===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
cwltool-3.0.20200807132242/PKG-INFO-234- Process objects (CommandLineTool and Workflow) in a list in the
cwltool-3.0.20200807132242/PKG-INFO:235: ``$graph`` field. Cross references (such as ``run:`` and ``source:``
cwltool-3.0.20200807132242/PKG-INFO-236- fields) are updated to internal references within the new packed
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cwltool-3.0.20200807132242/README.rst-225-Process objects (CommandLineTool and Workflow) in a list in the
cwltool-3.0.20200807132242/README.rst:226:``$graph`` field. Cross references (such as ``run:`` and ``source:``
cwltool-3.0.20200807132242/README.rst-227-fields) are updated to internal references within the new packed
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cwltool-3.0.20200807132242/cwltool/job.py-291- # appropriate MPI job launch command and flags before the
cwltool-3.0.20200807132242/cwltool/job.py:292: # execution.
cwltool-3.0.20200807132242/cwltool/job.py-293- if self.mpi_procs:
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cwltool-3.0.20200807132242/cwltool/schemas/v1.0/CommandLineTool.yml-559- be an absolute path, otherwise it is an error. If the program does not
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/CommandLineTool.yml:560: include a path separator, search the `$PATH` variable in the runtime
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/CommandLineTool.yml-561- environment of the workflow runner find the absolute path of the
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/Process.yml-265- File format ontologies may be provided in the "$schema" metadata at the
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/Process.yml:266: root of the document. If no ontologies are specified in `$schema`, the
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/Process.yml-267- runtime may perform exact file format matches.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-125-additional fields on any object. Such extensions fields must use a namespace
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md:126:prefix listed in the `$namespaces` section of the document as described in the
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-127-[Schema Salad specification](SchemaSalad.html#Explicit_context).
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-131-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md:132:# Execution model
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-133-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md:134:## Execution concepts
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-135-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-230-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md:231:Parameter references are denoted by the syntax `$(...)` and may be used in any
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-232-field permitting the pseudo-type `Expression`, as specified by this document.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-320-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md:321:Expressions are denoted by the syntax `$(...)` or `${...}`. A code
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md:322:fragment wrapped in the `$(...)` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-323-[ECMAScript expression](http://www.ecma-international.org/ecma-262/5.1/#sec-11). A
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md:324:code fragment wrapped in the `${...}` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-325-[ECMAScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13)
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-384-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md:385:`$XDG_DATA_HOME/commonwl/` (usually `$HOME/.local/share/commonwl`)
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-386-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md:387:`$XDG_DATA_HOME` is from the [XDG Base Directory
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/concepts.md-388-Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.0/invocation.md-123-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/invocation.md:124:## Execution
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/invocation.md-125-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res.yml-19- * If an identifier URI begins with a namespace prefix declared in
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res.yml:20: `$namespaces` followed by a colon `:`, the prefix and colon must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res.yml:21: replaced by the namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/ident_res.yml-22-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-2-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:3:During preprocessing traversal, an implementation must resolve `$import`
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:4:directives. An `$import` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:5:field `$import` specifying resource by URI string. It is an error if there
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:6:are additional fields in the `$import` object, such additional fields must
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-7-be ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-11-loading from `file`, `http` and `https` resources. The URI referenced by
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:12:`$import` must be loaded and recursively preprocessed as a Salad document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-13-The external imported document does not inherit the context of the
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-15-document must be the URI used to retrieve the imported document. If the
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:16:`$import` URI includes a document fragment, the fragment must be excluded
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-17-from the base URI used to preprocess the imported document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-18-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:19:Once loaded and processed, the `$import` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-20-structure by the object or array yielded from the import operation.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-22-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:23:the target document. This indicates that the `$import` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-24-replaced by only the object with the appropriate fragment identifier.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-64-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:65:During preprocessing traversal, an implementation must resolve `$include`
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:66:directives. An `$include` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:67:field `$include` specifying a URI string. It is an error if there are
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:68:additional fields in the `$include` object, such additional fields must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-69-ignored.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-71-The URI string must be resolved to an absolute URI using the link
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:72:resolution rules described previously. The URI referenced by `$include` must
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-73-be loaded as a text data. Implementations must support loading from
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-77-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:78:Once loaded, the `$include` node is replaced in the document structure by a
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-79-string containing the text data loaded from the resource.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-116-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:117:During preprocessing traversal, an implementation must resolve `$mixin`
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:118:directives. An `$mixin` directive is an object consisting of the field
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:119:`$mixin` specifying resource by URI string. If there are additional fields in
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:120:the `$mixin` object, these fields override fields in the object which is loaded
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:121:from the `$mixin` URI.
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-122-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-124-rules described previously. Implementations must support loading from `file`,
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:125:`http` and `https` resources. The URI referenced by `$mixin` must be loaded
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-126-and recursively preprocessed as a Salad document. The external imported
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-128-URI for processing the imported document must be the URI used to retrieve the
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:129:imported document. The `$mixin` URI must not include a document fragment.
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-130-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:131:Once loaded and processed, the `$mixin` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-132-structure by the object or array yielded from the import operation.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-134-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md:135:the target document. This indicates that the `$mixin` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/import_include.md-136-replaced by only the object with the appropriate fragment identifier.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res.yml-23-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res.yml:24: * If a reference URI begins with a namespace prefix declared in `$namespaces`
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res.yml-25- followed by a colon `:`, the prefix and colon must be replaced by the
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res.yml:26: namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/link_res.yml-27-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-179-If a document consists of a root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md:180:fields `$base`, `$namespaces`, `$schemas`, and `$graph`:
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-181-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md:182: * `$base`: Must be a string. Set the base URI for the document used to
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-183- resolve relative references.
