guppy_basecaller: env/lib/python3.7/site-packages/cwltool/schemas/v1.1/CommandLineTool.yml annotate

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

rev	line source
0 26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1 saladVersion: v1.1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	2 $base: "https://w3id.org/cwl/cwl#"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	3
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	4 $namespaces:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	5 cwl: "https://w3id.org/cwl/cwl#"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	7 $graph:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	8
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	9 - name: CommandLineToolDoc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	10 type: documentation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	11 doc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	12 - \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	13 # Common Workflow Language (CWL) Command Line Tool Description, v1.1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	14
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	15 This version:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	16 * https://w3id.org/cwl/v1.1/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	17
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	18 Current version:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	19 * https://w3id.org/cwl/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	20 - "\n\n"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	21 - {$include: contrib.md}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	22 - "\n\n"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	23 - \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	24 # Abstract
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	25
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	26 A Command Line Tool is a non-interactive executable program that reads
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	27 some input, performs a computation, and terminates after producing some
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	28 output. Command line programs are a flexible unit of code sharing and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	29 reuse, unfortunately the syntax and input/output semantics among command
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	30 line programs is extremely heterogeneous. A common layer for describing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	31 the syntax and semantics of programs can reduce this incidental
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	32 complexity by providing a consistent way to connect programs together.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	33 This specification defines the Common Workflow Language (CWL) Command
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	34 Line Tool Description, a vendor-neutral standard for describing the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	35 syntax and input/output semantics of command line programs.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	36
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	37 - {$include: intro.md}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	38
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	39 - \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	40 ## Introduction to the CWL Command Line Tool standard v1.1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	41
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	42 This specification represents the latest development release from the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	43 CWL group. Since the v1.0 release, v1.1 introduces the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	44 following updates to the CWL Command Line Tool standard.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	45 Documents should use `cwlVersion: v1.1` to make use of new
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	46 syntax and features introduced in v1.1. Existing v1.0 documents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	47 should be trivially updatable by changing `cwlVersion`, however
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	48 CWL documents that relied on previously undefined or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	49 underspecified behavior may have slightly different behavior in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	50 v1.1.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	51
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	52 ## Changelog
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	53
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	54 * Clarify behavior around `ENTRYPOINT` and `CMD` in containers.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	55 * Clarify documentation around `valueFrom` and `null` inputs.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	56 * Default values for some fields are now expressed in the schema.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	57 * When defining record types with `CommandInputRecordSchema`, fields of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	58 type `File` may now include `format`, `loadContents`,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	59 `secondaryFiles` and `streamable`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	60 * `CommandInputRecordSchema`, `CommandOutputRecordSchema`,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	61 `CommandInputEnumSchema and `CommandInputArraySchema` now have an optional
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	62 `doc` field.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	63 * `inputBinding` has been added as an optional field for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	64 `CommandInputRecordSchema` (was previously in CWL `draft-3` but
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	65 disappeared in `v1.0`).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	66 * Any `doc` field may be an array of strings in addition to the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	67 previously allowed single string.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	68 * Addition of `stdin` type shortcut for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	69 [`CommandInputParameter`](#CommandInputParameter).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	70 * Clarify that the designated output directory should be empty
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	71 except for files or directories specified using
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	72 [InitialWorkDirRequirement](#InitialWorkDirRequirement).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	73 * Clarify semantics of `shellQuote`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	74 * Expressions are now allowed to evaluate to `null` or `Dirent` in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	75 [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	76 * Items in [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	77 are now allowed to be `null` and `array<File \| Directory>`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	78 * Clarify behavior of secondaryFiles on output.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	79 * [Addition](#Requirements_and_hints) of `cwl:requirements` field to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	80 input object documents.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	81 * Clarify behavior of `glob` for absolute paths and symlinks.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	82 * Clarify behavior of `glob` to include directories.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	83 * `secondaryFiles` can now be explicitly marked as `required` or not.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	84 * Clarify `CommandLineTool.arguments` documentation.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	85 * Clarify that `runtime.outdir` and `runtime.tmpdir` must be distinct
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	86 directories.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	87 * Clarify that unspecified details related to execution are left open to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	88 the platform.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	89 * Added `InputParameter.loadContents` field. Use of `loadContents` in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	90 `InputBinding` is deprecated; it is preserved for v1.0 backwards
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	91 compatability and will be removed in CWL v2.0.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	92 * [Added](#ToolTimeLimit) `ToolTimeLimit` feature, allows setting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	93 an upper limit on the execution time of a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	94 * [Added](#WorkReuse) `WorkReuse` feature, allowing to enable or disable the reuse
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	95 behavior for a particular tool or step for implementations that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	96 support reusing output from past work.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	97 * [Added](#NetworkAccess) `NetworkAccess` feature, allowing to indicate whether a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	98 process requires outgoing network access.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	99 * [Added](#InplaceUpdateRequirement) `InplaceUpdateRequirement` feature, allowing tools to directly
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	100 update files with `writable: true` in `InitialWorkDirRequirement`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	101 * [Added](#LoadListingRequirement) `LoadListingRequirement`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	102 and [loadListing](#LoadContents) to control whether and how
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	103 `Directory` listings should be loaded for use in expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	104 * The position field of the [CommandLineBinding](#CommandLineBinding) can
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	105 now be calculated from a CWL Expression.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	106 * The exit code of a CommandLineTool invocation is now
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	107 available to expressions in `outputEval` as `runtime.exitCode`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	108 * [Better explain](#map) the `map<…>` notation that has existed since v1.0.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	109 * Fixed schema error where the `type` field inside the `inputs` and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	110 `outputs` field was incorrectly listed as optional.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	111 * For multi-Process CWL documents, if no particular process is named then
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	112 the process with the `id` of `#main` is chosen.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	113 * Added explicit defaults for [ResourceRequirement](#ResourceRequirement)s.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	114 * [Made explicit](#Generic_execution_process) that the `$namespaces` of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	115 the top level CWL document are also available to the input object as
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	116 well.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	117 * Fields with type "Expression" no longer include "string" in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	118 the type union unless a string is semantically valid. Where
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	119 a bare string is not semantically valid, these fields must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	120 contain either a non-string value accepted by the field
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	121 type, or a valid expression which returns a value having one
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	122 of the the other types defined for that field.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	123
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	124 See also the [CWL Workflow Description, v1.1 changelog](Workflow.html#Changelog).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	125
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	126 ## Purpose
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	127
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	128 Standalone programs are a flexible and interoperable form of code reuse.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	129 Unlike monolithic applications, applications and analysis workflows which
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	130 are composed of multiple separate programs can be written in multiple
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	131 languages and execute concurrently on multiple hosts. However, POSIX
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	132 does not dictate computer-readable grammar or semantics for program input
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	133 and output, resulting in extremely heterogeneous command line grammar and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	134 input/output semantics among program. This is a particular problem in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	135 distributed computing (multi-node compute clusters) and virtualized
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	136 environments (such as Docker containers) where it is often necessary to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	137 provision resources such as input files before executing the program.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	138
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	139 Often this gap is filled by hard coding program invocation and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	140 implicitly assuming requirements will be met, or abstracting program
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	141 invocation with wrapper scripts or descriptor documents. Unfortunately,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	142 where these approaches are application or platform specific it creates a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	143 significant barrier to reproducibility and portability, as methods
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	144 developed for one platform must be manually ported to be used on new
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	145 platforms. Similarly it creates redundant work, as wrappers for popular
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	146 tools must be rewritten for each application or platform in use.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	147
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	148 The Common Workflow Language Command Line Tool Description is designed to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	149 provide a common standard description of grammar and semantics for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	150 invoking programs used in data-intensive fields such as Bioinformatics,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	151 Chemistry, Physics, Astronomy, and Statistics. This specification
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	152 attempts to define a precise data and execution model for Command Line Tools that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	153 can be implemented on a variety of computing platforms, ranging from a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	154 single workstation to cluster, grid, cloud, and high performance
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	155 computing platforms. Details related to execution of these programs not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	156 laid out in this specification are open to interpretation by the computing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	157 platform implementing this specification.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	158
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	159 - {$include: concepts.md}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	160 - {$include: invocation.md}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	161
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	162
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	163 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	164 name: EnvironmentDef
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	165 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	166 Define an environment variable that will be set in the runtime environment
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	167 by the workflow platform when executing the command line tool. May be the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	168 result of executing an expression, such as getting a parameter from input.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	169 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	170 - name: envName
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	171 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	172 doc: The environment variable name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	173 - name: envValue
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	174 type: [string, Expression]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	175 doc: The environment variable value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	176
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	177 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	178 name: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	179 extends: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	180 docParent: "#CommandInputParameter"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	181 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	182
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	183 When listed under `inputBinding` in the input schema, the term
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	184 "value" refers to the the corresponding value in the input object. For
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	185 binding objects listed in `CommandLineTool.arguments`, the term "value"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	186 refers to the effective value after evaluating `valueFrom`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	187
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	188 The binding behavior when building the command line depends on the data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	189 type of the value. If there is a mismatch between the type described by
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	190 the input schema and the effective value, such as resulting from an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	191 expression evaluation, an implementation must use the data type of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	192 effective value.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	193
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	194 - string: Add `prefix` and the string to the command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	195
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	196 - number: Add `prefix` and decimal representation to command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	197
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	198 - boolean: If true, add `prefix` to the command line. If false, add
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	199 nothing.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	200
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	201 - File: Add `prefix` and the value of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	202 [`File.path`](#File) to the command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	203
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	204 - Directory: Add `prefix` and the value of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	205 [`Directory.path`](#Directory) to the command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	206
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	207 - array: If `itemSeparator` is specified, add `prefix` and the join
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	208 the array into a single string with `itemSeparator` separating the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	209 items. Otherwise first add `prefix`, then recursively process
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	210 individual elements.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	211 If the array is empty, it does not add anything to command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	212
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	213 - object: Add `prefix` only, and recursively add object fields for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	214 which `inputBinding` is specified.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	215
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	216 - null: Add nothing.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	217
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	218 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	219 - name: position
