must be written to a file.

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277

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278 If `loadContents` of `inputBinding` or `outputBinding` is true and

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279 `location` is valid, the implementation must read up to the first 64

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280 KiB of text from the file and place it in the "contents" field.

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281

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282

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283 - name: Directory

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284 type: record

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285 docAfter: "#File"

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286 doc: |

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287 Represents a directory to present to a command line tool.

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288

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289 Directories are represented as objects with `class` of `Directory`. Directory objects have

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290 a number of properties that provide metadata about the directory.

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291

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292 The `location` property of a Directory is a URI that uniquely identifies

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293 the directory. Implementations must support the file:// URI scheme and may

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294 support other schemes such as http://. Alternately to `location`,

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295 implementations must also accept the `path` property on Direcotry, which

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296 must be a filesystem path available on the same host as the CWL runner (for

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297 inputs) or the runtime environment of a command line tool execution (for

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298 command line tool outputs).

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299

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300 A Directory object may have a `listing` field. This is a list of File and

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301 Directory objects that are contained in the Directory. For each entry in

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302 `listing`, the `basename` property defines the name of the File or

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303 Subdirectory when staged to disk. If `listing` is not provided, the

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304 implementation must have some way of fetching the Directory listing at

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305 runtime based on the `location` field.

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306

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307 If a Directory does not have `location`, it is a Directory literal. A

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308 Directory literal must provide `listing`. Directory literals must be

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309 created on disk at runtime as needed.

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310

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311 The resources in a Directory literal do not need to have any implied

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312 relationship in their `location`. For example, a Directory listing may

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313 contain two files located on different hosts. It is the responsibility of

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314 the runtime to ensure that those files are staged to disk appropriately.

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315 Secondary files associated with files in `listing` must also be staged to

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316 the same Directory.

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317

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318 When executing a CommandLineTool, Directories must be recursively staged

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319 first and have local values of `path` assigend.

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320

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321 Directory objects in CommandLineTool output must provide either a

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322 `location` URI or a `path` property in the context of the tool execution

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323 runtime (local to the compute node, or within the executing container).

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324

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325 An ExpressionTool may forward file references from input to output by using

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326 the same value for `location`.

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327

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328 Name conflicts (the same `basename` appearing multiple times in `listing`

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329 or in any entry in `secondaryFiles` in the listing) is a fatal error.

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330

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331 fields:

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332 - name: class

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333 type:

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334 type: enum

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335 name: Directory_class

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336 symbols:

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337 - cwl:Directory

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338 jsonldPredicate:

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339 _id: "@type"

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340 _type: "@vocab"

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341 doc: Must be `Directory` to indicate this object describes a Directory.

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342 - name: location

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343 type: string?

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344 doc: |

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345 An IRI that identifies the directory resource. This may be a relative

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346 reference, in which case it must be resolved using the base IRI of the

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347 document. The location may refer to a local or remote resource. If

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348 the `listing` field is not set, the implementation must use the

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349 location IRI to retrieve directory listing. If an implementation is

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350 unable to retrieve the directory listing stored at a remote resource (due to

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351 unsupported protocol, access denied, or other issue) it must signal an

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352 error.

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353

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354 If the `location` field is not provided, the `listing` field must be

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355 provided. The implementation must assign a unique identifier for

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356 the `location` field.

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357

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358 If the `path` field is provided but the `location` field is not, an

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359 implementation may assign the value of the `path` field to `location`,

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360 then follow the rules above.

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361 jsonldPredicate:

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362 _id: "@id"

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363 _type: "@id"

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364 - name: path

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365 type: string?

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366 doc: |

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367 The local path where the Directory is made available prior to executing a

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368 CommandLineTool. This must be set by the implementation. This field

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369 must not be used in any other context. The command line tool being

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370 executed must be able to to access the directory at `path` using the POSIX

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371 `opendir(2)` syscall.

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372

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373 If the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)

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374 (`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\`, `"`, `'`,

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375 `<space>`, `<tab>`, and `<newline>`) or characters

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376 [not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)

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377 for [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)

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378 then implementations may terminate the process with a

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379 `permanentFailure`.

