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annotate env/lib/python3.7/site-packages/cwltool/schemas/v1.1/CommandLineTool.yml @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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0
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1 saladVersion: v1.1
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2 $base: "https://w3id.org/cwl/cwl#"
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3
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4 $namespaces:
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5 cwl: "https://w3id.org/cwl/cwl#"
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6
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7 $graph:
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8
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9 - name: CommandLineToolDoc
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10 type: documentation
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11 doc:
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12 - |
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13 # Common Workflow Language (CWL) Command Line Tool Description, v1.1
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14
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15 This version:
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16 * https://w3id.org/cwl/v1.1/
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17
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18 Current version:
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19 * https://w3id.org/cwl/
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20 - "\n\n"
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21 - {$include: contrib.md}
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22 - "\n\n"
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23 - |
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24 # Abstract
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25
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26 A Command Line Tool is a non-interactive executable program that reads
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27 some input, performs a computation, and terminates after producing some
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28 output. Command line programs are a flexible unit of code sharing and
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29 reuse, unfortunately the syntax and input/output semantics among command
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30 line programs is extremely heterogeneous. A common layer for describing
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31 the syntax and semantics of programs can reduce this incidental
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32 complexity by providing a consistent way to connect programs together.
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33 This specification defines the Common Workflow Language (CWL) Command
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34 Line Tool Description, a vendor-neutral standard for describing the
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35 syntax and input/output semantics of command line programs.
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36
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37 - {$include: intro.md}
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38
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39 - |
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40 ## Introduction to the CWL Command Line Tool standard v1.1
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41
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42 This specification represents the latest development release from the
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43 CWL group. Since the v1.0 release, v1.1 introduces the
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44 following updates to the CWL Command Line Tool standard.
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45 Documents should use `cwlVersion: v1.1` to make use of new
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46 syntax and features introduced in v1.1. Existing v1.0 documents
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47 should be trivially updatable by changing `cwlVersion`, however
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48 CWL documents that relied on previously undefined or
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49 underspecified behavior may have slightly different behavior in
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50 v1.1.
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51
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52 ## Changelog
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53
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54 * Clarify behavior around `ENTRYPOINT` and `CMD` in containers.
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55 * Clarify documentation around `valueFrom` and `null` inputs.
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56 * Default values for some fields are now expressed in the schema.
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57 * When defining record types with `CommandInputRecordSchema`, fields of
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58 type `File` may now include `format`, `loadContents`,
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59 `secondaryFiles` and `streamable`.
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60 * `CommandInputRecordSchema`, `CommandOutputRecordSchema`,
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61 `CommandInputEnumSchema and `CommandInputArraySchema` now have an optional
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62 `doc` field.
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63 * `inputBinding` has been added as an optional field for
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64 `CommandInputRecordSchema` (was previously in CWL `draft-3` but
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65 disappeared in `v1.0`).
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66 * Any `doc` field may be an array of strings in addition to the
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67 previously allowed single string.
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68 * Addition of `stdin` type shortcut for
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69 [`CommandInputParameter`](#CommandInputParameter).
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70 * Clarify that the designated output directory should be empty
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71 except for files or directories specified using
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72 [InitialWorkDirRequirement](#InitialWorkDirRequirement).
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73 * Clarify semantics of `shellQuote`.
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74 * Expressions are now allowed to evaluate to `null` or `Dirent` in
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75 [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement).
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76 * Items in [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement)
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77 are now allowed to be `null` and `array<File | Directory>`.
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78 * Clarify behavior of secondaryFiles on output.
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79 * [Addition](#Requirements_and_hints) of `cwl:requirements` field to
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80 input object documents.
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81 * Clarify behavior of `glob` for absolute paths and symlinks.
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82 * Clarify behavior of `glob` to include directories.
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83 * `secondaryFiles` can now be explicitly marked as `required` or not.
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84 * Clarify `CommandLineTool.arguments` documentation.
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85 * Clarify that `runtime.outdir` and `runtime.tmpdir` must be distinct
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86 directories.
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87 * Clarify that unspecified details related to execution are left open to
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88 the platform.