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	220 type: [ "null", int, Expression ]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	221 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	222 The sorting key. Default position is 0. If the inputBinding is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	223 associated with an input parameter, then the value of `self` in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	224 expression will be the value of the input parameter. Input parameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	225 defaults (as specified by the `InputParameter.default` field) must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	226 applied before evaluating the expression. Expressions must return a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	227 single value of type int or a null.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	228 - name: prefix
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	229 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	230 doc: "Command line prefix to add before the value."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	231 - name: separate
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	232 type: boolean?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	233 default: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	234 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	235 If true (default), then the prefix and value must be added as separate
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	236 command line arguments; if false, prefix and value must be concatenated
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	237 into a single command line argument.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	238 - name: itemSeparator
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	239 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	240 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	241 Join the array elements into a single string with the elements
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	242 separated by by `itemSeparator`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	243 - name: valueFrom
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	244 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	245 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	246 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	247 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	248 jsonldPredicate: "cwl:valueFrom"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	249 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	250 If `valueFrom` is a constant string value, use this as the value and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	251 apply the binding rules above.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	252
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	253 If `valueFrom` is an expression, evaluate the expression to yield the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	254 actual value to use to build the command line and apply the binding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	255 rules above. If the inputBinding is associated with an input
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	256 parameter, the value of `self` in the expression will be the value of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	257 the input parameter. Input parameter defaults (as specified by the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	258 `InputParameter.default` field) must be applied before evaluating the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	259 expression.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	260
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	261 If the value of the associated input parameter is `null`, `valueFrom` is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	262 not evaluated and nothing is added to the command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	263
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	264 When a binding is part of the `CommandLineTool.arguments` field,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	265 the `valueFrom` field is required.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	266
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	267 - name: shellQuote
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	268 type: boolean?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	269 default: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	270 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	271 If `ShellCommandRequirement` is in the requirements for the current command,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	272 this controls whether the value is quoted on the command line (default is true).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	273 Use `shellQuote: false` to inject metacharacters for operations such as pipes.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	274
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	275 If `shellQuote` is true or not provided, the implementation must not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	276 permit interpretation of any shell metacharacters or directives.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	277
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	278
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	279 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	280 name: CommandOutputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	281 extends: LoadContents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	282 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	283 Describes how to generate an output parameter based on the files produced
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	284 by a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	285
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	286 The output parameter value is generated by applying these operations in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	287 following order:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	288
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	289 - glob
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	290 - loadContents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	291 - outputEval
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	292 - secondaryFiles
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	293 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	294 - name: glob
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	295 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	296 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	297 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	298 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	299 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	300 items: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	301 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	302 Find files or directories relative to the output directory, using POSIX
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	303 glob(3) pathname matching. If an array is provided, find files or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	304 directories that match any pattern in the array. If an expression is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	305 provided, the expression must return a string or an array of strings,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	306 which will then be evaluated as one or more glob patterns. Must only
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	307 match and return files/directories which actually exist.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	308
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	309 If the value of glob is a relative path pattern (does not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	310 begin with a slash '/') then it is resolved relative to the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	311 output directory. If the value of the glob is an absolute
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	312 path pattern (it does begin with a slash '/') then it must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	313 refer to a path within the output directory. It is an error
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	314 if any glob resolves to a path outside the output directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	315 Specifically this means globs with relative paths containing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	316 '..' or absolute paths that refer outside the output directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	317 are illegal.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	318
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	319 A glob may match a path within the output directory which is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	320 actually a symlink to another file. In this case, the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	321 expected behavior is for the resulting File/Directory object to take the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	322 `basename` (and corresponding `nameroot` and `nameext`) of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	323 symlink. The `location` of the File/Directory is implementation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	324 dependent, but logically the File/Directory should have the same content
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	325 as the symlink target. Platforms may stage output files/directories to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	326 cloud storage that lack the concept of a symlink. In
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	327 this case file content and directories may be duplicated, or (to avoid
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	328 duplication) the File/Directory `location` may refer to the symlink
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	329 target.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	330
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	331 It is an error if a symlink in the output directory (or any
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	332 symlink in a chain of links) refers to any file or directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	333 that is not under an input or output directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	334
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	335 Implementations may shut down a container before globbing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	336 output, so globs and expressions must not assume access to the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	337 container filesystem except for declared input and output.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	338
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	339 - name: outputEval
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	340 type: Expression?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	341 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	342 Evaluate an expression to generate the output value. If
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	343 `glob` was specified, the value of `self` must be an array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	344 containing file objects that were matched. If no files were
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	345 matched, `self` must be a zero length array; if a single file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	346 was matched, the value of `self` is an array of a single
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	347 element. Additionally, if `loadContents` is `true`, the File
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	348 objects must include up to the first 64 KiB of file contents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	349 in the `contents` field. The exit code of the process is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	350 available in the expression as `runtime.exitCode`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	351
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	352 - name: CommandLineBindable
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	353 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	354 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	355 inputBinding:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	356 type: CommandLineBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	357 jsonldPredicate: "cwl:inputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	358 doc: Describes how to turn this object into command line arguments.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	359
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	360 - name: CommandInputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	361 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	362 extends: [InputRecordField, CommandLineBindable]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	363 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	364 - specializeFrom: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	365 specializeTo: CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	366 - specializeFrom: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	367 specializeTo: CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	368 - specializeFrom: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	369 specializeTo: CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	370 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	371 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	372
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	373
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	374 - name: CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	375 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	376 extends: [InputRecordSchema, CommandInputSchema, CommandLineBindable]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	377 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	378 - specializeFrom: InputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	379 specializeTo: CommandInputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	380 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	381 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	382
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	383
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	384 - name: CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	385 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	386 extends: [InputEnumSchema, CommandInputSchema, CommandLineBindable]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	387 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	388 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	389 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	390
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	391
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	392 - name: CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	393 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	394 extends: [InputArraySchema, CommandInputSchema, CommandLineBindable]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	395 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	396 - specializeFrom: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	397 specializeTo: CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	398 - specializeFrom: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	399 specializeTo: CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	400 - specializeFrom: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	401 specializeTo: CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	402 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	403 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	404
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	405
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	406 - name: CommandOutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	407 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	408 extends: OutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	409 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	410 - specializeFrom: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	411 specializeTo: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	412 - specializeFrom: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	413 specializeTo: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	414 - specializeFrom: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	415 specializeTo: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	416 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	417 - name: outputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	418 type: CommandOutputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	419 jsonldPredicate: "cwl:outputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	420 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	421 Describes how to generate this output object based on the files
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	422 produced by a CommandLineTool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	423
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	424
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	425 - name: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	426 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	427 extends: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	428 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	429 - specializeFrom: OutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	430 specializeTo: CommandOutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	431
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	432
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	433 - name: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	434 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	435 extends: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	436 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	437 - specializeFrom: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	438 specializeTo: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	439 - specializeFrom: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	440 specializeTo: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	441 - specializeFrom: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	442 specializeTo: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	443
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	444
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	445 - name: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	446 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	447 extends: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	448 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	449 - specializeFrom: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	450 specializeTo: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	451 - specializeFrom: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	452 specializeTo: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	453 - specializeFrom: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	454 specializeTo: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	455
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	456
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	457 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	458 name: CommandInputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	459 extends: InputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	460 doc: An input parameter for a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	461 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	462 - name: type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	463 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	464 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	465 - stdin
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	466 - CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	467 - CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	468 - CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	469 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	470 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	471 items:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	472 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	473 - CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	474 - CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	475 - CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	476 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	477 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	478 "_id": "sld:type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	479 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	480 refScope: 2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	481 typeDSL: True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	482 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	483 Specify valid types of data that may be assigned to this parameter.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	484 - name: inputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	485 type: CommandLineBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	486 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	487 Describes how to turns the input parameters of a process into
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	488 command line arguments.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	489 jsonldPredicate: "cwl:inputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	490
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	491 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	492 name: CommandOutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	493 extends: OutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	494 doc: An output parameter for a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	495 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	496 - name: type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	497 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	498 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	499 - stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	500 - stderr