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380 jsonldPredicate:

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381 _id: "cwl:path"

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382 _type: "@id"

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383 - name: basename

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384 type: string?

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385 doc: |

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386 The base name of the directory, that is, the name of the file without any

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387 leading directory path. The base name must not contain a slash `/`.

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388

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389 If not provided, the implementation must set this field based on the

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390 `location` field by taking the final path component after parsing

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391 `location` as an IRI. If `basename` is provided, it is not required to

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392 match the value from `location`.

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393

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394 When this file is made available to a CommandLineTool, it must be named

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395 with `basename`, i.e. the final component of the `path` field must match

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396 `basename`.

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397 jsonldPredicate: "cwl:basename"

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398 - name: listing

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399 type:

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400 - "null"

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401 - type: array

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402 items: [File, Directory]

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403 doc: |

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404 List of files or subdirectories contained in this directory. The name

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405 of each file or subdirectory is determined by the `basename` field of

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406 each `File` or `Directory` object. It is an error if a `File` shares a

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407 `basename` with any other entry in `listing`. If two or more

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408 `Directory` object share the same `basename`, this must be treated as

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409 equivalent to a single subdirectory with the listings recursively

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410 merged.

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411 jsonldPredicate:

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412 _id: "cwl:listing"

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413

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414 - name: SchemaBase

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415 type: record

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416 abstract: true

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417 fields:

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418 - name: label

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419 type:

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420 - "null"

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421 - string

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422 jsonldPredicate: "rdfs:label"

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423 doc: "A short, human-readable label of this object."

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424

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425

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426 - name: Parameter

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427 type: record

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428 extends: SchemaBase

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429 abstract: true

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430 doc: |

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431 Define an input or output parameter to a process.

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432

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433 fields:

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434 - name: secondaryFiles

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diff changeset

435 type:

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parents:

diff changeset

436 - "null"

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shellac

parents:

diff changeset

437 - string

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parents:

diff changeset

438 - Expression

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

439 - type: array

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parents:

diff changeset

440 items: [string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

441 jsonldPredicate: "cwl:secondaryFiles"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

442 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

443 Only valid when `type: File` or is an array of `items: File`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

444

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

445 Provides a pattern or expression specifying files or directories that

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

446 must be included alongside the primary file. All listed secondary

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

447 files must be present. An implementation may fail workflow execution

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

448 if an expected secondary file does not exist.

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parents:

diff changeset

449

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

450 If the value is an expression, the value of `self` in the expression

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

451 must be the primary input or output File object to which this binding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

452 applies. The `basename`, `nameroot` and `nameext` fields must be

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

453 present in `self`. For `CommandLineTool` outputs the `path` field must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

454 also be present. The expression must return a filename string relative

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

455 to the path to the primary File, a File or Directory object with either

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

456 `path` or `location` and `basename` fields set, or an array consisting

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

457 of strings or File or Directory objects. It is legal to reference an

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parents:

diff changeset

458 unchanged File or Directory object taken from input as a secondaryFile.

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parents:

diff changeset

459

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

460 To work on non-filename-preserving storage systems, portable tool

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

461 descriptions should avoid constructing new values from `location`, but

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

462 should construct relative references using `basename` or `nameroot`

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

463 instead.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

464

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

465 If a value in `secondaryFiles` is a string that is not an expression,

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

466 it specifies that the following pattern should be applied to the path

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parents:

diff changeset

467 of the primary file to yield a filename relative to the primary File:

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parents:

diff changeset

468

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parents:

diff changeset

469 1. If string begins with one or more caret `^` characters, for each

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

470 caret, remove the last file extension from the path (the last

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

471 period `.` and all following characters). If there are no file

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parents:

diff changeset

472 extensions, the path is unchanged.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

473 2. Append the remainder of the string to the end of the file path.

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parents:

diff changeset

474

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

475 - name: streamable

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shellac

parents:

diff changeset

476 type: boolean?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

477 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

478 Only valid when `type: File` or is an array of `items: File`.

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parents:

diff changeset

479

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parents:

diff changeset

480 A value of `true` indicates that the file is read or written

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parents:

diff changeset

481 sequentially without seeking. An implementation may use this flag to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

482 indicate whether it is valid to stream file contents using a named

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parents:

diff changeset

483 pipe. Default: `false`.