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-184-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md:185: * `$namespaces`: Must be an object with strings as values. The keys of
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-186- the object are namespace prefixes used in the document; the values of
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-188-
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md:189: * `$schemas`: Must be an array of strings. This field may list URI
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-190- references to documents in RDF-XML format which will be queried for RDF
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-199-If a document consists of a single root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md:200:field `$graph`. This field must be an array of objects. If present, this
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-201-field holds the primary content of the document. A document that consists
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-258-depth-first. For each visited object, field names, identifier fields, link
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md:259:fields, vocabulary fields, and `$import` and `$include` directives must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.0/salad/schema_salad/metaschema/salad.md-260-processed as described in this section. The order of traversal of child
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/CommandLineTool.yml-113- * Added explicit defaults for [ResourceRequirement](#ResourceRequirement)s.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/CommandLineTool.yml:114: * [Made explicit](#Generic_execution_process) that the `$namespaces` of
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/CommandLineTool.yml-115- the top level CWL document are also available to the input object as
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/CommandLineTool.yml-677- be an absolute path, otherwise it is an error. If the program does not
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/CommandLineTool.yml:678: include a path separator, search the `$PATH` variable in the runtime
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/CommandLineTool.yml-679- environment of the workflow runner find the absolute path of the
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/Process.yml-270- File format ontologies may be provided in the "$schema" metadata at the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/Process.yml:271: root of the document. If no ontologies are specified in `$schema`, the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/Process.yml-272- runtime may perform exact file format matches.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1/Workflow.yml-96- the process with the `id` of `#main` is chosen.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/Workflow.yml:97: * [Made explicit](#Generic_execution_process) that the `$namespaces` of
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/Workflow.yml-98- the top level CWL document are also available to the input object as
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-304-additional fields on any object. Such extensions fields must use a namespace
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:305:prefix listed in the `$namespaces` section of the document as described in the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-306-[Schema Salad specification](SchemaSalad.html#Explicit_context).
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-310-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:311:# Execution model
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-312-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:313:## Execution concepts
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-314-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-370-1. Load, process and validate a CWL document, yielding one or more process objects.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:371:The [`$namespaces`](SchemaSalad.html#Explicit_context) present in the CWL document
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-372-are also used when validating and processing the input object.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:373:1. If there are multiple process objects (due to [`$graph`](SchemaSalad.html#Document_graph))
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-374-and which process object to start with is not specified in the input object (via
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-426-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:427:Parameter references are denoted by the syntax `$(...)` and may be used in any
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-428-field permitting the pseudo-type `Expression`, as specified by this document.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-517-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:518:Expressions are denoted by the syntax `$(...)` or `${...}`. A code
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:519:fragment wrapped in the `$(...)` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-520-[ECMAScript expression](http://www.ecma-international.org/ecma-262/5.1/#sec-11). A
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:521:code fragment wrapped in the `${...}` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-522-[ECMAScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-584-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:585:`$XDG_DATA_HOME/commonwl/` (usually `$HOME/.local/share/commonwl`)
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-586-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md:587:`$XDG_DATA_HOME` is from the [XDG Base Directory
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/concepts.md-588-Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html)
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/invocation.md-126-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/invocation.md:127:## Execution
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/invocation.md-128-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/ident_res.yml-19- * If an identifier URI begins with a namespace prefix declared in
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/ident_res.yml:20: `$namespaces` followed by a colon `:`, the prefix and colon must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/ident_res.yml:21: replaced by the namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/ident_res.yml-22-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-2-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:3:During preprocessing traversal, an implementation must resolve `$import`
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:4:directives. An `$import` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:5:field `$import` specifying resource by URI string. It is an error if there
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:6:are additional fields in the `$import` object, such additional fields must
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-7-be ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-11-loading from `file`, `http` and `https` resources. The URI referenced by
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:12:`$import` must be loaded and recursively preprocessed as a Salad document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-13-The external imported document does not inherit the context of the
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-15-document must be the URI used to retrieve the imported document. If the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:16:`$import` URI includes a document fragment, the fragment must be excluded
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-17-from the base URI used to preprocess the imported document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-18-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:19:Once loaded and processed, the `$import` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-20-structure by the object or array yielded from the import operation.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-22-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:23:the target document. This indicates that the `$import` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-24-replaced by only the object with the appropriate fragment identifier.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-64-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:65:During preprocessing traversal, an implementation must resolve `$include`
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:66:directives. An `$include` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:67:field `$include` specifying a URI string. It is an error if there are
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:68:additional fields in the `$include` object, such additional fields must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-69-ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-71-The URI string must be resolved to an absolute URI using the link
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:72:resolution rules described previously. The URI referenced by `$include` must
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-73-be loaded as a text data. Implementations must support loading from
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-77-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:78:Once loaded, the `$include` node is replaced in the document structure by a
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-79-string containing the text data loaded from the resource.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-116-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:117:During preprocessing traversal, an implementation must resolve `$mixin`
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:118:directives. An `$mixin` directive is an object consisting of the field
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:119:`$mixin` specifying resource by URI string. If there are additional fields in
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:120:the `$mixin` object, these fields override fields in the object which is loaded
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:121:from the `$mixin` URI.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-122-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-124-rules described previously. Implementations must support loading from `file`,
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:125:`http` and `https` resources. The URI referenced by `$mixin` must be loaded
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-126-and recursively preprocessed as a Salad document. The external imported
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-128-URI for processing the imported document must be the URI used to retrieve the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:129:imported document. The `$mixin` URI must not include a document fragment.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-130-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:131:Once loaded and processed, the `$mixin` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-132-structure by the object or array yielded from the import operation.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-134-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md:135:the target document. This indicates that the `$mixin` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/import_include.md-136-replaced by only the object with the appropriate fragment identifier.
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/link_res.yml-23-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/link_res.yml:24: * If a reference URI begins with a namespace prefix declared in `$namespaces`
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/link_res.yml-25- followed by a colon `:`, the prefix and colon must be replaced by the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/link_res.yml:26: namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/link_res.yml-27-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-179-If a document consists of a root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md:180:fields `$base`, `$namespaces`, `$schemas`, and `$graph`:
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-181-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md:182: * `$base`: Must be a string. Set the base URI for the document used to
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-183- resolve relative references.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-184-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md:185: * `$namespaces`: Must be an object with strings as values. The keys of
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-186- the object are namespace prefixes used in the document; the values of
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-188-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md:189: * `$schemas`: Must be an array of strings. This field may list URI
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-190- references to documents in RDF-XML format which will be queried for RDF
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-199-If a document consists of a single root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md:200:field `$graph`. This field must be an array of objects. If present, this
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-201-field holds the primary content of the document. A document that consists
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-258-depth-first. For each visited object, field names, identifier fields, link
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md:259:fields, vocabulary fields, and `$import` and `$include` directives must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.1/salad/schema_salad/metaschema/salad.md-260-processed as described in this section. The order of traversal of child
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/CommandLineTool.yml-670- be an absolute path, otherwise it is an error. If the program does not
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/CommandLineTool.yml:671: include a path separator, search the `$PATH` variable in the runtime
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/CommandLineTool.yml-672- environment of the workflow runner find the absolute path of the
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/Process.yml-269- File format ontologies may be provided in the "$schema" metadata at the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/Process.yml:270: root of the document. If no ontologies are specified in `$schema`, the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/Process.yml-271- runtime may perform exact file format matches.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-304-additional fields on any object. Such extensions fields must use a namespace
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md:305:prefix listed in the `$namespaces` section of the document as described in the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-306-[Schema Salad specification](SchemaSalad.html#Explicit_context).