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89 * Added `InputParameter.loadContents` field. Use of `loadContents` in
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90 `InputBinding` is deprecated; it is preserved for v1.0 backwards
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91 compatability and will be removed in CWL v2.0.
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92 * [Added](#ToolTimeLimit) `ToolTimeLimit` feature, allows setting
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93 an upper limit on the execution time of a CommandLineTool.
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94 * [Added](#WorkReuse) `WorkReuse` feature, allowing to enable or disable the reuse
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95 behavior for a particular tool or step for implementations that
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96 support reusing output from past work.
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97 * [Added](#NetworkAccess) `NetworkAccess` feature, allowing to indicate whether a
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98 process requires outgoing network access.
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99 * [Added](#InplaceUpdateRequirement) `InplaceUpdateRequirement` feature, allowing tools to directly
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100 update files with `writable: true` in `InitialWorkDirRequirement`.
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101 * [Added](#LoadListingRequirement) `LoadListingRequirement`
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102 and [loadListing](#LoadContents) to control whether and how
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103 `Directory` listings should be loaded for use in expressions.
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104 * The position field of the [CommandLineBinding](#CommandLineBinding) can
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105 now be calculated from a CWL Expression.
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106 * The exit code of a CommandLineTool invocation is now
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107 available to expressions in `outputEval` as `runtime.exitCode`
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108 * [Better explain](#map) the `map<…>` notation that has existed since v1.0.
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109 * Fixed schema error where the `type` field inside the `inputs` and
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110 `outputs` field was incorrectly listed as optional.
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111 * For multi-Process CWL documents, if no particular process is named then
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112 the process with the `id` of `#main` is chosen.
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113 * Added explicit defaults for [ResourceRequirement](#ResourceRequirement)s.
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114 * [Made explicit](#Generic_execution_process) that the `$namespaces` of
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115 the top level CWL document are also available to the input object as
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116 well.
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117 * Fields with type "Expression" no longer include "string" in
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118 the type union unless a string is semantically valid. Where
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119 a bare string is not semantically valid, these fields must
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120 contain either a non-string value accepted by the field
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121 type, or a valid expression which returns a value having one
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122 of the the other types defined for that field.
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123
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124 See also the [CWL Workflow Description, v1.1 changelog](Workflow.html#Changelog).
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125
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126 ## Purpose
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127
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128 Standalone programs are a flexible and interoperable form of code reuse.
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129 Unlike monolithic applications, applications and analysis workflows which
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130 are composed of multiple separate programs can be written in multiple
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131 languages and execute concurrently on multiple hosts. However, POSIX
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132 does not dictate computer-readable grammar or semantics for program input
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133 and output, resulting in extremely heterogeneous command line grammar and
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134 input/output semantics among program. This is a particular problem in
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135 distributed computing (multi-node compute clusters) and virtualized
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136 environments (such as Docker containers) where it is often necessary to
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137 provision resources such as input files before executing the program.
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138
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139 Often this gap is filled by hard coding program invocation and
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140 implicitly assuming requirements will be met, or abstracting program
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141 invocation with wrapper scripts or descriptor documents. Unfortunately,
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142 where these approaches are application or platform specific it creates a
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143 significant barrier to reproducibility and portability, as methods
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144 developed for one platform must be manually ported to be used on new
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145 platforms. Similarly it creates redundant work, as wrappers for popular
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146 tools must be rewritten for each application or platform in use.
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147
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148 The Common Workflow Language Command Line Tool Description is designed to
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149 provide a common standard description of grammar and semantics for
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150 invoking programs used in data-intensive fields such as Bioinformatics,
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151 Chemistry, Physics, Astronomy, and Statistics. This specification
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152 attempts to define a precise data and execution model for Command Line Tools that
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153 can be implemented on a variety of computing platforms, ranging from a
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154 single workstation to cluster, grid, cloud, and high performance
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155 computing platforms. Details related to execution of these programs not
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156 laid out in this specification are open to interpretation by the computing
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157 platform implementing this specification.
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158
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159 - {$include: concepts.md}
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160 - {$include: invocation.md}
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161
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162
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163 - type: record
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164 name: EnvironmentDef
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165 doc: |
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166 Define an environment variable that will be set in the runtime environment
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167 by the workflow platform when executing the command line tool. May be the
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168 result of executing an expression, such as getting a parameter from input.