0

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1 saladVersion: v1.1

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

2 $base: "https://w3id.org/cwl/cwl#"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

3

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

4 $namespaces:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

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

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

6

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

7 $graph:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

8

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

9 - name: CommandLineToolDoc

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

10 type: documentation

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

11 doc:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

12 - |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

13 # Common Workflow Language (CWL) Command Line Tool Description, v1.1

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

14

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

15 This version:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

16 * https://w3id.org/cwl/v1.1/

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

17

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

18 Current version:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

19 * https://w3id.org/cwl/

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

20 - "\n\n"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

21 - {$include: contrib.md}

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

22 - "\n\n"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

23 - |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

24 # Abstract

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

25

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

26 A Command Line Tool is a non-interactive executable program that reads

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

27 some input, performs a computation, and terminates after producing some

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

28 output. Command line programs are a flexible unit of code sharing and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

29 reuse, unfortunately the syntax and input/output semantics among command

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

30 line programs is extremely heterogeneous. A common layer for describing

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

31 the syntax and semantics of programs can reduce this incidental

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

32 complexity by providing a consistent way to connect programs together.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

33 This specification defines the Common Workflow Language (CWL) Command

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

34 Line Tool Description, a vendor-neutral standard for describing the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

35 syntax and input/output semantics of command line programs.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

36

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

37 - {$include: intro.md}

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

38

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

39 - |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

40 ## Introduction to the CWL Command Line Tool standard v1.1

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

41

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

42 This specification represents the latest development release from the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

43 CWL group. Since the v1.0 release, v1.1 introduces the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

44 following updates to the CWL Command Line Tool standard.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

45 Documents should use `cwlVersion: v1.1` to make use of new

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

46 syntax and features introduced in v1.1. Existing v1.0 documents

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

47 should be trivially updatable by changing `cwlVersion`, however

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

48 CWL documents that relied on previously undefined or

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

49 underspecified behavior may have slightly different behavior in

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

50 v1.1.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

51

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

52 ## Changelog

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

53

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

54 * Clarify behavior around `ENTRYPOINT` and `CMD` in containers.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

55 * Clarify documentation around `valueFrom` and `null` inputs.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

56 * Default values for some fields are now expressed in the schema.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

57 * When defining record types with `CommandInputRecordSchema`, fields of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

58 type `File` may now include `format`, `loadContents`,

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

59 `secondaryFiles` and `streamable`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

60 * `CommandInputRecordSchema`, `CommandOutputRecordSchema`,

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

61 `CommandInputEnumSchema and `CommandInputArraySchema` now have an optional

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

62 `doc` field.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

63 * `inputBinding` has been added as an optional field for

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

64 `CommandInputRecordSchema` (was previously in CWL `draft-3` but

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

65 disappeared in `v1.0`).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

66 * Any `doc` field may be an array of strings in addition to the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

67 previously allowed single string.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

68 * Addition of `stdin` type shortcut for

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

69 [`CommandInputParameter`](#CommandInputParameter).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

70 * Clarify that the designated output directory should be empty

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

71 except for files or directories specified using

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

72 [InitialWorkDirRequirement](#InitialWorkDirRequirement).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

73 * Clarify semantics of `shellQuote`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

74 * Expressions are now allowed to evaluate to `null` or `Dirent` in

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

75 [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

76 * Items in [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement)

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

77 are now allowed to be `null` and `array<File | Directory>`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

78 * Clarify behavior of secondaryFiles on output.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

79 * [Addition](#Requirements_and_hints) of `cwl:requirements` field to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

80 input object documents.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

81 * Clarify behavior of `glob` for absolute paths and symlinks.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

82 * Clarify behavior of `glob` to include directories.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

83 * `secondaryFiles` can now be explicitly marked as `required` or not.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

84 * Clarify `CommandLineTool.arguments` documentation.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

85 * Clarify that `runtime.outdir` and `runtime.tmpdir` must be distinct

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

86 directories.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

87 * Clarify that unspecified details related to execution are left open to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

88 the platform.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

89 * Added `InputParameter.loadContents` field. Use of `loadContents` in

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

90 `InputBinding` is deprecated; it is preserved for v1.0 backwards

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

91 compatability and will be removed in CWL v2.0.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

92 * [Added](#ToolTimeLimit) `ToolTimeLimit` feature, allows setting

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

93 an upper limit on the execution time of a CommandLineTool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

94 * [Added](#WorkReuse) `WorkReuse` feature, allowing to enable or disable the reuse

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

95 behavior for a particular tool or step for implementations that

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

96 support reusing output from past work.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