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-310-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md:311:# Execution model
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-312-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md:313:## Execution concepts
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-314-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-370-1. Load, process and validate a CWL document, yielding one or more process objects.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md:371:1. If there are multiple process objects (due to [`$graph`](SchemaSalad.html#Document_graph))
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-372-and which process object to start with is not specified in the input object (via
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-424-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md:425:Parameter references are denoted by the syntax `$(...)` and may be used in any
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-426-field permitting the pseudo-type `Expression`, as specified by this document.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-515-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md:516:Expressions are denoted by the syntax `$(...)` or `${...}`. A code
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md:517:fragment wrapped in the `$(...)` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-518-[ECMAScript expression](http://www.ecma-international.org/ecma-262/5.1/#sec-11). A
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md:519:code fragment wrapped in the `${...}` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-520-[ECMAScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13)
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-582-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md:583:`$XDG_DATA_HOME/commonwl/` (usually `$HOME/.local/share/commonwl`)
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-584-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md:585:`$XDG_DATA_HOME` is from the [XDG Base Directory
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/concepts.md-586-Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/invocation.md-126-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/invocation.md:127:## Execution
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/invocation.md-128-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/ident_res.yml-19- * If an identifier URI begins with a namespace prefix declared in
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/ident_res.yml:20: `$namespaces` followed by a colon `:`, the prefix and colon must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/ident_res.yml:21: replaced by the namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/ident_res.yml-22-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-2-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:3:During preprocessing traversal, an implementation must resolve `$import`
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:4:directives. An `$import` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:5:field `$import` specifying resource by URI string. It is an error if there
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:6:are additional fields in the `$import` object, such additional fields must
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-7-be ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-11-loading from `file`, `http` and `https` resources. The URI referenced by
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:12:`$import` must be loaded and recursively preprocessed as a Salad document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-13-The external imported document does not inherit the context of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-15-document must be the URI used to retrieve the imported document. If the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:16:`$import` URI includes a document fragment, the fragment must be excluded
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-17-from the base URI used to preprocess the imported document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-18-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:19:Once loaded and processed, the `$import` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-20-structure by the object or array yielded from the import operation.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-22-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:23:the target document. This indicates that the `$import` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-24-replaced by only the object with the appropriate fragment identifier.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-64-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:65:During preprocessing traversal, an implementation must resolve `$include`
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:66:directives. An `$include` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:67:field `$include` specifying a URI string. It is an error if there are
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:68:additional fields in the `$include` object, such additional fields must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-69-ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-71-The URI string must be resolved to an absolute URI using the link
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:72:resolution rules described previously. The URI referenced by `$include` must
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-73-be loaded as a text data. Implementations must support loading from
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-77-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:78:Once loaded, the `$include` node is replaced in the document structure by a
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-79-string containing the text data loaded from the resource.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-116-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:117:During preprocessing traversal, an implementation must resolve `$mixin`
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:118:directives. An `$mixin` directive is an object consisting of the field
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:119:`$mixin` specifying resource by URI string. If there are additional fields in
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:120:the `$mixin` object, these fields override fields in the object which is loaded
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:121:from the `$mixin` URI.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-122-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-124-rules described previously. Implementations must support loading from `file`,
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:125:`http` and `https` resources. The URI referenced by `$mixin` must be loaded
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-126-and recursively preprocessed as a Salad document. The external imported
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-128-URI for processing the imported document must be the URI used to retrieve the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:129:imported document. The `$mixin` URI must not include a document fragment.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-130-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:131:Once loaded and processed, the `$mixin` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-132-structure by the object or array yielded from the import operation.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-134-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md:135:the target document. This indicates that the `$mixin` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/import_include.md-136-replaced by only the object with the appropriate fragment identifier.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/link_res.yml-23-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/link_res.yml:24: * If a reference URI begins with a namespace prefix declared in `$namespaces`
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/link_res.yml-25- followed by a colon `:`, the prefix and colon must be replaced by the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/link_res.yml:26: namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/link_res.yml-27-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-179-If a document consists of a root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md:180:fields `$base`, `$namespaces`, `$schemas`, and `$graph`:
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-181-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md:182: * `$base`: Must be a string. Set the base URI for the document used to
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-183- resolve relative references.
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-184-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md:185: * `$namespaces`: Must be an object with strings as values. The keys of
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-186- the object are namespace prefixes used in the document; the values of
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-188-
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md:189: * `$schemas`: Must be an array of strings. This field may list URI
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-190- references to documents in RDF-XML format which will be queried for RDF
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-199-If a document consists of a single root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md:200:field `$graph`. This field must be an array of objects. If present, this
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-201-field holds the primary content of the document. A document that consists
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cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-258-depth-first. For each visited object, field names, identifier fields, link
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md:259:fields, vocabulary fields, and `$import` and `$include` directives must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.1.0-dev1/salad/schema_salad/metaschema/salad.md-260-processed as described in this section. The order of traversal of child
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/CommandLineTool.yml-648- be an absolute path, otherwise it is an error. If the program does not
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/CommandLineTool.yml:649: include a path separator, search the `$PATH` variable in the runtime
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/CommandLineTool.yml-650- environment of the workflow runner find the absolute path of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/Process.yml-276- File format ontologies may be provided in the "$schema" metadata at the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/Process.yml:277: root of the document. If no ontologies are specified in `$schema`, the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/Process.yml-278- runtime may perform exact file format matches.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/Process.yml-920- - Type definitions may be shared by defining them in a file and then
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/Process.yml:921: `$include`-ing them in the `types` field.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/Process.yml-922- - A file can contain a list of type definitions
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-317-additional fields on any object. Such extensions fields must use a namespace
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:318:prefix listed in the `$namespaces` section of the document as described in the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-319-[Schema Salad specification](SchemaSalad.html#Explicit_context).