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169 fields:
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170 - name: envName
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171 type: string
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172 doc: The environment variable name
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173 - name: envValue
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174 type: [string, Expression]
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175 doc: The environment variable value
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176
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177 - type: record
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178 name: CommandLineBinding
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179 extends: InputBinding
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180 docParent: "#CommandInputParameter"
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181 doc: |
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182
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183 When listed under `inputBinding` in the input schema, the term
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184 "value" refers to the the corresponding value in the input object. For
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185 binding objects listed in `CommandLineTool.arguments`, the term "value"
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186 refers to the effective value after evaluating `valueFrom`.
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187
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188 The binding behavior when building the command line depends on the data
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189 type of the value. If there is a mismatch between the type described by
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190 the input schema and the effective value, such as resulting from an
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191 expression evaluation, an implementation must use the data type of the
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192 effective value.
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193
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194 - **string**: Add `prefix` and the string to the command line.
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195
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196 - **number**: Add `prefix` and decimal representation to command line.
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197
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198 - **boolean**: If true, add `prefix` to the command line. If false, add
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199 nothing.
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200
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201 - **File**: Add `prefix` and the value of
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202 [`File.path`](#File) to the command line.
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203
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204 - **Directory**: Add `prefix` and the value of
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205 [`Directory.path`](#Directory) to the command line.
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206
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207 - **array**: If `itemSeparator` is specified, add `prefix` and the join
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208 the array into a single string with `itemSeparator` separating the
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209 items. Otherwise first add `prefix`, then recursively process
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210 individual elements.
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211 If the array is empty, it does not add anything to command line.
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212
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213 - **object**: Add `prefix` only, and recursively add object fields for
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214 which `inputBinding` is specified.
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215
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216 - **null**: Add nothing.
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217
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218 fields:
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219 - name: position
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220 type: [ "null", int, Expression ]
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221 doc: |
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222 The sorting key. Default position is 0. If the inputBinding is
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223 associated with an input parameter, then the value of `self` in the
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224 expression will be the value of the input parameter. Input parameter
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225 defaults (as specified by the `InputParameter.default` field) must be
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226 applied before evaluating the expression. Expressions must return a
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227 single value of type int or a null.
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228 - name: prefix
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229 type: string?
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230 doc: "Command line prefix to add before the value."
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231 - name: separate
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232 type: boolean?
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233 default: true
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234 doc: |
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235 If true (default), then the prefix and value must be added as separate
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236 command line arguments; if false, prefix and value must be concatenated
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237 into a single command line argument.
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238 - name: itemSeparator
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239 type: string?
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240 doc: |
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241 Join the array elements into a single string with the elements
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242 separated by by `itemSeparator`.
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243 - name: valueFrom
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244 type:
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245 - "null"
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246 - string
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247 - Expression
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248 jsonldPredicate: "cwl:valueFrom"
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249 doc: |
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250 If `valueFrom` is a constant string value, use this as the value and
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251 apply the binding rules above.
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252
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253 If `valueFrom` is an expression, evaluate the expression to yield the
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254 actual value to use to build the command line and apply the binding
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255 rules above. If the inputBinding is associated with an input
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256 parameter, the value of `self` in the expression will be the value of
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257 the input parameter. Input parameter defaults (as specified by the
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258 `InputParameter.default` field) must be applied before evaluating the
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259 expression.
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260
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261 If the value of the associated input parameter is `null`, `valueFrom` is
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262 not evaluated and nothing is added to the command line.
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263
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264 When a binding is part of the `CommandLineTool.arguments` field,
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265 the `valueFrom` field is required.
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266
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267 - name: shellQuote
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268 type: boolean?
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269 default: true
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270 doc: |
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271 If `ShellCommandRequirement` is in the requirements for the current command,
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272 this controls whether the value is quoted on the command line (default is true).
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273 Use `shellQuote: false` to inject metacharacters for operations such as pipes.
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274
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275 If `shellQuote` is true or not provided, the implementation must not
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276 permit interpretation of any shell metacharacters or directives.
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277
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278
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279 - type: record
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280 name: CommandOutputBinding
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281 extends: LoadContents
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282 doc: |
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283 Describes how to generate an output parameter based on the files produced
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284 by a CommandLineTool.