97 * [Added](#NetworkAccess) `NetworkAccess` feature, allowing to indicate whether a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

98 process requires outgoing network access.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

99 * [Added](#InplaceUpdateRequirement) `InplaceUpdateRequirement` feature, allowing tools to directly

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

100 update files with `writable: true` in `InitialWorkDirRequirement`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

101 * [Added](#LoadListingRequirement) `LoadListingRequirement`

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

102 and [loadListing](#LoadContents) to control whether and how

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

103 `Directory` listings should be loaded for use in expressions.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

104 * The position field of the [CommandLineBinding](#CommandLineBinding) can

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

105 now be calculated from a CWL Expression.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

106 * The exit code of a CommandLineTool invocation is now

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

107 available to expressions in `outputEval` as `runtime.exitCode`

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

108 * [Better explain](#map) the `map<…>` notation that has existed since v1.0.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

109 * Fixed schema error where the `type` field inside the `inputs` and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

110 `outputs` field was incorrectly listed as optional.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

111 * For multi-Process CWL documents, if no particular process is named then

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

112 the process with the `id` of `#main` is chosen.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

113 * Added explicit defaults for [ResourceRequirement](#ResourceRequirement)s.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

114 * [Made explicit](#Generic_execution_process) that the `$namespaces` of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

115 the top level CWL document are also available to the input object as

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

116 well.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

117 * Fields with type "Expression" no longer include "string" in

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

118 the type union unless a string is semantically valid. Where

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

119 a bare string is not semantically valid, these fields must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

120 contain either a non-string value accepted by the field

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

121 type, or a valid expression which returns a value having one

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

122 of the the other types defined for that field.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

123

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

124 See also the [CWL Workflow Description, v1.1 changelog](Workflow.html#Changelog).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

125

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

126 ## Purpose

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

127

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

128 Standalone programs are a flexible and interoperable form of code reuse.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

129 Unlike monolithic applications, applications and analysis workflows which

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

130 are composed of multiple separate programs can be written in multiple

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

131 languages and execute concurrently on multiple hosts. However, POSIX

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

132 does not dictate computer-readable grammar or semantics for program input

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

133 and output, resulting in extremely heterogeneous command line grammar and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

134 input/output semantics among program. This is a particular problem in

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

135 distributed computing (multi-node compute clusters) and virtualized

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

136 environments (such as Docker containers) where it is often necessary to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

137 provision resources such as input files before executing the program.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

138

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

139 Often this gap is filled by hard coding program invocation and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

140 implicitly assuming requirements will be met, or abstracting program

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

141 invocation with wrapper scripts or descriptor documents. Unfortunately,

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

142 where these approaches are application or platform specific it creates a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

143 significant barrier to reproducibility and portability, as methods

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

144 developed for one platform must be manually ported to be used on new

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

145 platforms. Similarly it creates redundant work, as wrappers for popular

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

146 tools must be rewritten for each application or platform in use.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

147

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

148 The Common Workflow Language Command Line Tool Description is designed to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

149 provide a common standard description of grammar and semantics for

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

150 invoking programs used in data-intensive fields such as Bioinformatics,

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

151 Chemistry, Physics, Astronomy, and Statistics. This specification

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

152 attempts to define a precise data and execution model for Command Line Tools that

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

153 can be implemented on a variety of computing platforms, ranging from a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

154 single workstation to cluster, grid, cloud, and high performance

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

155 computing platforms. Details related to execution of these programs not

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

156 laid out in this specification are open to interpretation by the computing

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

157 platform implementing this specification.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

158

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

159 - {$include: concepts.md}

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

160 - {$include: invocation.md}

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

161

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

162

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

163 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

164 name: EnvironmentDef

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

165 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

166 Define an environment variable that will be set in the runtime environment

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

167 by the workflow platform when executing the command line tool. May be the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

168 result of executing an expression, such as getting a parameter from input.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

169 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

170 - name: envName

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

171 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

172 doc: The environment variable name

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

173 - name: envValue

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

174 type: [string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

175 doc: The environment variable value

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

176

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

177 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

178 name: CommandLineBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

179 extends: InputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

180 docParent: "#CommandInputParameter"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

181 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

182

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

183 When listed under `inputBinding` in the input schema, the term

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

184 "value" refers to the the corresponding value in the input object. For

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

185 binding objects listed in `CommandLineTool.arguments`, the term "value"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

186 refers to the effective value after evaluating `valueFrom`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

187

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

188 The binding behavior when building the command line depends on the data

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

189 type of the value. If there is a mismatch between the type described by

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

190 the input schema and the effective value, such as resulting from an

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

191 expression evaluation, an implementation must use the data type of the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

192 effective value.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

193

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

194 - **string**: Add `prefix` and the string to the command line.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

195

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

196 - **number**: Add `prefix` and decimal representation to command line.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

197

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

198 - **boolean**: If true, add `prefix` to the command line. If false, add

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

199 nothing.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

200

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

201 - **File**: Add `prefix` and the value of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

202 [`File.path`](#File) to the command line.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

203

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

204 - **Directory**: Add `prefix` and the value of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

205 [`Directory.path`](#Directory) to the command line.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

206

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

207 - **array**: If `itemSeparator` is specified, add `prefix` and the join

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

208 the array into a single string with `itemSeparator` separating the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

209 items. Otherwise first add `prefix`, then recursively process

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

210 individual elements.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

211 If the array is empty, it does not add anything to command line.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

212

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

213 - **object**: Add `prefix` only, and recursively add object fields for

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

214 which `inputBinding` is specified.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

215

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

216 - **null**: Add nothing.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

217

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

218 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

219 - name: position

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

220 type: [ "null", int, Expression ]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

221 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

222 The sorting key. Default position is 0. If the inputBinding is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

223 associated with an input parameter, then the value of `self` in the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

224 expression will be the value of the input parameter. Input parameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

225 defaults (as specified by the `InputParameter.default` field) must be

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

226 applied before evaluating the expression. Expressions must return a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

227 single value of type int or a null.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

228 - name: prefix

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

229 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

230 doc: "Command line prefix to add before the value."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

231 - name: separate

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

232 type: boolean?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

233 default: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

234 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

235 If true (default), then the prefix and value must be added as separate

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

236 command line arguments; if false, prefix and value must be concatenated

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

237 into a single command line argument.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

238 - name: itemSeparator

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

239 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

240 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

241 Join the array elements into a single string with the elements

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

242 separated by by `itemSeparator`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

243 - name: valueFrom

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

244 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

245 - "null"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

246 - string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

247 - Expression

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

248 jsonldPredicate: "cwl:valueFrom"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

249 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

250 If `valueFrom` is a constant string value, use this as the value and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

251 apply the binding rules above.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

252

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

253 If `valueFrom` is an expression, evaluate the expression to yield the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

254 actual value to use to build the command line and apply the binding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

255 rules above. If the inputBinding is associated with an input

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

256 parameter, the value of `self` in the expression will be the value of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

257 the input parameter. Input parameter defaults (as specified by the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

258 `InputParameter.default` field) must be applied before evaluating the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

259 expression.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

260

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

261 If the value of the associated input parameter is `null`, `valueFrom` is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

262 not evaluated and nothing is added to the command line.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

263

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

264 When a binding is part of the `CommandLineTool.arguments` field,

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

265 the `valueFrom` field is required.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

266

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

267 - name: shellQuote

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

268 type: boolean?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

269 default: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

270 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

271 If `ShellCommandRequirement` is in the requirements for the current command,

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

272 this controls whether the value is quoted on the command line (default is true).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

