Mercurial > repos > shellac > guppy_basecaller
annotate env/lib/python3.7/site-packages/cwltool/schemas/v1.0/CommandLineTool.yml @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author | shellac |
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date | Thu, 14 May 2020 14:56:58 -0400 |
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1 $base: "https://w3id.org/cwl/cwl#" |
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2 |
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3 $namespaces: |
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4 cwl: "https://w3id.org/cwl/cwl#" |
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5 |
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6 $graph: |
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7 |
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8 - name: CommandLineToolDoc |
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9 type: documentation |
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10 doc: |
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11 - | |
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12 # Common Workflow Language (CWL) Command Line Tool Description, v1.0.2 |
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13 |
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14 This version: |
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15 * https://w3id.org/cwl/v1.0/ |
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16 |
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17 Current version: |
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18 * https://w3id.org/cwl/ |
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19 - "\n\n" |
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20 - {$include: contrib.md} |
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21 - "\n\n" |
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22 - | |
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23 # Abstract |
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24 |
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25 A Command Line Tool is a non-interactive executable program that reads |
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26 some input, performs a computation, and terminates after producing some |
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27 output. Command line programs are a flexible unit of code sharing and |
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28 reuse, unfortunately the syntax and input/output semantics among command |
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29 line programs is extremely heterogeneous. A common layer for describing |
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30 the syntax and semantics of programs can reduce this incidental |
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31 complexity by providing a consistent way to connect programs together. |
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32 This specification defines the Common Workflow Language (CWL) Command |
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33 Line Tool Description, a vendor-neutral standard for describing the |
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34 syntax and input/output semantics of command line programs. |
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35 |
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36 - {$include: intro.md} |
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37 |
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38 - | |
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39 ## Introduction to CWL Command Line Tool standard v1.0.2 |
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40 |
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41 This specification represents the third stable release from the CWL |
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42 group. Since the initial v1.0 release, v1.0.2 introduces the following |
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43 updates to the CWL Command Line Tool standard. Documents should continue |
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44 to use `cwlVersion: v1.0` and existing v1.0 documents remain valid, |
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45 however CWL documents that relied on previously undefined or |
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46 underspecified behavior may have slightly different behavior in v1.0.2. |
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47 |
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48 * 13 July 2016: Mark `baseCommand` as optional and update descriptive text. |
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49 * 14 November 2016: Clarify [SoftwareRequirement](#SoftwareRequirement) |
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50 `spec` fields. |
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51 * 12 March 2017: |
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52 * Mark `default` as not required for link checking. |
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53 * Add note that files in InitialWorkDir must have path in output directory. |
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54 * Add note that writable: true applies recursively. |
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55 * 23 July 2017: (v1.0.1) |
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56 * Add clarification about scattering over empty arrays. |
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57 * Clarify interpretation of `secondaryFiles` on inputs. |
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58 * Expanded discussion of semantics of `File` and `Directory` types |
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59 * Fixed typo "EMACScript" to "ECMAScript" |
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60 * Clarified application of input parameter default values when the input is `null` or undefined. |
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61 * Clarified valid types and meaning of the format field on inputs versus outputs |
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62 * Clarify that command line arguments must not interpreted as shell except when shellQuote: false |
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63 * Clarify behavior of `entryname` |
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64 * 10 August 2017: (v1.0.2) |
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65 * Clarify behavior resolving expressions in `secondaryFile` |
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66 |
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67 Since draft-3, v1.0 introduces the following changes and additions |
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68 to the CWL Command Line Tool standard: |
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69 |
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70 * The [Directory](#Directory) type. |
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71 * Syntax simplifcations: denoted by the `map<>` syntax. Example: inputs |
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72 contains a list of items, each with an id. Now one can specify |
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73 a mapping of that identifier to the corresponding |
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74 `CommandInputParamater`. |
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75 ``` |
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76 inputs: |
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77 - id: one |
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78 type: string |
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79 doc: First input parameter |
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80 - id: two |
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81 type: int |
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82 doc: Second input parameter |
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83 ``` |
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84 can be |
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85 ``` |
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86 inputs: |
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87 one: |
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88 type: string |
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89 doc: First input parameter |
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90 two: |
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91 type: int |
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92 doc: Second input parameter |
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93 ``` |
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94 * [InitialWorkDirRequirement](#InitialWorkDirRequirement): list of |
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95 files and subdirectories to be present in the output directory prior |
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96 to execution. |
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97 * Shortcuts for specifying the standard [output](#stdout) and/or |
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98 [error](#stderr) streams as a (streamable) File output. |
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99 * [SoftwareRequirement](#SoftwareRequirement) for describing software |
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100 dependencies of a tool. |
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101 * The common `description` field has been renamed to `doc`. |
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102 |
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103 |
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104 ## Purpose |
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105 |
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106 Standalone programs are a flexible and interoperable form of code reuse. |
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107 Unlike monolithic applications, applications and analysis workflows which |
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108 are composed of multiple separate programs can be written in multiple |
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109 languages and execute concurrently on multiple hosts. However, POSIX |
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110 does not dictate computer-readable grammar or semantics for program input |