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285
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286 The output parameter value is generated by applying these operations in the
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287 following order:
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288
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289 - glob
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290 - loadContents
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291 - outputEval
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292 - secondaryFiles
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293 fields:
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294 - name: glob
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295 type:
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296 - "null"
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297 - string
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298 - Expression
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299 - type: array
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300 items: string
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301 doc: |
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302 Find files or directories relative to the output directory, using POSIX
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303 glob(3) pathname matching. If an array is provided, find files or
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304 directories that match any pattern in the array. If an expression is
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305 provided, the expression must return a string or an array of strings,
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306 which will then be evaluated as one or more glob patterns. Must only
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307 match and return files/directories which actually exist.
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308
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309 If the value of glob is a relative path pattern (does not
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310 begin with a slash '/') then it is resolved relative to the
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311 output directory. If the value of the glob is an absolute
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312 path pattern (it does begin with a slash '/') then it must
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313 refer to a path within the output directory. It is an error
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314 if any glob resolves to a path outside the output directory.
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315 Specifically this means globs with relative paths containing
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316 '..' or absolute paths that refer outside the output directory
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317 are illegal.
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318
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319 A glob may match a path within the output directory which is
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320 actually a symlink to another file. In this case, the
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321 expected behavior is for the resulting File/Directory object to take the
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322 `basename` (and corresponding `nameroot` and `nameext`) of the
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323 symlink. The `location` of the File/Directory is implementation
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324 dependent, but logically the File/Directory should have the same content
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325 as the symlink target. Platforms may stage output files/directories to
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326 cloud storage that lack the concept of a symlink. In
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327 this case file content and directories may be duplicated, or (to avoid
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328 duplication) the File/Directory `location` may refer to the symlink
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329 target.
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330
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331 It is an error if a symlink in the output directory (or any
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332 symlink in a chain of links) refers to any file or directory
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333 that is not under an input or output directory.
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334
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335 Implementations may shut down a container before globbing
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336 output, so globs and expressions must not assume access to the
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337 container filesystem except for declared input and output.
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338
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339 - name: outputEval
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340 type: Expression?
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341 doc: |
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342 Evaluate an expression to generate the output value. If
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343 `glob` was specified, the value of `self` must be an array
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344 containing file objects that were matched. If no files were
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345 matched, `self` must be a zero length array; if a single file
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346 was matched, the value of `self` is an array of a single
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347 element. Additionally, if `loadContents` is `true`, the File
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348 objects must include up to the first 64 KiB of file contents
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349 in the `contents` field. The exit code of the process is
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350 available in the expression as `runtime.exitCode`.
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351
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352 - name: CommandLineBindable
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353 type: record
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354 fields:
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355 inputBinding:
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356 type: CommandLineBinding?
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357 jsonldPredicate: "cwl:inputBinding"
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358 doc: Describes how to turn this object into command line arguments.