273 Use `shellQuote: false` to inject metacharacters for operations such as pipes.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

274

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

275 If `shellQuote` is true or not provided, the implementation must not

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

276 permit interpretation of any shell metacharacters or directives.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

277

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

278

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

279 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

280 name: CommandOutputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

281 extends: LoadContents

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

282 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

283 Describes how to generate an output parameter based on the files produced

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

284 by a CommandLineTool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

285

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

286 The output parameter value is generated by applying these operations in the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

287 following order:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

288

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

289 - glob

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

290 - loadContents

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

291 - outputEval

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

292 - secondaryFiles

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

293 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

294 - name: glob

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

295 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

296 - "null"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

297 - string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

298 - Expression

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

299 - type: array

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

300 items: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

301 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

302 Find files or directories relative to the output directory, using POSIX

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

303 glob(3) pathname matching. If an array is provided, find files or

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

304 directories that match any pattern in the array. If an expression is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

305 provided, the expression must return a string or an array of strings,

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

306 which will then be evaluated as one or more glob patterns. Must only

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

307 match and return files/directories which actually exist.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

308

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

309 If the value of glob is a relative path pattern (does not

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

310 begin with a slash '/') then it is resolved relative to the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

311 output directory. If the value of the glob is an absolute

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

312 path pattern (it does begin with a slash '/') then it must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

313 refer to a path within the output directory. It is an error

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

314 if any glob resolves to a path outside the output directory.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

315 Specifically this means globs with relative paths containing

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

316 '..' or absolute paths that refer outside the output directory

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

317 are illegal.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

318

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

319 A glob may match a path within the output directory which is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

320 actually a symlink to another file. In this case, the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

321 expected behavior is for the resulting File/Directory object to take the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

322 `basename` (and corresponding `nameroot` and `nameext`) of the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

323 symlink. The `location` of the File/Directory is implementation

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

324 dependent, but logically the File/Directory should have the same content

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

325 as the symlink target. Platforms may stage output files/directories to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

326 cloud storage that lack the concept of a symlink. In

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

327 this case file content and directories may be duplicated, or (to avoid

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

328 duplication) the File/Directory `location` may refer to the symlink

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

329 target.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

330

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

331 It is an error if a symlink in the output directory (or any

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

332 symlink in a chain of links) refers to any file or directory

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

333 that is not under an input or output directory.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

334

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

335 Implementations may shut down a container before globbing

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

336 output, so globs and expressions must not assume access to the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

337 container filesystem except for declared input and output.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

338

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

339 - name: outputEval

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

340 type: Expression?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

341 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

342 Evaluate an expression to generate the output value. If

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

343 `glob` was specified, the value of `self` must be an array

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

344 containing file objects that were matched. If no files were

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

345 matched, `self` must be a zero length array; if a single file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

346 was matched, the value of `self` is an array of a single

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

347 element. Additionally, if `loadContents` is `true`, the File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

348 objects must include up to the first 64 KiB of file contents

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

349 in the `contents` field. The exit code of the process is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

350 available in the expression as `runtime.exitCode`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

351

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

352 - name: CommandLineBindable

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

353 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

354 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

355 inputBinding:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

356 type: CommandLineBinding?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

357 jsonldPredicate: "cwl:inputBinding"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

358 doc: Describes how to turn this object into command line arguments.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

359

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

360 - name: CommandInputRecordField

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

361 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

362 extends: [InputRecordField, CommandLineBindable]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

363 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

364 - specializeFrom: InputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

365 specializeTo: CommandInputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

366 - specializeFrom: InputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

367 specializeTo: CommandInputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

368 - specializeFrom: InputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

369 specializeTo: CommandInputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

370 - specializeFrom: InputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

371 specializeTo: CommandLineBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

372

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

373

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

374 - name: CommandInputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

375 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

376 extends: [InputRecordSchema, CommandInputSchema, CommandLineBindable]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

377 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

378 - specializeFrom: InputRecordField

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

379 specializeTo: CommandInputRecordField

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

380 - specializeFrom: InputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

381 specializeTo: CommandLineBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

382

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

383

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

384 - name: CommandInputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

385 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

386 extends: [InputEnumSchema, CommandInputSchema, CommandLineBindable]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

387 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

388 - specializeFrom: InputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

389 specializeTo: CommandLineBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

390

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

391

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

392 - name: CommandInputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

393 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

394 extends: [InputArraySchema, CommandInputSchema, CommandLineBindable]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

395 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

396 - specializeFrom: InputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

397 specializeTo: CommandInputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

398 - specializeFrom: InputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

399 specializeTo: CommandInputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

400 - specializeFrom: InputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

401 specializeTo: CommandInputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

402 - specializeFrom: InputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

403 specializeTo: CommandLineBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

404

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

405

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

406 - name: CommandOutputRecordField

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

407 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

408 extends: OutputRecordField

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

409 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

410 - specializeFrom: OutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

411 specializeTo: CommandOutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

412 - specializeFrom: OutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

413 specializeTo: CommandOutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

414 - specializeFrom: OutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

415 specializeTo: CommandOutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

416 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

417 - name: outputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

418 type: CommandOutputBinding?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

419 jsonldPredicate: "cwl:outputBinding"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

420 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

421 Describes how to generate this output object based on the files

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

422 produced by a CommandLineTool

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

423

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

424

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

425 - name: CommandOutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

426 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

427 extends: OutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

428 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

429 - specializeFrom: OutputRecordField

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

430 specializeTo: CommandOutputRecordField

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

431

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

432

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

433 - name: CommandOutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

434 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

435 extends: OutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

436 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

437 - specializeFrom: OutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

438 specializeTo: CommandOutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

439 - specializeFrom: OutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

440 specializeTo: CommandOutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

441 - specializeFrom: OutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

442 specializeTo: CommandOutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

443

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

444

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

445 - name: CommandOutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

446 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

447 extends: OutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

448 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

449 - specializeFrom: OutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

450 specializeTo: CommandOutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

451 - specializeFrom: OutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

452 specializeTo: CommandOutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

453 - specializeFrom: OutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

454 specializeTo: CommandOutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

455

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

456

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

457 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

458 name: CommandInputParameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

459 extends: InputParameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

460 doc: An input parameter for a CommandLineTool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

461 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

462 - name: type

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

463 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

464 - CWLType

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

465 - stdin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

466 - CommandInputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

467 - CommandInputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

468 - CommandInputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

469 - string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

470 - type: array

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

471 items:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

472 - CWLType

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

473 - CommandInputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

474 - CommandInputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

475 - CommandInputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

476 - string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

477 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

478 "_id": "sld:type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

479 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

480 refScope: 2

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

481 typeDSL: True

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

482 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

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

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

484 - name: inputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

485 type: CommandLineBinding?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

486 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

487 Describes how to turns the input parameters of a process into

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

488 command line arguments.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

489 jsonldPredicate: "cwl:inputBinding"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

490

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

491 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

492 name: CommandOutputParameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

493 extends: OutputParameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

494 doc: An output parameter for a CommandLineTool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

495 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

496 - name: type

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

497 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

498 - CWLType

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

499 - stdout

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

500 - stderr

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

501 - CommandOutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

502 - CommandOutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

503 - CommandOutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

504 - string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

505 - type: array

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

506 items:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

507 - CWLType

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

508 - CommandOutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

509 - CommandOutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

510 - CommandOutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

511 - string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

512 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

513 "_id": "sld:type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

514 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

515 refScope: 2

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

516 typeDSL: True

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

517 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

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

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

519 - name: outputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

520 type: CommandOutputBinding?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