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111 and output, resulting in extremely heterogeneous command line grammar and |
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112 input/output semantics among program. This is a particular problem in |
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113 distributed computing (multi-node compute clusters) and virtualized |
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114 environments (such as Docker containers) where it is often necessary to |
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115 provision resources such as input files before executing the program. |
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116 |
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117 Often this gap is filled by hard coding program invocation and |
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118 implicitly assuming requirements will be met, or abstracting program |
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119 invocation with wrapper scripts or descriptor documents. Unfortunately, |
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120 where these approaches are application or platform specific it creates a |
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121 significant barrier to reproducibility and portability, as methods |
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122 developed for one platform must be manually ported to be used on new |
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123 platforms. Similarly it creates redundant work, as wrappers for popular |
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124 tools must be rewritten for each application or platform in use. |
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125 |
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126 The Common Workflow Language Command Line Tool Description is designed to |
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127 provide a common standard description of grammar and semantics for |
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128 invoking programs used in data-intensive fields such as Bioinformatics, |
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129 Chemistry, Physics, Astronomy, and Statistics. This specification |
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130 defines a precise data and execution model for Command Line Tools that |
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131 can be implemented on a variety of computing platforms, ranging from a |
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132 single workstation to cluster, grid, cloud, and high performance |
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133 computing platforms. |
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134 |
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135 - {$include: concepts.md} |
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136 - {$include: invocation.md} |
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137 |
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138 |
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139 - type: record |
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140 name: EnvironmentDef |
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141 doc: | |
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142 Define an environment variable that will be set in the runtime environment |
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143 by the workflow platform when executing the command line tool. May be the |
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144 result of executing an expression, such as getting a parameter from input. |
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145 fields: |
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146 - name: envName |
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147 type: string |
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148 doc: The environment variable name |
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149 - name: envValue |
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150 type: [string, Expression] |
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151 doc: The environment variable value |
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152 |
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153 - type: record |
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154 name: CommandLineBinding |
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155 extends: InputBinding |
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156 doc: | |
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157 |
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158 When listed under `inputBinding` in the input schema, the term |
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159 "value" refers to the the corresponding value in the input object. For |
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160 binding objects listed in `CommandLineTool.arguments`, the term "value" |
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161 refers to the effective value after evaluating `valueFrom`. |
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162 |
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163 The binding behavior when building the command line depends on the data |
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164 type of the value. If there is a mismatch between the type described by |
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165 the input schema and the effective value, such as resulting from an |
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166 expression evaluation, an implementation must use the data type of the |
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167 effective value. |
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168 |
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169 - **string**: Add `prefix` and the string to the command line. |
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170 |
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171 - **number**: Add `prefix` and decimal representation to command line. |
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172 |
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173 - **boolean**: If true, add `prefix` to the command line. If false, add |
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174 nothing. |
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175 |
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176 - **File**: Add `prefix` and the value of |
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177 [`File.path`](#File) to the command line. |
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178 |
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179 - **array**: If `itemSeparator` is specified, add `prefix` and the join |
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180 the array into a single string with `itemSeparator` separating the |
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181 items. Otherwise first add `prefix`, then recursively process |
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182 individual elements. |
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183 |
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184 - **object**: Add `prefix` only, and recursively add object fields for |
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185 which `inputBinding` is specified. |
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186 |
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187 - **null**: Add nothing. |
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188 |
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189 fields: |
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190 - name: position |
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191 type: int? |
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192 doc: "The sorting key. Default position is 0." |
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193 - name: prefix |
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194 type: string? |
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195 doc: "Command line prefix to add before the value." |
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196 - name: separate |
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197 type: boolean? |
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198 doc: | |
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199 If true (default), then the prefix and value must be added as separate |
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200 command line arguments; if false, prefix and value must be concatenated |
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201 into a single command line argument. |
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202 - name: itemSeparator |
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203 type: string? |
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204 doc: | |
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205 Join the array elements into a single string with the elements |
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206 separated by by `itemSeparator`. |
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207 - name: valueFrom |
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208 type: |
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209 - "null" |
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210 - string |
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211 - Expression |
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212 jsonldPredicate: "cwl:valueFrom" |
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213 doc: | |
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214 If `valueFrom` is a constant string value, use this as the value and |
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215 apply the binding rules above. |
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216 |
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217 If `valueFrom` is an expression, evaluate the expression to yield the |
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218 actual value to use to build the command line and apply the binding |
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219 rules above. If the inputBinding is associated with an input |