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parents:

diff changeset

484

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

485 - name: doc

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

486 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

487 - string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

488 - string[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

489 doc: "A documentation string for this type, or an array of strings which should be concatenated."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

490 jsonldPredicate: "rdfs:comment"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

491

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

492

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

493 - type: enum

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

494 name: Expression

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

495 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

496 'Expression' is not a real type. It indicates that a field must allow

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

497 runtime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement)

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shellac

parents:

diff changeset

498 is declared and supported by the platform, the field must also allow

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

499 Javascript expressions.

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shellac

parents:

diff changeset

500 symbols:

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shellac

parents:

diff changeset

501 - cwl:ExpressionPlaceholder

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shellac

parents:

diff changeset

502

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

503

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

504 - name: InputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

505 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

506 abstract: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

507 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

508 - name: loadContents

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

509 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

510 - "null"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

511 - boolean

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

512 jsonldPredicate: "cwl:loadContents"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

513 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

514 Only valid when `type: File` or is an array of `items: File`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

515

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

516 Read up to the first 64 KiB of text from the file and place it in the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

517 "contents" field of the file object for use by expressions.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

518

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

519

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

520 - name: OutputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

521 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

522 abstract: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

523

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

524

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

525 - name: InputSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

526 extends: SchemaBase

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

527 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

528 abstract: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

529

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

530

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

531 - name: OutputSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

532 extends: SchemaBase

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

533 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

534 abstract: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

535

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

536

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

537 - name: InputRecordField

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

538 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

539 extends: "sld:RecordField"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

540 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

541 - specializeFrom: "sld:RecordSchema"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

542 specializeTo: InputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

543 - specializeFrom: "sld:EnumSchema"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

544 specializeTo: InputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

545 - specializeFrom: "sld:ArraySchema"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

546 specializeTo: InputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

547 - specializeFrom: "sld:PrimitiveType"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

548 specializeTo: CWLType

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

549 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

550 - name: inputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

551 type: InputBinding?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

552 jsonldPredicate: "cwl:inputBinding"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

553 - name: label

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

554 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

555 jsonldPredicate: "rdfs:label"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

556 doc: "A short, human-readable label of this process object."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

557

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

558

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

559 - name: InputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

560 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

561 extends: ["sld:RecordSchema", InputSchema]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

562 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

563 - specializeFrom: "sld:RecordField"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

564 specializeTo: InputRecordField

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

565

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

566

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

567 - name: InputEnumSchema

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parents:

diff changeset

568 type: record

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diff changeset

569 extends: ["sld:EnumSchema", InputSchema]

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diff changeset

570 fields:

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diff changeset

571 - name: inputBinding

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diff changeset

572 type: InputBinding?

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573 jsonldPredicate: "cwl:inputBinding"

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574

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diff changeset

575

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diff changeset

576 - name: InputArraySchema

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diff changeset

577 type: record

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diff changeset

578 extends: ["sld:ArraySchema", InputSchema]

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diff changeset

579 specialize:

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diff changeset

580 - specializeFrom: "sld:RecordSchema"

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581 specializeTo: InputRecordSchema

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parents:

diff changeset

582 - specializeFrom: "sld:EnumSchema"

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diff changeset

583 specializeTo: InputEnumSchema

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diff changeset

584 - specializeFrom: "sld:ArraySchema"

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diff changeset

585 specializeTo: InputArraySchema

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diff changeset

586 - specializeFrom: "sld:PrimitiveType"

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diff changeset

587 specializeTo: CWLType

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588 fields:

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parents:

diff changeset

589 - name: inputBinding

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diff changeset

590 type: InputBinding?