521 jsonldPredicate: "cwl:outputBinding"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

522 doc: Describes how to generate this output object based on the files

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

523 produced by a CommandLineTool

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

524

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

525 - name: stdin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

526 type: enum

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

527 symbols: [ "cwl:stdin" ]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

528 docParent: "#CommandOutputParameter"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

529 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

530 Only valid as a `type` for a `CommandLineTool` input with no

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

531 `inputBinding` set. `stdin` must not be specified at the `CommandLineTool`

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

532 level.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

533

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

534 The following

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

535 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

536 inputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

537 an_input_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

538 type: stdin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

539 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

540 is equivalent to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

541 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

542 inputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

543 an_input_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

544 type: File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

545 streamable: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

546

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

547 stdin: ${inputs.an_input_name.path}

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

548 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

549

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

550 - name: stdout

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

551 type: enum

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

552 symbols: [ "cwl:stdout" ]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

553 docParent: "#CommandOutputParameter"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

554 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

555 Only valid as a `type` for a `CommandLineTool` output with no

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

556 `outputBinding` set.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

557

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

558 The following

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

559 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

560 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

561 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

562 type: stdout

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

563

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

564 stdout: a_stdout_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

565 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

566 is equivalent to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

567 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

568 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

569 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

570 type: File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

571 streamable: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

572 outputBinding:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

573 glob: a_stdout_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

574

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

575 stdout: a_stdout_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

576 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

577

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

578 If there is no `stdout` name provided, a random filename will be created.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

579 For example, the following

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

580 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

581 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

582 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

583 type: stdout

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

584 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

585 is equivalent to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

586 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

587 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

588 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

589 type: File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

590 streamable: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

591 outputBinding:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

592 glob: random_stdout_filenameABCDEFG

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

593

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

594 stdout: random_stdout_filenameABCDEFG

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

595 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

596

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

597

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

598 - name: stderr

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

599 type: enum

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

600 symbols: [ "cwl:stderr" ]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

601 docParent: "#CommandOutputParameter"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

602 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

603 Only valid as a `type` for a `CommandLineTool` output with no

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

604 `outputBinding` set.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

605

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

606 The following

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

607 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

608 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

609 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

610 type: stderr

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

611

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

612 stderr: a_stderr_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

613 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

614 is equivalent to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

615 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

616 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

617 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

618 type: File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

619 streamable: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

620 outputBinding:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

621 glob: a_stderr_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

622

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

623 stderr: a_stderr_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

624 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

625

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

626 If there is no `stderr` name provided, a random filename will be created.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

627 For example, the following

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

628 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

629 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

630 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

631 type: stderr

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

632 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

633 is equivalent to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

634 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

635 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

636 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

637 type: File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

638 streamable: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

639 outputBinding:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

640 glob: random_stderr_filenameABCDEFG

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

641

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

642 stderr: random_stderr_filenameABCDEFG

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

643 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

644

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

645

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

646 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

647 name: CommandLineTool

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

648 extends: Process

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

649 documentRoot: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

650 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

651 - specializeFrom: InputParameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

652 specializeTo: CommandInputParameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

653 - specializeFrom: OutputParameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

654 specializeTo: CommandOutputParameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

655 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

656 This defines the schema of the CWL Command Line Tool Description document.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

657

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

658 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

659 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

660 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

661 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

662 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

663 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

664 - name: baseCommand

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

665 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

666 Specifies the program to execute. If an array, the first element of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

667 the array is the command to execute, and subsequent elements are

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

668 mandatory command line arguments. The elements in `baseCommand` must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

669 appear before any command line bindings from `inputBinding` or

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

670 `arguments`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

671

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

672 If `baseCommand` is not provided or is an empty array, the first

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

673 element of the command line produced after processing `inputBinding` or

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

674 `arguments` must be used as the program to execute.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

675

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

676 If the program includes a path separator character it must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

677 be an absolute path, otherwise it is an error. If the program does not

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

678 include a path separator, search the `$PATH` variable in the runtime

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

679 environment of the workflow runner find the absolute path of the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

680 executable.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

681 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

682 - string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

683 - string[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

684 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

685 "_id": "cwl:baseCommand"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

686 "_container": "@list"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

687 - name: arguments

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

688 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

689 Command line bindings which are not directly associated with input

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

690 parameters. If the value is a string, it is used as a string literal

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

691 argument. If it is an Expression, the result of the evaluation is used

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

692 as an argument.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

693 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

694 - "null"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

695 - type: array

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

696 items: [string, Expression, CommandLineBinding]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

697 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

698 "_id": "cwl:arguments"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

699 "_container": "@list"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

700 - name: stdin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

701 type: ["null", string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

702 jsonldPredicate: "https://w3id.org/cwl/cwl#stdin"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

703 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

704 A path to a file whose contents must be piped into the command's

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

705 standard input stream.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

706 - name: stderr

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

707 type: ["null", string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

708 jsonldPredicate: "https://w3id.org/cwl/cwl#stderr"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

709 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

710 Capture the command's standard error stream to a file written to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

711 the designated output directory.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

712

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

713 If `stderr` is a string, it specifies the file name to use.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

714

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

715 If `stderr` is an expression, the expression is evaluated and must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

716 return a string with the file name to use to capture stderr. If the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

717 return value is not a string, or the resulting path contains illegal

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

718 characters (such as the path separator `/`) it is an error.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

719 - name: stdout

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

720 type: ["null", string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

721 jsonldPredicate: "https://w3id.org/cwl/cwl#stdout"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

722 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

723 Capture the command's standard output stream to a file written to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

724 the designated output directory.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

725

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

726 If `stdout` is a string, it specifies the file name to use.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

727

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

728 If `stdout` is an expression, the expression is evaluated and must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

729 return a string with the file name to use to capture stdout. If the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

730 return value is not a string, or the resulting path contains illegal

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

731 characters (such as the path separator `/`) it is an error.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

732 - name: successCodes

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

733 type: int[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

734 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

735 Exit codes that indicate the process completed successfully.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

736

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

737 - name: temporaryFailCodes

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

738 type: int[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

739 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

740 Exit codes that indicate the process failed due to a possibly

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

741 temporary condition, where executing the process with the same

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

742 runtime environment and inputs may produce different results.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

743

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

744 - name: permanentFailCodes

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

745 type: int[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

746 doc:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

747 Exit codes that indicate the process failed due to a permanent logic

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

748 error, where executing the process with the same runtime environment and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

749 same inputs is expected to always fail.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

750

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

751

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

752 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

753 name: DockerRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

754 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

755 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

756 Indicates that a workflow component should be run in a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

757 [Docker](http://docker.com) or Docker-compatible (such as

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

758 [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

759 specifies how to fetch or build the image.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

760

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

761 If a CommandLineTool lists `DockerRequirement` under

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

762 `hints` (or `requirements`), it may (or must) be run in the specified Docker

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

763 container.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

764

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

765 The platform must first acquire or install the correct Docker image as

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

766 specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

767

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

768 The platform must execute the tool in the container using `docker run` with

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

769 the appropriate Docker image and tool command line.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

770

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

771 The workflow platform may provide input files and the designated output

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

772 directory through the use of volume bind mounts. The platform should rewrite

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

773 file paths in the input object to correspond to the Docker bind mounted

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

774 locations. That is, the platform should rewrite values in the parameter context

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

775 such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

776 within the container. The platform must ensure that `runtime.outdir` and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

777 `runtime.tmpdir` are distinct directories.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

778

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

779 When running a tool contained in Docker, the workflow platform must not

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

780 assume anything about the contents of the Docker container, such as the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