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220 parameter, the value of `self` in the expression will be the value of |
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221 the input parameter. Input parameter defaults (as specified by the |
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222 `InputParameter.default` field) must be applied before evaluating the |
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223 expression. |
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224 |
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225 When a binding is part of the `CommandLineTool.arguments` field, |
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226 the `valueFrom` field is required. |
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227 |
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228 - name: shellQuote |
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229 type: boolean? |
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230 doc: | |
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231 If `ShellCommandRequirement` is in the requirements for the current command, |
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232 this controls whether the value is quoted on the command line (default is true). |
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233 Use `shellQuote: false` to inject metacharacters for operations such as pipes. |
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234 |
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235 If `shellQuote` is true or not provided, the implementation must not |
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236 permit interpretation of any shell metacharacters or directives. |
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237 |
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238 - type: record |
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239 name: CommandOutputBinding |
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240 extends: OutputBinding |
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241 doc: | |
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242 Describes how to generate an output parameter based on the files produced |
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243 by a CommandLineTool. |
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244 |
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245 The output parameter value is generated by applying these operations in the |
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246 following order: |
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247 |
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248 - glob |
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249 - loadContents |
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250 - outputEval |
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251 - secondaryFiles |
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252 fields: |
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253 - name: glob |
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254 type: |
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255 - "null" |
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256 - string |
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257 - Expression |
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258 - type: array |
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259 items: string |
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260 doc: | |
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261 Find files relative to the output directory, using POSIX glob(3) |
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262 pathname matching. If an array is provided, find files that match any |
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263 pattern in the array. If an expression is provided, the expression must |
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264 return a string or an array of strings, which will then be evaluated as |
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265 one or more glob patterns. Must only match and return files which |
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266 actually exist. |
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267 - name: loadContents |
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268 type: |
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269 - "null" |
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270 - boolean |
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271 jsonldPredicate: "cwl:loadContents" |
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272 doc: | |
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273 For each file matched in `glob`, read up to |
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274 the first 64 KiB of text from the file and place it in the `contents` |
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275 field of the file object for manipulation by `outputEval`. |
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276 - name: outputEval |
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277 type: |
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278 - "null" |
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279 - string |
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280 - Expression |
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281 doc: | |
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282 Evaluate an expression to generate the output value. If `glob` was |
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283 specified, the value of `self` must be an array containing file objects |
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284 that were matched. If no files were matched, `self` must be a zero |
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285 length array; if a single file was matched, the value of `self` is an |
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286 array of a single element. Additionally, if `loadContents` is `true`, |
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287 the File objects must include up to the first 64 KiB of file contents |
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288 in the `contents` field. |
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289 |
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290 |
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291 - name: CommandInputRecordField |
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292 type: record |
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293 extends: InputRecordField |
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294 specialize: |
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295 - specializeFrom: InputRecordSchema |
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296 specializeTo: CommandInputRecordSchema |
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297 - specializeFrom: InputEnumSchema |
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298 specializeTo: CommandInputEnumSchema |
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299 - specializeFrom: InputArraySchema |
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300 specializeTo: CommandInputArraySchema |
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301 - specializeFrom: InputBinding |
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302 specializeTo: CommandLineBinding |
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303 |
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304 |
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305 - name: CommandInputRecordSchema |
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306 type: record |
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307 extends: InputRecordSchema |
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308 specialize: |
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309 - specializeFrom: InputRecordField |
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310 specializeTo: CommandInputRecordField |
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311 |
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312 |
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313 - name: CommandInputEnumSchema |
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314 type: record |
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315 extends: InputEnumSchema |
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316 specialize: |
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317 - specializeFrom: InputBinding |
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318 specializeTo: CommandLineBinding |
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319 |
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320 |
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321 - name: CommandInputArraySchema |
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322 type: record |
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323 extends: InputArraySchema |
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324 specialize: |
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325 - specializeFrom: InputRecordSchema |
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326 specializeTo: CommandInputRecordSchema |
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327 - specializeFrom: InputEnumSchema |
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328 specializeTo: CommandInputEnumSchema |
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329 - specializeFrom: InputArraySchema |
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330 specializeTo: CommandInputArraySchema |
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331 - specializeFrom: InputBinding |
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332 specializeTo: CommandLineBinding |
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333 |
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334 |
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335 - name: CommandOutputRecordField |
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336 type: record |
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337 extends: OutputRecordField |
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338 specialize: |
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339 - specializeFrom: OutputRecordSchema |
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340 specializeTo: CommandOutputRecordSchema |