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-321-It is recommended that concepts from schema.org are used whenever possible.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:322:For the `$schema` field we recommend their RDF encoding: http://schema.org/version/latest/schema.rdf
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-323-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-342-A "$graph" document does not have a process object at the root.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:343:Instead there is a [`$graph`](SchemaSalad.html#Document_graph) field
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-344-which consists of a list of process objects. Each process object must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-345-have an `id` field. Workflow `run` fields cross-reference other
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:346:processes in the document `$graph` using the `id` of the process
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-347-object.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-359-entry point. If there is no top-level process object (as in the case
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:360:of `$graph`) then the runner must choose the process object with an id
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-361-of `#main`. If there is no `#main` object, the runner must return an
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-363-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:364:# Execution model
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-365-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:366:## Execution concepts
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-367-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-429-1. Load, process and validate a CWL document, yielding one or more process objects.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:430:The [`$namespaces`](SchemaSalad.html#Explicit_context) present in the CWL document
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-431-are also used when validating and processing the input object.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:432:1. If there are multiple process objects (due to [`$graph`](SchemaSalad.html#Document_graph))
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-433-and which process object to start with is not specified in the input object (via
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-485-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:486:Parameter references are denoted by the syntax `$(...)` and may be used in any
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-487-field permitting the pseudo-type `Expression`, as specified by this document.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-564-When text embedded in a CWL file represents code for another
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:565:programming language, the use of `$(...)` (and `${...}` in the case of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-566-expressions) may conflict with the syntax of that language. For
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:567:example, when writing shell scripts, `$(...)` is used to execute a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-568-command in a subshell and replace a portion of the command line with
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-575-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:576: 1. The substrings `\$(` and `\${` are replaced by `$(` and `${`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-577- respectively. No parameter or expression evaluation
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-604-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:605:Expressions are denoted by the syntax `$(...)` or `${...}`. A code
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:606:fragment wrapped in the `$(...)` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-607-[ECMAScript expression](http://www.ecma-international.org/ecma-262/5.1/#sec-11). A
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:608:code fragment wrapped in the `${...}` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-609-[ECMAScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-673-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:674:Then check `$XDG_DATA_HOME/commonwl/`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-675-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-676-If the `XDG_DATA_HOME` environment variable is unset, its default value is
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:677:`$HOME/.local/share` (That is to say, check `$HOME/.local/share/commonwl`)
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-678-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md:679:`$XDG_DATA_HOME` and `$XDG_DATA_DIRS` are from the [XDG Base Directory
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/concepts.md-680-Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/invocation.md-128-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/invocation.md:129:## Execution
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/invocation.md-130-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/ident_res.yml-36- * If an identifier URI begins with a namespace prefix declared in
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/ident_res.yml:37: `$namespaces` followed by a colon `:`, the prefix and colon must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/ident_res.yml:38: replaced by the namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/ident_res.yml-39-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-2-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:3:During preprocessing traversal, an implementation must resolve `$import`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:4:directives. An `$import` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:5:field `$import` specifying resource by URI string. It is an error if there
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:6:are additional fields in the `$import` object, such additional fields must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-7-be ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-11-loading from `file`, `http` and `https` resources. The URI referenced by
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:12:`$import` must be loaded and recursively preprocessed as a Salad document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-13-The external imported document does not inherit the context of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-15-document must be the URI used to retrieve the imported document. If the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:16:`$import` URI includes a document fragment, the fragment must be excluded
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-17-from the base URI used to preprocess the imported document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-18-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:19:Once loaded and processed, the `$import` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-20-structure by the object or array yielded from the import operation.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-22-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:23:the target document. This indicates that the `$import` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-24-replaced by only the object with the appropriate fragment identifier.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-64-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:65:During preprocessing traversal, an implementation must resolve `$include`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:66:directives. An `$include` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:67:field `$include` specifying a URI string. It is an error if there are
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:68:additional fields in the `$include` object, such additional fields must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-69-ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-71-The URI string must be resolved to an absolute URI using the link
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:72:resolution rules described previously. The URI referenced by `$include` must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-73-be loaded as a text data. Implementations must support loading from
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-77-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md:78:Once loaded, the `$include` node is replaced in the document structure by a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/import_include.md-79-string containing the text data loaded from the resource.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/link_res.yml-23-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/link_res.yml:24: * If a reference URI begins with a namespace prefix declared in `$namespaces`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/link_res.yml-25- followed by a colon `:`, the prefix and colon must be replaced by the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/link_res.yml:26: namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/link_res.yml-27-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/metaschema.yml-48- 1. The document root must be an object or a list. If the document root is an
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/metaschema.yml:49: object containing the field `$graph` (which must be a list of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/metaschema.yml-50- objects), then validation applies to each object in the list.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/metaschema.yml-71- which contain a CWL parameter reference or expression in the form
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/metaschema.yml:72: `$(...)` or `${...}`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/metaschema.yml-73-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-84-* Add *secondaryFilesDSL* micro DSL (domain specific language) to convert text strings to a secondaryFiles record type used in CWL
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md:85:* The `$mixin` feature has been removed from the specification, as it
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-86- is poorly documented, not included in conformance testing,
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-191-If a document consists of a root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md:192:fields `$base`, `$namespaces`, `$schemas`, and `$graph`:
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-193-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md:194: * `$base`: Must be a string. Set the base URI for the document used to
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-195- resolve relative references.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-196-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md:197: * `$namespaces`: Must be an object with strings as values. The keys of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-198- the object are namespace prefixes used in the document; the values of
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-200-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md:201: * `$schemas`: Must be an array of strings. This field may list URI
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-202- references to documents in RDF-XML format which will be queried for RDF
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-211-If a document consists of a single root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md:212:field `$graph`. This field must be an array of objects. If present, this
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-213-field holds the primary content of the document. A document that consists
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-303-depth-first. For each visited object, field names, identifier fields, link
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md:304:fields, vocabulary fields, and `$import` and `$include` directives must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2/salad/schema_salad/metaschema/salad.md-305-processed as described in this section. The order of traversal of child
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/CommandLineTool.yml-611- be an absolute path, otherwise it is an error. If the program does not
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/CommandLineTool.yml:612: include a path separator, search the `$PATH` variable in the runtime
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/CommandLineTool.yml-613- environment of the workflow runner find the absolute path of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/Process.yml-272- File format ontologies may be provided in the "$schema" metadata at the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/Process.yml:273: root of the document. If no ontologies are specified in `$schema`, the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/Process.yml-274- runtime may perform exact file format matches.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-303-additional fields on any object. Such extensions fields must use a namespace
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:304:prefix listed in the `$namespaces` section of the document as described in the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-305-[Schema Salad specification](SchemaSalad.html#Explicit_context).