781 presence or absence of specific software, except to assume that the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

782 generated command line represents a valid command within the runtime

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

783 environment of the container.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

784

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

785 A container image may specify an

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

786 [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint)

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

787 and/or

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

788 [CMD](https://docs.docker.com/engine/reference/builder/#cmd).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

789 Command line arguments will be appended after all elements of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

790 ENTRYPOINT, and will override all elements specified using CMD (in

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

791 other words, CMD is only used when the CommandLineTool definition

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

792 produces an empty command line).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

793

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

794 Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

795 concerns of the implicit hidden execution point (For further discussion, see

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

796 [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

797 CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

798 CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

799 `requirements` section.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

800

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

801 ## Interaction with other requirements

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

802

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

803 If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

804 DockerRequirement, the environment variables must be provided to Docker

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

805 using `--env` or `--env-file` and interact with the container's preexisting

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

806 environment as defined by Docker.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

807

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

808 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

809 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

810 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

811 doc: "Always 'DockerRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

812 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

813 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

814 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

815 - name: dockerPull

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

816 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

817 doc: "Specify a Docker image to retrieve using `docker pull`."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

818 - name: dockerLoad

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

819 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

820 doc: "Specify a HTTP URL from which to download a Docker image using `docker load`."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

821 - name: dockerFile

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

822 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

823 doc: "Supply the contents of a Dockerfile which will be built using `docker build`."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

824 - name: dockerImport

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

825 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

826 doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

827 - name: dockerImageId

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

828 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

829 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

830 The image id that will be used for `docker run`. May be a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

831 human-readable image name or the image identifier hash. May be skipped

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

832 if `dockerPull` is specified, in which case the `dockerPull` image id

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

833 must be used.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

834 - name: dockerOutputDirectory

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

835 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

836 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

837 Set the designated output directory to a specific location inside the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

838 Docker container.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

839

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

840

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

841 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

842 name: SoftwareRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

843 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

844 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

845 A list of software packages that should be configured in the environment of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

846 the defined process.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

847 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

848 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

849 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

850 doc: "Always 'SoftwareRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

851 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

852 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

853 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

854 - name: packages

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

855 type: SoftwarePackage[]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

856 doc: "The list of software to be configured."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

857 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

858 mapSubject: package

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

859 mapPredicate: specs

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

860

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

861 - name: SoftwarePackage

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

862 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

863 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

864 - name: package

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

865 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

866 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

867 The name of the software to be made available. If the name is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

868 common, inconsistent, or otherwise ambiguous it should be combined with

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

869 one or more identifiers in the `specs` field.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

870 - name: version

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

871 type: string[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

872 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

873 The (optional) versions of the software that are known to be

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

874 compatible.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

875 - name: specs

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

876 type: string[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

877 jsonldPredicate: {_type: "@id", noLinkCheck: true}

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

878 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

879 One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

880 identifying resources for installing or enabling the software named in

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

881 the `package` field. Implementations may provide resolvers which map

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

882 these software identifer IRIs to some configuration action; or they can

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

883 use only the name from the `package` field on a best effort basis.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

884

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

885 For example, the IRI https://packages.debian.org/bowtie could

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

886 be resolved with `apt-get install bowtie`. The IRI

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

887 https://anaconda.org/bioconda/bowtie could be resolved with `conda

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

888 install -c bioconda bowtie`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

889

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

890 IRIs can also be system independent and used to map to a specific

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

891 software installation or selection mechanism.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

892 Using [RRID](https://www.identifiers.org/rrid/) as an example:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

893 https://identifiers.org/rrid/RRID:SCR_005476

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

894 could be fulfilled using the above mentioned Debian or bioconda

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

895 package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/),

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

896 or any other mechanism the platform chooses. IRIs can also be from

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

897 identifer sources that are discipline specific yet still system

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

898 independent. As an example, the equivalent [ELIXIR Tools and Data

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

899 Service Registry](https://bio.tools) IRI to the previous RRID example is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

900 https://bio.tools/tool/bowtie2/version/2.2.8.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

901 If supported by a given registry, implementations are encouraged to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

902 query these system independent sofware identifier IRIs directly for

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

903 links to packaging systems.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

904

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

905 A site specific IRI can be listed as well. For example, an academic

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

906 computing cluster using Environement Modules could list the IRI

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

907 `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

908 `module load bowtie-tbb/1.1.2` should be executed to make available

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

909 `bowtie` version 1.1.2 compiled with the TBB library prior to running

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

910 the accompanying Workflow or CommandLineTool. Note that the example IRI

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

911 is specific to a particular institution and computing environment as

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

912 the Environment Modules system does not have a common namespace or

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

913 standardized naming convention.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

914

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

915 This last example is the least portable and should only be used if

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

916 mechanisms based off of the `package` field or more generic IRIs are

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

917 unavailable or unsuitable. While harmless to other sites, site specific

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

918 software IRIs should be left out of shared CWL descriptions to avoid

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

919 clutter.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

920

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

921 - name: Dirent

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

922 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

923 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

924 Define a file or subdirectory that must be placed in the designated output

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

925 directory prior to executing the command line tool. May be the result of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

926 executing an expression, such as building a configuration file from a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

927 template.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

928 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

929 - name: entryname

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

930 type: ["null", string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

931 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

932 _id: cwl:entryname

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

933 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

934 The name of the file or subdirectory to create in the output directory.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

935 If `entry` is a File or Directory, the `entryname` field overrides the value

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

936 of `basename` of the File or Directory object. Optional.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

937 - name: entry

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

938 type: [string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

939 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

940 _id: cwl:entry

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

941 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

942 If the value is a string literal or an expression which evaluates to a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

943 string, a new file must be created with the string as the file contents.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

944

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

945 If the value is an expression that evaluates to a `File` object, this

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

946 indicates the referenced file should be added to the designated output

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

947 directory prior to executing the tool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

948

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

949 If the value is an expression that evaluates to a `Dirent` object, this

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

950 indicates that the File or Directory in `entry` should be added to the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

951 designated output directory with the name in `entryname`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

952

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

953 If `writable` is false, the file may be made available using a bind

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

954 mount or file system link to avoid unnecessary copying of the input

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

955 file.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

956 - name: writable

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

957 type: boolean?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

958 default: false

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

959 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

960 If true, the file or directory must be writable by the tool. Changes

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

961 to the file or directory must be isolated and not visible by any other

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

962 CommandLineTool process. This may be implemented by making a copy of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

963 the original file or directory. Default false (files and directories

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

964 read-only by default).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

965

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

966 A directory marked as `writable: true` implies that all files and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

967 subdirectories are recursively writable as well.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

968

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

969

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

970 - name: InitialWorkDirRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

971 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

972 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

973 doc:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

974 Define a list of files and subdirectories that must be created by the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

975 workflow platform in the designated output directory prior to executing the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

976 command line tool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

977 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

978 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

979 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

980 doc: InitialWorkDirRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

981 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

982 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

983 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

984 - name: listing

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

985 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

986 - type: array

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

987 items:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

988 - "null"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

989 - File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

990 - type: array

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

991 items:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

992 - File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

993 - Directory

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

994 - Directory

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

995 - Dirent

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

996 - Expression

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

997 - Expression

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

998 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

999 _id: "cwl:listing"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1000 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1001 The list of files or subdirectories that must be placed in the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1002 designated output directory prior to executing the command line tool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1003

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1004 May be an expression. If so, the expression return value must validate as

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1005 `{type: array, items: ["null", File, File[], Directory, Directory[], Dirent]}`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1006