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591 jsonldPredicate: "cwl:inputBinding"

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592

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parents:

diff changeset

593

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parents:

diff changeset

594 - name: OutputRecordField

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diff changeset

595 type: record

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diff changeset

596 extends: "sld:RecordField"

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diff changeset

597 specialize:

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diff changeset

598 - specializeFrom: "sld:RecordSchema"

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diff changeset

599 specializeTo: OutputRecordSchema

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diff changeset

600 - specializeFrom: "sld:EnumSchema"

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diff changeset

601 specializeTo: OutputEnumSchema

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diff changeset

602 - specializeFrom: "sld:ArraySchema"

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diff changeset

603 specializeTo: OutputArraySchema

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diff changeset

604 - specializeFrom: "sld:PrimitiveType"

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diff changeset

605 specializeTo: CWLType

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606 fields:

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diff changeset

607 - name: outputBinding

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diff changeset

608 type: OutputBinding?

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diff changeset

609 jsonldPredicate: "cwl:outputBinding"

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610

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611

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parents:

diff changeset

612 - name: OutputRecordSchema

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diff changeset

613 type: record

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614 extends: ["sld:RecordSchema", "#OutputSchema"]

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615 docParent: "#OutputParameter"

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616 specialize:

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617 - specializeFrom: "sld:RecordField"

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diff changeset

618 specializeTo: OutputRecordField

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diff changeset

619

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620

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621 - name: OutputEnumSchema

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diff changeset

622 type: record

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623 extends: ["sld:EnumSchema", OutputSchema]

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624 docParent: "#OutputParameter"

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625 fields:

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626 - name: outputBinding

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diff changeset

627 type: OutputBinding?

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628 jsonldPredicate: "cwl:outputBinding"

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629

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parents:

diff changeset

630 - name: OutputArraySchema

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parents:

diff changeset

631 type: record

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diff changeset

632 extends: ["sld:ArraySchema", OutputSchema]

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diff changeset

633 docParent: "#OutputParameter"

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diff changeset

634 specialize:

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635 - specializeFrom: "sld:RecordSchema"

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636 specializeTo: OutputRecordSchema

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diff changeset

637 - specializeFrom: "sld:EnumSchema"

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diff changeset

638 specializeTo: OutputEnumSchema

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diff changeset

639 - specializeFrom: "sld:ArraySchema"

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diff changeset

640 specializeTo: OutputArraySchema

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diff changeset

641 - specializeFrom: "sld:PrimitiveType"

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diff changeset

642 specializeTo: CWLType

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diff changeset

643 fields:

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parents:

diff changeset

644 - name: outputBinding

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diff changeset

645 type: OutputBinding?

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diff changeset

646 jsonldPredicate: "cwl:outputBinding"

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647

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diff changeset

648

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diff changeset

649 - name: InputParameter

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diff changeset

650 type: record

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diff changeset

651 extends: Parameter

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652 fields:

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diff changeset

653 - name: id

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654 type: string

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655 jsonldPredicate: "@id"

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656 doc: "The unique identifier for this parameter object."

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657

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658 - name: format

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659 type:

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660 - "null"

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661 - string

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662 - type: array

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663 items: string

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664 - Expression

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665 jsonldPredicate:

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666 _id: cwl:format

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667 _type: "@id"

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668 identity: true

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669 doc: |

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670 Only valid when `type: File` or is an array of `items: File`.

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671

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672 This must be one or more IRIs of concept nodes

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673 that represents file formats which are allowed as input to this

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674 parameter, preferrably defined within an ontology. If no ontology is

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675 available, file formats may be tested by exact match.

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676

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diff changeset

677

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678 - name: inputBinding

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679 type: InputBinding?

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680 jsonldPredicate: "cwl:inputBinding"

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681 doc: |

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682 Describes how to handle the inputs of a process and convert them

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683 into a concrete form for execution, such as command line parameters.

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684

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685 - name: default

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686 type: Any?

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687 jsonldPredicate:

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688 _id: cwl:default

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689 noLinkCheck: true

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690 doc: |

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691 The default value to use for this parameter if the parameter is missing

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692 from the input object, or if the value of the parameter in the input

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693 object is `null`. Default values are applied before evaluating expressions

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694 (e.g. dependent `valueFrom` fields).