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-307-It is recommended that concepts from schema.org are used whenever possible.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:308:For the `$schema` field we recommend their RDF encoding: http://schema.org/version/latest/schema.rdf
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-309-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-312-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:313:# Execution model
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-314-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:315:## Execution concepts
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-316-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-370-1. Load, process and validate a CWL document, yielding one or more process objects.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:371:The [`$namespaces`](SchemaSalad.html#Explicit_context) present in the CWL document
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-372-are also used when validating and processing the input object.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:373:1. If there are multiple process objects (due to [`$graph`](SchemaSalad.html#Document_graph))
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-374-and which process object to start with is not specified in the input object (via
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-426-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:427:Parameter references are denoted by the syntax `$(...)` and may be used in any
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-428-field permitting the pseudo-type `Expression`, as specified by this document.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-523-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:524:Expressions are denoted by the syntax `$(...)` or `${...}`. A code
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:525:fragment wrapped in the `$(...)` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-526-[ECMAScript expression](http://www.ecma-international.org/ecma-262/5.1/#sec-11). A
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:527:code fragment wrapped in the `${...}` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-528-[ECMAScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-592-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:593:Then check `$XDG_DATA_HOME/commonwl/`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-594-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-595-If the `XDG_DATA_HOME` environment variable is unset, its default value is
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:596:`$HOME/.local/share` (That is to say, check `$HOME/.local/share/commonwl`)
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-597-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md:598:`$XDG_DATA_HOME` and `$XDG_DATA_DIRS` are from the [XDG Base Directory
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/concepts.md-599-Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/invocation.md-128-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/invocation.md:129:## Execution
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/invocation.md-130-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/ident_res.yml-36- * If an identifier URI begins with a namespace prefix declared in
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/ident_res.yml:37: `$namespaces` followed by a colon `:`, the prefix and colon must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/ident_res.yml:38: replaced by the namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/ident_res.yml-39-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-2-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:3:During preprocessing traversal, an implementation must resolve `$import`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:4:directives. An `$import` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:5:field `$import` specifying resource by URI string. It is an error if there
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:6:are additional fields in the `$import` object, such additional fields must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-7-be ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-11-loading from `file`, `http` and `https` resources. The URI referenced by
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:12:`$import` must be loaded and recursively preprocessed as a Salad document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-13-The external imported document does not inherit the context of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-15-document must be the URI used to retrieve the imported document. If the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:16:`$import` URI includes a document fragment, the fragment must be excluded
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-17-from the base URI used to preprocess the imported document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-18-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:19:Once loaded and processed, the `$import` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-20-structure by the object or array yielded from the import operation.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-22-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:23:the target document. This indicates that the `$import` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-24-replaced by only the object with the appropriate fragment identifier.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-64-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:65:During preprocessing traversal, an implementation must resolve `$include`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:66:directives. An `$include` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:67:field `$include` specifying a URI string. It is an error if there are
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:68:additional fields in the `$include` object, such additional fields must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-69-ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-71-The URI string must be resolved to an absolute URI using the link
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:72:resolution rules described previously. The URI referenced by `$include` must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-73-be loaded as a text data. Implementations must support loading from
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-77-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md:78:Once loaded, the `$include` node is replaced in the document structure by a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/import_include.md-79-string containing the text data loaded from the resource.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/link_res.yml-23-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/link_res.yml:24: * If a reference URI begins with a namespace prefix declared in `$namespaces`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/link_res.yml-25- followed by a colon `:`, the prefix and colon must be replaced by the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/link_res.yml:26: namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/link_res.yml-27-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/metaschema.yml-48- 1. The document root must be an object or a list. If the document root is an
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/metaschema.yml:49: object containing the field `$graph` (which must be a list of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/metaschema.yml-50- objects), then validation applies to each object in the list.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/metaschema.yml-71- which contain a CWL parameter reference or expression in the form
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/metaschema.yml:72: `$(...)` or `${...}`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/metaschema.yml-73-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-84-* Add *secondaryFilesDSL* micro DSL (domain specific language) to convert text strings to a secondaryFiles record type used in CWL
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md:85:* The `$mixin` feature has been removed from the specification, as it
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-86- is poorly documented, not included in conformance testing,
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-191-If a document consists of a root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md:192:fields `$base`, `$namespaces`, `$schemas`, and `$graph`:
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-193-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md:194: * `$base`: Must be a string. Set the base URI for the document used to
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-195- resolve relative references.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-196-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md:197: * `$namespaces`: Must be an object with strings as values. The keys of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-198- the object are namespace prefixes used in the document; the values of
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-200-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md:201: * `$schemas`: Must be an array of strings. This field may list URI
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-202- references to documents in RDF-XML format which will be queried for RDF
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-211-If a document consists of a single root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md:212:field `$graph`. This field must be an array of objects. If present, this
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-213-field holds the primary content of the document. A document that consists
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-303-depth-first. For each visited object, field names, identifier fields, link
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md:304:fields, vocabulary fields, and `$import` and `$include` directives must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev2/salad/schema_salad/metaschema/salad.md-305-processed as described in this section. The order of traversal of child
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/CommandLineTool.yml-613- be an absolute path, otherwise it is an error. If the program does not
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/CommandLineTool.yml:614: include a path separator, search the `$PATH` variable in the runtime
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/CommandLineTool.yml-615- environment of the workflow runner find the absolute path of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/Process.yml-273- File format ontologies may be provided in the "$schema" metadata at the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/Process.yml:274: root of the document. If no ontologies are specified in `$schema`, the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/Process.yml-275- runtime may perform exact file format matches.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-303-additional fields on any object. Such extensions fields must use a namespace
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:304:prefix listed in the `$namespaces` section of the document as described in the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-305-[Schema Salad specification](SchemaSalad.html#Explicit_context).