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359
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360 - name: CommandInputRecordField
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361 type: record
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362 extends: [InputRecordField, CommandLineBindable]
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363 specialize:
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364 - specializeFrom: InputRecordSchema
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365 specializeTo: CommandInputRecordSchema
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366 - specializeFrom: InputEnumSchema
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367 specializeTo: CommandInputEnumSchema
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368 - specializeFrom: InputArraySchema
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369 specializeTo: CommandInputArraySchema
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370 - specializeFrom: InputBinding
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371 specializeTo: CommandLineBinding
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372
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373
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374 - name: CommandInputRecordSchema
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375 type: record
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376 extends: [InputRecordSchema, CommandInputSchema, CommandLineBindable]
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377 specialize:
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378 - specializeFrom: InputRecordField
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379 specializeTo: CommandInputRecordField
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diff changeset
380 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
381 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
382
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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parents:
diff changeset
386 extends: [InputEnumSchema, CommandInputSchema, CommandLineBindable]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
387 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
388 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
389 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
390
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
391
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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392 - name: CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
393 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
394 extends: [InputArraySchema, CommandInputSchema, CommandLineBindable]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
395 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
396 - specializeFrom: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
397 specializeTo: CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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parents:
diff changeset
404
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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405
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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406 - name: CommandOutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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407 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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408 extends: OutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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409 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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410 - specializeFrom: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
411 specializeTo: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
412 - specializeFrom: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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413 specializeTo: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
414 - specializeFrom: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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415 specializeTo: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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416 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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417 - name: outputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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418 type: CommandOutputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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419 jsonldPredicate: "cwl:outputBinding"
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420 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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421 Describes how to generate this output object based on the files
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parents:
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422 produced by a CommandLineTool
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423
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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424
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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425 - name: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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426 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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427 extends: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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428 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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429 - specializeFrom: OutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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430 specializeTo: CommandOutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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431
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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432
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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433 - name: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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434 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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435 extends: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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436 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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437 - specializeFrom: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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438 specializeTo: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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439 - specializeFrom: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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440 specializeTo: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
441 - specializeFrom: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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442 specializeTo: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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443
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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444
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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445 - name: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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446 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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447 extends: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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448 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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449 - specializeFrom: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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450 specializeTo: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
451 - specializeFrom: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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452 specializeTo: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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453 - specializeFrom: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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454 specializeTo: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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455
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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456
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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457 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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458 name: CommandInputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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459 extends: InputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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460 doc: An input parameter for a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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461 fields:
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parents:
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462 - name: type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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463 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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464 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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465 - stdin
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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466 - CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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467 - CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
468 - CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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469 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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470 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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471 items:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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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"
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parents:
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475 - CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
476 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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477 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
478 "_id": "sld:type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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479 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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480 refScope: 2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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481 typeDSL: True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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482 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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483 Specify valid types of data that may be assigned to this parameter.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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484 - name: inputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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485 type: CommandLineBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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486 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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487 Describes how to turns the input parameters of a process into
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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488 command line arguments.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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489 jsonldPredicate: "cwl:inputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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490
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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491 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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492 name: CommandOutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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493 extends: OutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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494 doc: An output parameter for a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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495 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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496 - name: type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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497 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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498 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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499 - stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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500 - stderr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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501 - CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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502 - CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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503 - CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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504 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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505 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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506 items:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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parents:
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510 - CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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511 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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512 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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513 "_id": "sld:type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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514 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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parents:
diff changeset
653 - specializeFrom: OutputParameter
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parents:
diff changeset
654 specializeTo: CommandOutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
655 doc: |
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parents:
diff changeset
656 This defines the schema of the CWL Command Line Tool Description document.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
657
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
658 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
659 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
660 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
661 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
662 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
663 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
664 - name: baseCommand
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
665 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
666 Specifies the program to execute. If an array, the first element of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
667 the array is the command to execute, and subsequent elements are
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
668 mandatory command line arguments. The elements in `baseCommand` must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
669 appear before any command line bindings from `inputBinding` or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
670 `arguments`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
671
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
672 If `baseCommand` is not provided or is an empty array, the first
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
673 element of the command line produced after processing `inputBinding` or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
674 `arguments` must be used as the program to execute.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
675
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parents:
diff changeset
676 If the program includes a path separator character it must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
677 be an absolute path, otherwise it is an error. If the program does not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
678 include a path separator, search the `$PATH` variable in the runtime
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
679 environment of the workflow runner find the absolute path of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
680 executable.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
681 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
682 - string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
683 - string[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
684 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
685 "_id": "cwl:baseCommand"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
686 "_container": "@list"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
687 - name: arguments
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
688 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
689 Command line bindings which are not directly associated with input
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
690 parameters. If the value is a string, it is used as a string literal
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
691 argument. If it is an Expression, the result of the evaluation is used
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
692 as an argument.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
693 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
694 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
695 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
696 items: [string, Expression, CommandLineBinding]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
697 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
698 "_id": "cwl:arguments"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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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"
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parents:
diff changeset
784
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
785 A container image may specify an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
786 [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
787 and/or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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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"
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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"
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parents:
diff changeset
795 concerns of the implicit hidden execution point (For further discussion, see
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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parents:
diff changeset
798 CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
799 `requirements` section.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
800
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
801 ## Interaction with other requirements
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
802
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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parents:
diff changeset
807
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
808 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
809 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
810 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
811 doc: "Always 'DockerRequirement'"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
812 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
813 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
814 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
815 - name: dockerPull
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
816 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
817 doc: "Specify a Docker image to retrieve using `docker pull`."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
818 - name: dockerLoad
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
819 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
820 doc: "Specify a HTTP URL from which to download a Docker image using `docker load`."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
821 - name: dockerFile
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
822 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
823 doc: "Supply the contents of a Dockerfile which will be built using `docker build`."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
824 - name: dockerImport
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
825 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
826 doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
827 - name: dockerImageId
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
828 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
829 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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parents:
diff changeset
835 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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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"
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parents:
diff changeset
852 "_id": "@type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
853 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
854 - name: packages
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
855 type: SoftwarePackage[]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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parents:
diff changeset
859 mapPredicate: specs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
860
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
861 - name: SoftwarePackage
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
862 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
863 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
864 - name: package
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
865 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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parents:
diff changeset
871 type: string[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
872 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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parents:
diff changeset
876 type: string[]?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
877 jsonldPredicate: {_type: "@id", noLinkCheck: true}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
878 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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"
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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"
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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"
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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"
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parents:
diff changeset
904
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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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.