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341 - specializeFrom: OutputEnumSchema |
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342 specializeTo: CommandOutputEnumSchema |
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343 - specializeFrom: OutputArraySchema |
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344 specializeTo: CommandOutputArraySchema |
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345 - specializeFrom: OutputBinding |
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346 specializeTo: CommandOutputBinding |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
347 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
348 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
349 - name: CommandOutputRecordSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
350 type: record |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
351 extends: OutputRecordSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
352 specialize: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
353 - specializeFrom: OutputRecordField |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
354 specializeTo: CommandOutputRecordField |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
355 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
356 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
357 - name: CommandOutputEnumSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
358 type: record |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
359 extends: OutputEnumSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
360 specialize: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
361 - specializeFrom: OutputRecordSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
362 specializeTo: CommandOutputRecordSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
363 - specializeFrom: OutputEnumSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
364 specializeTo: CommandOutputEnumSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
365 - specializeFrom: OutputArraySchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
366 specializeTo: CommandOutputArraySchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
367 - specializeFrom: OutputBinding |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
368 specializeTo: CommandOutputBinding |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
369 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
370 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
371 - name: CommandOutputArraySchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
372 type: record |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
373 extends: OutputArraySchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
374 specialize: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
375 - specializeFrom: OutputRecordSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
376 specializeTo: CommandOutputRecordSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
377 - specializeFrom: OutputEnumSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
378 specializeTo: CommandOutputEnumSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
379 - specializeFrom: OutputArraySchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
380 specializeTo: CommandOutputArraySchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
381 - specializeFrom: OutputBinding |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
382 specializeTo: CommandOutputBinding |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
383 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
384 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
385 - type: record |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
386 name: CommandInputParameter |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
387 extends: InputParameter |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
388 doc: An input parameter for a CommandLineTool. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
389 specialize: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
390 - specializeFrom: InputRecordSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
391 specializeTo: CommandInputRecordSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
392 - specializeFrom: InputEnumSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
393 specializeTo: CommandInputEnumSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
394 - specializeFrom: InputArraySchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
395 specializeTo: CommandInputArraySchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
396 - specializeFrom: InputBinding |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
397 specializeTo: CommandLineBinding |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
398 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
399 - type: record |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
400 name: CommandOutputParameter |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
401 extends: OutputParameter |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
402 doc: An output parameter for a CommandLineTool. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
403 specialize: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
404 - specializeFrom: OutputBinding |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
405 specializeTo: CommandOutputBinding |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
406 fields: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
407 - name: type |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
408 type: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
409 - "null" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
410 - CWLType |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
411 - stdout |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
412 - stderr |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
413 - CommandOutputRecordSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
414 - CommandOutputEnumSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
415 - CommandOutputArraySchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
416 - string |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
417 - type: array |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
418 items: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
419 - CWLType |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
420 - CommandOutputRecordSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
421 - CommandOutputEnumSchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
422 - CommandOutputArraySchema |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
423 - string |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
424 jsonldPredicate: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
425 "_id": "sld:type" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
426 "_type": "@vocab" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
427 refScope: 2 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
428 typeDSL: True |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
429 doc: | |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
430 Specify valid types of data that may be assigned to this parameter. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
431 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
432 - name: stdout |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
433 type: enum |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
434 symbols: [ "cwl:stdout" ] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
435 docParent: "#CommandOutputParameter" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
436 doc: | |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
437 Only valid as a `type` for a `CommandLineTool` output with no |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
438 `outputBinding` set. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
439 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
440 The following |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
441 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
442 outputs: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
443 an_output_name: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
444 type: stdout |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
445 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
446 stdout: a_stdout_file |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
447 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
448 is equivalent to |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
449 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
450 outputs: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
451 an_output_name: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
452 type: File |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
453 streamable: true |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
454 outputBinding: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
455 glob: a_stdout_file |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
456 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
457 stdout: a_stdout_file |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
458 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
459 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
460 If there is no `stdout` name provided, a random filename will be created. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
461 For example, the following |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
462 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
463 outputs: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
464 an_output_name: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
465 type: stdout |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
466 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
467 is equivalent to |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
468 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
469 outputs: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
470 an_output_name: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
471 type: File |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
472 streamable: true |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
473 outputBinding: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
474 glob: random_stdout_filenameABCDEFG |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
475 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
476 stdout: random_stdout_filenameABCDEFG |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