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-307-It is recommended that concepts from schema.org are used whenever possible.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:308:For the `$schema` field we recommend their RDF encoding: http://schema.org/version/latest/schema.rdf
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-309-
##############################################
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-312-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:313:# Execution model
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-314-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:315:## Execution concepts
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-316-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-370-1. Load, process and validate a CWL document, yielding one or more process objects.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:371:The [`$namespaces`](SchemaSalad.html#Explicit_context) present in the CWL document
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-372-are also used when validating and processing the input object.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:373:1. If there are multiple process objects (due to [`$graph`](SchemaSalad.html#Document_graph))
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-374-and which process object to start with is not specified in the input object (via
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-426-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:427:Parameter references are denoted by the syntax `$(...)` and may be used in any
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-428-field permitting the pseudo-type `Expression`, as specified by this document.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-523-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:524:Expressions are denoted by the syntax `$(...)` or `${...}`. A code
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:525:fragment wrapped in the `$(...)` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-526-[ECMAScript expression](http://www.ecma-international.org/ecma-262/5.1/#sec-11). A
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:527:code fragment wrapped in the `${...}` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-528-[ECMAScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-592-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:593:Then check `$XDG_DATA_HOME/commonwl/`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-594-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-595-If the `XDG_DATA_HOME` environment variable is unset, its default value is
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:596:`$HOME/.local/share` (That is to say, check `$HOME/.local/share/commonwl`)
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-597-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md:598:`$XDG_DATA_HOME` and `$XDG_DATA_DIRS` are from the [XDG Base Directory
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/concepts.md-599-Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/invocation.md-128-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/invocation.md:129:## Execution
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/invocation.md-130-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/ident_res.yml-36- * If an identifier URI begins with a namespace prefix declared in
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/ident_res.yml:37: `$namespaces` followed by a colon `:`, the prefix and colon must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/ident_res.yml:38: replaced by the namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/ident_res.yml-39-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-2-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:3:During preprocessing traversal, an implementation must resolve `$import`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:4:directives. An `$import` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:5:field `$import` specifying resource by URI string. It is an error if there
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:6:are additional fields in the `$import` object, such additional fields must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-7-be ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-11-loading from `file`, `http` and `https` resources. The URI referenced by
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:12:`$import` must be loaded and recursively preprocessed as a Salad document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-13-The external imported document does not inherit the context of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-15-document must be the URI used to retrieve the imported document. If the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:16:`$import` URI includes a document fragment, the fragment must be excluded
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-17-from the base URI used to preprocess the imported document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-18-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:19:Once loaded and processed, the `$import` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-20-structure by the object or array yielded from the import operation.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-22-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:23:the target document. This indicates that the `$import` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-24-replaced by only the object with the appropriate fragment identifier.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-64-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:65:During preprocessing traversal, an implementation must resolve `$include`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:66:directives. An `$include` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:67:field `$include` specifying a URI string. It is an error if there are
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:68:additional fields in the `$include` object, such additional fields must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-69-ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-71-The URI string must be resolved to an absolute URI using the link
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:72:resolution rules described previously. The URI referenced by `$include` must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-73-be loaded as a text data. Implementations must support loading from
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-77-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md:78:Once loaded, the `$include` node is replaced in the document structure by a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/import_include.md-79-string containing the text data loaded from the resource.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/link_res.yml-23-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/link_res.yml:24: * If a reference URI begins with a namespace prefix declared in `$namespaces`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/link_res.yml-25- followed by a colon `:`, the prefix and colon must be replaced by the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/link_res.yml:26: namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/link_res.yml-27-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/metaschema.yml-48- 1. The document root must be an object or a list. If the document root is an
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/metaschema.yml:49: object containing the field `$graph` (which must be a list of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/metaschema.yml-50- objects), then validation applies to each object in the list.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/metaschema.yml-71- which contain a CWL parameter reference or expression in the form
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/metaschema.yml:72: `$(...)` or `${...}`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/metaschema.yml-73-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-84-* Add *secondaryFilesDSL* micro DSL (domain specific language) to convert text strings to a secondaryFiles record type used in CWL
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md:85:* The `$mixin` feature has been removed from the specification, as it
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-86- is poorly documented, not included in conformance testing,
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-191-If a document consists of a root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md:192:fields `$base`, `$namespaces`, `$schemas`, and `$graph`:
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-193-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md:194: * `$base`: Must be a string. Set the base URI for the document used to
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-195- resolve relative references.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-196-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md:197: * `$namespaces`: Must be an object with strings as values. The keys of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-198- the object are namespace prefixes used in the document; the values of
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-200-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md:201: * `$schemas`: Must be an array of strings. This field may list URI
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-202- references to documents in RDF-XML format which will be queried for RDF
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-211-If a document consists of a single root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md:212:field `$graph`. This field must be an array of objects. If present, this
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-213-field holds the primary content of the document. A document that consists
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-303-depth-first. For each visited object, field names, identifier fields, link
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md:304:fields, vocabulary fields, and `$import` and `$include` directives must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev3/salad/schema_salad/metaschema/salad.md-305-processed as described in this section. The order of traversal of child
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/CommandLineTool.yml-648- be an absolute path, otherwise it is an error. If the program does not
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/CommandLineTool.yml:649: include a path separator, search the `$PATH` variable in the runtime
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/CommandLineTool.yml-650- environment of the workflow runner find the absolute path of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/Process.yml-274- File format ontologies may be provided in the "$schema" metadata at the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/Process.yml:275: root of the document. If no ontologies are specified in `$schema`, the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/Process.yml-276- runtime may perform exact file format matches.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/Process.yml-918- - Type definitions may be shared by defining them in a file and then
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/Process.yml:919: `$include`-ing them in the `types` field.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/Process.yml-920- - A file can contain a list of type definitions
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-303-additional fields on any object. Such extensions fields must use a namespace
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:304:prefix listed in the `$namespaces` section of the document as described in the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-305-[Schema Salad specification](SchemaSalad.html#Explicit_context).