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1165
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1166 fields:
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1167 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1168 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1169 doc: "Always 'NetworkAccess'"
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1170 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1171 "_id": "@type"
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1172 "_type": "@vocab"
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1173 - name: networkAccess
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1174 type: [boolean, Expression]
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1175
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1176 - name: InplaceUpdateRequirement
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1177 type: record
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1178 extends: cwl:ProcessRequirement
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1179 doc: |
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1180
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1181 If `inplaceUpdate` is true, then an implementation supporting this
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1182 feature may permit tools to directly update files with `writable:
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1183 true` in InitialWorkDirRequirement. That is, as an optimization,
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1184 files may be destructively modified in place as opposed to copied
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1185 and updated.
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1186
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1187 An implementation must ensure that only one workflow step may
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1188 access a writable file at a time. It is an error if a file which
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1189 is writable by one workflow step file is accessed (for reading or
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1190 writing) by any other workflow step running independently.
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1191 However, a file which has been updated in a previous completed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1192 step may be used as input to multiple steps, provided it is
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1193 read-only in every step.
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1194
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1195 Workflow steps which modify a file must produce the modified file
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1196 as output. Downstream steps which futher process the file must
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1197 use the output of previous steps, and not refer to a common input
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1198 (this is necessary for both ordering and correctness).
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1199
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1200 Workflow authors should provide this in the `hints` section. The
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1201 intent of this feature is that workflows produce the same results
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1202 whether or not InplaceUpdateRequirement is supported by the
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1203 implementation, and this feature is primarily available as an
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1204 optimization for particular environments.
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1205
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1206 Users and implementers should be aware that workflows that
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1207 destructively modify inputs may not be repeatable or reproducible.
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1208 In particular, enabling this feature implies that WorkReuse should
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1209 not be enabled.
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1210
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1211 fields:
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1212 class:
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1213 type: string
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1214 doc: "Always 'InplaceUpdateRequirement'"
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1215 jsonldPredicate:
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1216 "_id": "@type"
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1217 "_type": "@vocab"
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1218 inplaceUpdate:
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1219 type: boolean
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1220
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1221 - type: record
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1222 name: ToolTimeLimit
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1223 extends: ProcessRequirement
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1224 doc: |
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1225 Set an upper limit on the execution time of a CommandLineTool.
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1226 A CommandLineTool whose execution duration exceeds the time
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1227 limit may be preemptively terminated and considered failed.
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1228 May also be used by batch systems to make scheduling decisions.
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1229 The execution duration excludes external operations, such as
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1230 staging of files, pulling a docker image etc, and only counts
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1231 wall-time for the execution of the command line itself.
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1232 fields:
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1233 - name: class
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1234 type: string
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1235 doc: "Always 'ToolTimeLimit'"
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1236 jsonldPredicate:
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1237 "_id": "@type"
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1238 "_type": "@vocab"
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1239 - name: timelimit
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1240 type: [long, Expression]
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1241 doc: |
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1242 The time limit, in seconds. A time limit of zero means no
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1243 time limit. Negative time limits are an error.