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695

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696 - name: type

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697 type:

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698 - "null"

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699 - CWLType

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diff changeset

700 - InputRecordSchema

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diff changeset

701 - InputEnumSchema

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diff changeset

702 - InputArraySchema

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diff changeset

703 - string

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diff changeset

704 - type: array

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diff changeset

705 items:

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diff changeset

706 - CWLType

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diff changeset

707 - InputRecordSchema

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diff changeset

708 - InputEnumSchema

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diff changeset

709 - InputArraySchema

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diff changeset

710 - string

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diff changeset

711 jsonldPredicate:

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diff changeset

712 "_id": "sld:type"

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diff changeset

713 "_type": "@vocab"

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diff changeset

714 refScope: 2

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715 typeDSL: True

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716 doc: |

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717 Specify valid types of data that may be assigned to this parameter.

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diff changeset

718

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719 - name: OutputParameter

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diff changeset

720 type: record

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diff changeset

721 extends: Parameter

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722 fields:

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723 - name: id

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724 type: string

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725 jsonldPredicate: "@id"

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diff changeset

726 doc: "The unique identifier for this parameter object."

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diff changeset

727 - name: outputBinding

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diff changeset

728 type: OutputBinding?

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diff changeset

729 jsonldPredicate: "cwl:outputBinding"

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diff changeset

730 doc: |

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diff changeset

731 Describes how to handle the outputs of a process.

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diff changeset

732 - name: format

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diff changeset

733 type:

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diff changeset

734 - "null"

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diff changeset

735 - string

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diff changeset

736 - Expression

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737 jsonldPredicate:

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diff changeset

738 _id: cwl:format

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diff changeset

739 _type: "@id"

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diff changeset

740 identity: true

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741 doc: |

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742 Only valid when `type: File` or is an array of `items: File`.

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diff changeset

743

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diff changeset

744 This is the file format that will be assigned to

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diff changeset

745 the output parameter.

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diff changeset

746

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747

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748

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diff changeset

749 - type: record

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diff changeset

750 name: ProcessRequirement

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diff changeset

751 abstract: true

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diff changeset

752 doc: |

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diff changeset

753 A process requirement declares a prerequisite that may or must be fulfilled

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diff changeset

754 before executing a process. See [`Process.hints`](#process) and

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diff changeset

755 [`Process.requirements`](#process).

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diff changeset

756

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757 Process requirements are the primary mechanism for specifying extensions to

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diff changeset

758 the CWL core specification.

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diff changeset

759

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diff changeset

760

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diff changeset

761 - type: record

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diff changeset

762 name: Process

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diff changeset

763 abstract: true

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diff changeset

764 doc: |

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diff changeset

765

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diff changeset

766 The base executable type in CWL is the `Process` object defined by the

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diff changeset

767 document. Note that the `Process` object is abstract and cannot be

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diff changeset

768 directly executed.

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diff changeset

769

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diff changeset

770 fields:

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diff changeset

771 - name: id

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parents:

diff changeset

772 type: string?

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diff changeset

773 jsonldPredicate: "@id"

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diff changeset

774 doc: "The unique identifier for this process object."

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diff changeset

775 - name: inputs

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parents:

diff changeset

776 type:

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diff changeset

777 type: array

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parents:

diff changeset

778 items: InputParameter

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diff changeset

779 jsonldPredicate:

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diff changeset

780 _id: "cwl:inputs"

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diff changeset

781 mapSubject: id

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parents:

diff changeset

782 mapPredicate: type

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diff changeset

783 doc: |

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diff changeset

784 Defines the input parameters of the process. The process is ready to

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diff changeset

785 run when all required input parameters are associated with concrete

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diff changeset

786 values. Input parameters include a schema for each parameter which is

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diff changeset

787 used to validate the input object. It may also be used to build a user

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parents:

diff changeset

788 interface for constructing the input object.

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diff changeset

789

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790 When accepting an input object, all input parameters must have a value.

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diff changeset

791 If an input parameter is missing from the input object, it must be

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792 assigned a value of `null` (or the value of `default` for that

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diff changeset

793 parameter, if provided) for the purposes of validation and evaluation

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diff changeset

794 of expressions.