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-307-It is recommended that concepts from schema.org are used whenever possible.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:308:For the `$schema` field we recommend their RDF encoding: http://schema.org/version/latest/schema.rdf
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-309-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-312-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:313:# Execution model
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-314-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:315:## Execution concepts
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-316-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-370-1. Load, process and validate a CWL document, yielding one or more process objects.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:371:The [`$namespaces`](SchemaSalad.html#Explicit_context) present in the CWL document
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-372-are also used when validating and processing the input object.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:373:1. If there are multiple process objects (due to [`$graph`](SchemaSalad.html#Document_graph))
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-374-and which process object to start with is not specified in the input object (via
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-426-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:427:Parameter references are denoted by the syntax `$(...)` and may be used in any
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-428-field permitting the pseudo-type `Expression`, as specified by this document.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-505-When text embedded in a CWL file represents code for another
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:506:programming language, the use of `$(...)` (and `${...}` in the case of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-507-expressions) may conflict with the syntax of that language. For
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:508:example, when writing shell scripts, `$(...)` is used to execute a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-509-command in a subshell and replace a portion of the command line with
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-516-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:517: 1. The substrings `\$(` and `\${` are replaced by `$(` and `${`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-518- respectively. No parameter or expression evaluation
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-545-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:546:Expressions are denoted by the syntax `$(...)` or `${...}`. A code
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:547:fragment wrapped in the `$(...)` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-548-[ECMAScript expression](http://www.ecma-international.org/ecma-262/5.1/#sec-11). A
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:549:code fragment wrapped in the `${...}` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-550-[ECMAScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-614-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:615:Then check `$XDG_DATA_HOME/commonwl/`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-616-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-617-If the `XDG_DATA_HOME` environment variable is unset, its default value is
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:618:`$HOME/.local/share` (That is to say, check `$HOME/.local/share/commonwl`)
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-619-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md:620:`$XDG_DATA_HOME` and `$XDG_DATA_DIRS` are from the [XDG Base Directory
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/concepts.md-621-Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/invocation.md-128-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/invocation.md:129:## Execution
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/invocation.md-130-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/ident_res.yml-36- * If an identifier URI begins with a namespace prefix declared in
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/ident_res.yml:37: `$namespaces` followed by a colon `:`, the prefix and colon must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/ident_res.yml:38: replaced by the namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/ident_res.yml-39-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-2-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:3:During preprocessing traversal, an implementation must resolve `$import`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:4:directives. An `$import` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:5:field `$import` specifying resource by URI string. It is an error if there
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:6:are additional fields in the `$import` object, such additional fields must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-7-be ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-11-loading from `file`, `http` and `https` resources. The URI referenced by
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:12:`$import` must be loaded and recursively preprocessed as a Salad document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-13-The external imported document does not inherit the context of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-15-document must be the URI used to retrieve the imported document. If the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:16:`$import` URI includes a document fragment, the fragment must be excluded
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-17-from the base URI used to preprocess the imported document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-18-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:19:Once loaded and processed, the `$import` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-20-structure by the object or array yielded from the import operation.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-22-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:23:the target document. This indicates that the `$import` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-24-replaced by only the object with the appropriate fragment identifier.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-64-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:65:During preprocessing traversal, an implementation must resolve `$include`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:66:directives. An `$include` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:67:field `$include` specifying a URI string. It is an error if there are
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:68:additional fields in the `$include` object, such additional fields must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-69-ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-71-The URI string must be resolved to an absolute URI using the link
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:72:resolution rules described previously. The URI referenced by `$include` must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-73-be loaded as a text data. Implementations must support loading from
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-77-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md:78:Once loaded, the `$include` node is replaced in the document structure by a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/import_include.md-79-string containing the text data loaded from the resource.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/link_res.yml-23-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/link_res.yml:24: * If a reference URI begins with a namespace prefix declared in `$namespaces`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/link_res.yml-25- followed by a colon `:`, the prefix and colon must be replaced by the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/link_res.yml:26: namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/link_res.yml-27-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/metaschema.yml-48- 1. The document root must be an object or a list. If the document root is an
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/metaschema.yml:49: object containing the field `$graph` (which must be a list of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/metaschema.yml-50- objects), then validation applies to each object in the list.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/metaschema.yml-71- which contain a CWL parameter reference or expression in the form
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/metaschema.yml:72: `$(...)` or `${...}`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/metaschema.yml-73-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-84-* Add *secondaryFilesDSL* micro DSL (domain specific language) to convert text strings to a secondaryFiles record type used in CWL
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md:85:* The `$mixin` feature has been removed from the specification, as it
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-86- is poorly documented, not included in conformance testing,
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-191-If a document consists of a root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md:192:fields `$base`, `$namespaces`, `$schemas`, and `$graph`:
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-193-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md:194: * `$base`: Must be a string. Set the base URI for the document used to
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-195- resolve relative references.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-196-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md:197: * `$namespaces`: Must be an object with strings as values. The keys of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-198- the object are namespace prefixes used in the document; the values of
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-200-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md:201: * `$schemas`: Must be an array of strings. This field may list URI
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-202- references to documents in RDF-XML format which will be queried for RDF
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-211-If a document consists of a single root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md:212:field `$graph`. This field must be an array of objects. If present, this
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-213-field holds the primary content of the document. A document that consists
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-303-depth-first. For each visited object, field names, identifier fields, link
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md:304:fields, vocabulary fields, and `$import` and `$include` directives must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev4/salad/schema_salad/metaschema/salad.md-305-processed as described in this section. The order of traversal of child
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/CommandLineTool.yml-648- be an absolute path, otherwise it is an error. If the program does not
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/CommandLineTool.yml:649: include a path separator, search the `$PATH` variable in the runtime
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/CommandLineTool.yml-650- environment of the workflow runner find the absolute path of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/Process.yml-275- File format ontologies may be provided in the "$schema" metadata at the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/Process.yml:276: root of the document. If no ontologies are specified in `$schema`, the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/Process.yml-277- runtime may perform exact file format matches.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/Process.yml-919- - Type definitions may be shared by defining them in a file and then
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/Process.yml:920: `$include`-ing them in the `types` field.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/Process.yml-921- - A file can contain a list of type definitions
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-317-additional fields on any object. Such extensions fields must use a namespace
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:318:prefix listed in the `$namespaces` section of the document as described in the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-319-[Schema Salad specification](SchemaSalad.html#Explicit_context).