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1007 Files or Directories which are listed in the input parameters and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1008 appear in the `InitialWorkDirRequirement` listing must have their

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1009 `path` set to their staged location in the designated output directory.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1010 If the same File or Directory appears more than once in the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1011 `InitialWorkDirRequirement` listing, the implementation must choose

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1012 exactly one value for `path`; how this value is chosen is undefined.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1013

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1014

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1015 - name: EnvVarRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1016 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1017 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1018 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1019 Define a list of environment variables which will be set in the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1020 execution environment of the tool. See `EnvironmentDef` for details.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1021 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1022 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1023 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1024 doc: "Always 'EnvVarRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1025 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1026 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1027 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1028 - name: envDef

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1029 type: EnvironmentDef[]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1030 doc: The list of environment variables.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1031 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1032 mapSubject: envName

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1033 mapPredicate: envValue

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1034

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1035

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1036 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1037 name: ShellCommandRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1038 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1039 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1040 Modify the behavior of CommandLineTool to generate a single string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1041 containing a shell command line. Each item in the argument list must be

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1042 joined into a string separated by single spaces and quoted to prevent

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1043 intepretation by the shell, unless `CommandLineBinding` for that argument

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1044 contains `shellQuote: false`. If `shellQuote: false` is specified, the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1045 argument is joined into the command string without quoting, which allows

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1046 the use of shell metacharacters such as `|` for pipes.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1047 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1048 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1049 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1050 doc: "Always 'ShellCommandRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1051 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1052 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1053 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1054

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1055

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1056 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1057 name: ResourceRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1058 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1059 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1060 Specify basic hardware resource requirements.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1061

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1062 "min" is the minimum amount of a resource that must be reserved to schedule

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1063 a job. If "min" cannot be satisfied, the job should not be run.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1064

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1065 "max" is the maximum amount of a resource that the job shall be permitted

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1066 to use. If a node has sufficient resources, multiple jobs may be scheduled

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1067 on a single node provided each job's "max" resource requirements are

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1068 met. If a job attempts to exceed its "max" resource allocation, an

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1069 implementation may deny additional resources, which may result in job

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1070 failure.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1071

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1072 If "min" is specified but "max" is not, then "max" == "min"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1073 If "max" is specified by "min" is not, then "min" == "max".

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1074

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1075 It is an error if max < min.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1076

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1077 It is an error if the value of any of these fields is negative.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1078

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1079 If neither "min" nor "max" is specified for a resource, use the default values below.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1080

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1081 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1082 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1083 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1084 doc: "Always 'ResourceRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1085 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1086 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1087 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1088 - name: coresMin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1089 type: ["null", long, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1090 doc: Minimum reserved number of CPU cores (default is 1)

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1091

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1092 - name: coresMax

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1093 type: ["null", int, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1094 doc: Maximum reserved number of CPU cores

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1095

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1096 - name: ramMin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1097 type: ["null", long, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1098 doc: Minimum reserved RAM in mebibytes (2**20) (default is 256)

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1099

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1100 - name: ramMax

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1101 type: ["null", long, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1102 doc: Maximum reserved RAM in mebibytes (2**20)

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1103

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1104 - name: tmpdirMin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1105 type: ["null", long, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1106 doc: Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) (default is 1024)

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1107

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1108 - name: tmpdirMax

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1109 type: ["null", long, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1110 doc: Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1111

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1112 - name: outdirMin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1113 type: ["null", long, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1114 doc: Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) (default is 1024)

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1115

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1116 - name: outdirMax

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1117 type: ["null", long, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1118 doc: Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1119

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1120

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1121 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1122 name: WorkReuse

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1123 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1124 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1125 For implementations that support reusing output from past work (on

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1126 the assumption that same code and same input produce same

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1127 results), control whether to enable or disable the reuse behavior

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1128 for a particular tool or step (to accomodate situations where that

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1129 assumption is incorrect). A reused step is not executed but

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1130 instead returns the same output as the original execution.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1131

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1132 If `enableReuse` is not specified, correct tools should assume it

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1133 is enabled by default.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1134 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1135 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1136 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1137 doc: "Always 'WorkReuse'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1138 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1139 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1140 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1141 - name: enableReuse

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1142 type: [boolean, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1143 default: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1144

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1145

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1146 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1147 name: NetworkAccess

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1148 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1149 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1150 Indicate whether a process requires outgoing IPv4/IPv6 network

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1151 access. Choice of IPv4 or IPv6 is implementation and site

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1152 specific, correct tools must support both.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1153

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1154 If `networkAccess` is false or not specified, tools must not

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1155 assume network access, except for localhost (the loopback device).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1156

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1157 If `networkAccess` is true, the tool must be able to make outgoing

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1158 connections to network resources. Resources may be on a private

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1159 subnet or the public Internet. However, implementations and sites

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1160 may apply their own security policies to restrict what is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1161 accessible by the tool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1162

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1163 Enabling network access does not imply a publically routable IP

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1164 address or the ability to accept inbound connections.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1165

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1166 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1167 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1168 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1169 doc: "Always 'NetworkAccess'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1170 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1171 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1172 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1173 - name: networkAccess

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1174 type: [boolean, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1175

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1176 - name: InplaceUpdateRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1177 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1178 extends: cwl:ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1179 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1180

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1181 If `inplaceUpdate` is true, then an implementation supporting this

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1182 feature may permit tools to directly update files with `writable:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1183 true` in InitialWorkDirRequirement. That is, as an optimization,

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1184 files may be destructively modified in place as opposed to copied

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1185 and updated.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1186

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1187 An implementation must ensure that only one workflow step may

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1188 access a writable file at a time. It is an error if a file which

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1189 is writable by one workflow step file is accessed (for reading or

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1190 writing) by any other workflow step running independently.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1191 However, a file which has been updated in a previous completed

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1192 step may be used as input to multiple steps, provided it is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1193 read-only in every step.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1194

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1195 Workflow steps which modify a file must produce the modified file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1196 as output. Downstream steps which futher process the file must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1197 use the output of previous steps, and not refer to a common input

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1198 (this is necessary for both ordering and correctness).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1199

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1200 Workflow authors should provide this in the `hints` section. The

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1201 intent of this feature is that workflows produce the same results

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1202 whether or not InplaceUpdateRequirement is supported by the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1203 implementation, and this feature is primarily available as an

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1204 optimization for particular environments.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1205

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1206 Users and implementers should be aware that workflows that

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1207 destructively modify inputs may not be repeatable or reproducible.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1208 In particular, enabling this feature implies that WorkReuse should

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1209 not be enabled.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1210

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1211 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1212 class:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1213 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1214 doc: "Always 'InplaceUpdateRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1215 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1216 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1217 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1218 inplaceUpdate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1219 type: boolean

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1220

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1221 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1222 name: ToolTimeLimit

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1223 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1224 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1225 Set an upper limit on the execution time of a CommandLineTool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1226 A CommandLineTool whose execution duration exceeds the time

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1227 limit may be preemptively terminated and considered failed.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1228 May also be used by batch systems to make scheduling decisions.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1229 The execution duration excludes external operations, such as

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1230 staging of files, pulling a docker image etc, and only counts

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1231 wall-time for the execution of the command line itself.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1232 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1233 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1234 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1235 doc: "Always 'ToolTimeLimit'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1236 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1237 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1238 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1239 - name: timelimit

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1240 type: [long, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1241 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1242 The time limit, in seconds. A time limit of zero means no

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1243 time limit. Negative time limits are an error.

Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/schemas/v1.1/CommandLineTool.yml @ 0:26e78fe6e8c4 draft