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diff changeset

795

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diff changeset

796 - name: outputs

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parents:

diff changeset

797 type:

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diff changeset

798 type: array

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parents:

diff changeset

799 items: OutputParameter

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diff changeset

800 jsonldPredicate:

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diff changeset

801 _id: "cwl:outputs"

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parents:

diff changeset

802 mapSubject: id

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parents:

diff changeset

803 mapPredicate: type

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diff changeset

804 doc: |

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diff changeset

805 Defines the parameters representing the output of the process. May be

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diff changeset

806 used to generate and/or validate the output object.

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diff changeset

807 - name: requirements

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parents:

diff changeset

808 type: ProcessRequirement[]?

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diff changeset

809 jsonldPredicate:

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diff changeset

810 _id: "cwl:requirements"

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diff changeset

811 mapSubject: class

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diff changeset

812 doc: |

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diff changeset

813 Declares requirements that apply to either the runtime environment or the

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diff changeset

814 workflow engine that must be met in order to execute this process. If

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diff changeset

815 an implementation cannot satisfy all requirements, or a requirement is

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diff changeset

816 listed which is not recognized by the implementation, it is a fatal

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diff changeset

817 error and the implementation must not attempt to run the process,

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diff changeset

818 unless overridden at user option.

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diff changeset

819 - name: hints

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diff changeset

820 type: Any[]?

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diff changeset

821 doc: |

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diff changeset

822 Declares hints applying to either the runtime environment or the

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parents:

diff changeset

823 workflow engine that may be helpful in executing this process. It is

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parents:

diff changeset

824 not an error if an implementation cannot satisfy all hints, however

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parents:

diff changeset

825 the implementation may report a warning.

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diff changeset

826 jsonldPredicate:

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diff changeset

827 _id: cwl:hints

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diff changeset

828 noLinkCheck: true

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diff changeset

829 mapSubject: class

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parents:

diff changeset

830 - name: label

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parents:

diff changeset

831 type: string?

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parents:

diff changeset

832 jsonldPredicate: "rdfs:label"

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833 doc: "A short, human-readable label of this process object."

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834 - name: doc

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835 type: string?

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836 jsonldPredicate: "rdfs:comment"

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837 doc: "A long, human-readable description of this process object."

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838 - name: cwlVersion

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839 type: CWLVersion?

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840 doc: |

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841 CWL document version. Always required at the document root. Not

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842 required for a Process embedded inside another Process.

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843 jsonldPredicate:

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844 "_id": "cwl:cwlVersion"

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845 "_type": "@vocab"

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846

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847 - name: InlineJavascriptRequirement

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848 type: record

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849 extends: ProcessRequirement

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850 doc: |

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851 Indicates that the workflow platform must support inline Javascript expressions.

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852 If this requirement is not present, the workflow platform must not perform expression

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853 interpolatation.

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854 fields:

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855 - name: class

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856 type: string

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857 doc: "Always 'InlineJavascriptRequirement'"

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858 jsonldPredicate:

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859 "_id": "@type"

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860 "_type": "@vocab"

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861 - name: expressionLib

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862 type: string[]?

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863 doc: |

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864 Additional code fragments that will also be inserted

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865 before executing the expression code. Allows for function definitions that may

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866 be called from CWL expressions.

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867

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868

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869 - name: SchemaDefRequirement

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870 type: record

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871 extends: ProcessRequirement

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872 doc: |

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873 This field consists of an array of type definitions which must be used when

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874 interpreting the `inputs` and `outputs` fields. When a `type` field

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875 contain a IRI, the implementation must check if the type is defined in

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876 `schemaDefs` and use that definition. If the type is not found in

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877 `schemaDefs`, it is an error. The entries in `schemaDefs` must be

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878 processed in the order listed such that later schema definitions may refer

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879 to earlier schema definitions.

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880 fields:

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881 - name: class

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882 type: string

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883 doc: "Always 'SchemaDefRequirement'"

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884 jsonldPredicate:

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885 "_id": "@type"

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886 "_type": "@vocab"

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887 - name: types

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888 type:

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889 type: array

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890 items: InputSchema

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891 doc: The list of type definitions.

Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/schemas/v1.0/Process.yml @ 0:26e78fe6e8c4 draft