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-321-It is recommended that concepts from schema.org are used whenever possible.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:322:For the `$schema` field we recommend their RDF encoding: http://schema.org/version/latest/schema.rdf
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-323-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-342-A "$graph" document does not have a process object at the root.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:343:Instead there is a [`$graph`](SchemaSalad.html#Document_graph) field
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-344-which consists of a list of process objects. Each process object must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-345-have an `id` field. Workflow `run` fields cross-reference other
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:346:processes in the document `$graph` using the `id` of the process
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-347-object.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-359-entry point. If there is no top-level process object (as in the case
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:360:of `$graph`) then the runner must choose the process object with an id
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-361-of `#main`. If there is no `#main` object, the runner must return an
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-363-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:364:# Execution model
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-365-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:366:## Execution concepts
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-367-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-429-1. Load, process and validate a CWL document, yielding one or more process objects.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:430:The [`$namespaces`](SchemaSalad.html#Explicit_context) present in the CWL document
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-431-are also used when validating and processing the input object.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:432:1. If there are multiple process objects (due to [`$graph`](SchemaSalad.html#Document_graph))
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-433-and which process object to start with is not specified in the input object (via
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-485-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:486:Parameter references are denoted by the syntax `$(...)` and may be used in any
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-487-field permitting the pseudo-type `Expression`, as specified by this document.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-564-When text embedded in a CWL file represents code for another
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:565:programming language, the use of `$(...)` (and `${...}` in the case of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-566-expressions) may conflict with the syntax of that language. For
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:567:example, when writing shell scripts, `$(...)` is used to execute a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-568-command in a subshell and replace a portion of the command line with
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-575-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:576: 1. The substrings `\$(` and `\${` are replaced by `$(` and `${`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-577- respectively. No parameter or expression evaluation
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-604-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:605:Expressions are denoted by the syntax `$(...)` or `${...}`. A code
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:606:fragment wrapped in the `$(...)` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-607-[ECMAScript expression](http://www.ecma-international.org/ecma-262/5.1/#sec-11). A
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:608:code fragment wrapped in the `${...}` syntax must be evaluated as a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-609-[ECMAScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-673-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:674:Then check `$XDG_DATA_HOME/commonwl/`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-675-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-676-If the `XDG_DATA_HOME` environment variable is unset, its default value is
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:677:`$HOME/.local/share` (That is to say, check `$HOME/.local/share/commonwl`)
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-678-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md:679:`$XDG_DATA_HOME` and `$XDG_DATA_DIRS` are from the [XDG Base Directory
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/concepts.md-680-Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html)
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/invocation.md-128-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/invocation.md:129:## Execution
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/invocation.md-130-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/ident_res.yml-36- * If an identifier URI begins with a namespace prefix declared in
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/ident_res.yml:37: `$namespaces` followed by a colon `:`, the prefix and colon must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/ident_res.yml:38: replaced by the namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/ident_res.yml-39-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-2-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:3:During preprocessing traversal, an implementation must resolve `$import`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:4:directives. An `$import` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:5:field `$import` specifying resource by URI string. It is an error if there
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:6:are additional fields in the `$import` object, such additional fields must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-7-be ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-11-loading from `file`, `http` and `https` resources. The URI referenced by
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:12:`$import` must be loaded and recursively preprocessed as a Salad document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-13-The external imported document does not inherit the context of the
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-15-document must be the URI used to retrieve the imported document. If the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:16:`$import` URI includes a document fragment, the fragment must be excluded
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-17-from the base URI used to preprocess the imported document.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-18-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:19:Once loaded and processed, the `$import` node is replaced in the document
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-20-structure by the object or array yielded from the import operation.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-22-URIs may reference document fragments which refer to specific an object in
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:23:the target document. This indicates that the `$import` node must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-24-replaced by only the object with the appropriate fragment identifier.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-64-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:65:During preprocessing traversal, an implementation must resolve `$include`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:66:directives. An `$include` directive is an object consisting of exactly one
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:67:field `$include` specifying a URI string. It is an error if there are
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:68:additional fields in the `$include` object, such additional fields must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-69-ignored.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-71-The URI string must be resolved to an absolute URI using the link
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:72:resolution rules described previously. The URI referenced by `$include` must
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-73-be loaded as a text data. Implementations must support loading from
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-77-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md:78:Once loaded, the `$include` node is replaced in the document structure by a
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/import_include.md-79-string containing the text data loaded from the resource.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/link_res.yml-23-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/link_res.yml:24: * If a reference URI begins with a namespace prefix declared in `$namespaces`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/link_res.yml-25- followed by a colon `:`, the prefix and colon must be replaced by the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/link_res.yml:26: namespace declared in `$namespaces`.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/link_res.yml-27-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/metaschema.yml-48- 1. The document root must be an object or a list. If the document root is an
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/metaschema.yml:49: object containing the field `$graph` (which must be a list of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/metaschema.yml-50- objects), then validation applies to each object in the list.
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/metaschema.yml-71- which contain a CWL parameter reference or expression in the form
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/metaschema.yml:72: `$(...)` or `${...}`
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/metaschema.yml-73-
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-84-* Add *secondaryFilesDSL* micro DSL (domain specific language) to convert text strings to a secondaryFiles record type used in CWL
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md:85:* The `$mixin` feature has been removed from the specification, as it
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-86- is poorly documented, not included in conformance testing,
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-191-If a document consists of a root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md:192:fields `$base`, `$namespaces`, `$schemas`, and `$graph`:
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-193-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md:194: * `$base`: Must be a string. Set the base URI for the document used to
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-195- resolve relative references.
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-196-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md:197: * `$namespaces`: Must be an object with strings as values. The keys of
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-198- the object are namespace prefixes used in the document; the values of
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-200-
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md:201: * `$schemas`: Must be an array of strings. This field may list URI
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-202- references to documents in RDF-XML format which will be queried for RDF
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-211-If a document consists of a single root object, this object may contain the
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md:212:field `$graph`. This field must be an array of objects. If present, this
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-213-field holds the primary content of the document. A document that consists
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cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-303-depth-first. For each visited object, field names, identifier fields, link
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md:304:fields, vocabulary fields, and `$import` and `$include` directives must be
cwltool-3.0.20200807132242/cwltool/schemas/v1.2.0-dev5/salad/schema_salad/metaschema/salad.md-305-processed as described in this section. The order of traversal of child
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cwltool-3.0.20200807132242/cwltool.egg-info/PKG-INFO-234- Process objects (CommandLineTool and Workflow) in a list in the
cwltool-3.0.20200807132242/cwltool.egg-info/PKG-INFO:235: ``$graph`` field. Cross references (such as ``run:`` and ``source:``
cwltool-3.0.20200807132242/cwltool.egg-info/PKG-INFO-236- fields) are updated to internal references within the new packed