477 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
478 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
479 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
480 - name: stderr |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
481 type: enum |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
482 symbols: [ "cwl:stderr" ] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
483 docParent: "#CommandOutputParameter" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
484 doc: | |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
485 Only valid as a `type` for a `CommandLineTool` output with no |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
486 `outputBinding` set. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
487 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
488 The following |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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changeset
|
489 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
490 outputs: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
491 an_output_name: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
492 type: stderr |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
493 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
494 stderr: a_stderr_file |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
495 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
496 is equivalent to |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
497 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
498 outputs: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
499 an_output_name: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
500 type: File |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
501 streamable: true |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
502 outputBinding: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
503 glob: a_stderr_file |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
504 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
505 stderr: a_stderr_file |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
506 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
507 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
508 If there is no `stderr` name provided, a random filename will be created. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
509 For example, the following |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
510 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
511 outputs: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
512 an_output_name: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
513 type: stderr |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
514 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
515 is equivalent to |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
516 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
517 outputs: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
518 an_output_name: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
519 type: File |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
520 streamable: true |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
521 outputBinding: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
522 glob: random_stderr_filenameABCDEFG |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
523 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
524 stderr: random_stderr_filenameABCDEFG |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
525 ``` |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
526 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
527 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
528 - type: record |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
529 name: CommandLineTool |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
530 extends: Process |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
531 documentRoot: true |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
532 specialize: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
533 - specializeFrom: InputParameter |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
534 specializeTo: CommandInputParameter |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
535 - specializeFrom: OutputParameter |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
536 specializeTo: CommandOutputParameter |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
537 doc: | |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
538 This defines the schema of the CWL Command Line Tool Description document. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
539 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
540 fields: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
541 - name: class |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
542 jsonldPredicate: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
543 "_id": "@type" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
544 "_type": "@vocab" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
545 type: string |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
546 - name: baseCommand |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
547 doc: | |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
548 Specifies the program to execute. If an array, the first element of |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
549 the array is the command to execute, and subsequent elements are |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
550 mandatory command line arguments. The elements in `baseCommand` must |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
551 appear before any command line bindings from `inputBinding` or |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
552 `arguments`. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
553 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
554 If `baseCommand` is not provided or is an empty array, the first |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
555 element of the command line produced after processing `inputBinding` or |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
556 `arguments` must be used as the program to execute. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
557 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
558 If the program includes a path separator character it must |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
559 be an absolute path, otherwise it is an error. If the program does not |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
560 include a path separator, search the `$PATH` variable in the runtime |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
561 environment of the workflow runner find the absolute path of the |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
562 executable. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
563 type: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
564 - string? |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
565 - string[]? |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
566 jsonldPredicate: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
567 "_id": "cwl:baseCommand" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
568 "_container": "@list" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
569 - name: arguments |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
570 doc: | |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
571 Command line bindings which are not directly associated with input parameters. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
572 type: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
573 - "null" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
574 - type: array |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
575 items: [string, Expression, CommandLineBinding] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
576 jsonldPredicate: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
577 "_id": "cwl:arguments" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
578 "_container": "@list" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
579 - name: stdin |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
580 type: ["null", string, Expression] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
581 doc: | |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
582 A path to a file whose contents must be piped into the command's |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
583 standard input stream. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
584 - name: stderr |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
585 type: ["null", string, Expression] |
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586 jsonldPredicate: "https://w3id.org/cwl/cwl#stderr" |
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587 doc: | |
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588 Capture the command's standard error stream to a file written to |
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589 the designated output directory. |
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590 |
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591 If `stderr` is a string, it specifies the file name to use. |
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592 |
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593 If `stderr` is an expression, the expression is evaluated and must |
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594 return a string with the file name to use to capture stderr. If the |
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595 return value is not a string, or the resulting path contains illegal |
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596 characters (such as the path separator `/`) it is an error. |
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597 - name: stdout |
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598 type: ["null", string, Expression] |
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599 jsonldPredicate: "https://w3id.org/cwl/cwl#stdout" |
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600 doc: | |
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601 Capture the command's standard output stream to a file written to |
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602 the designated output directory. |
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603 |
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604 If `stdout` is a string, it specifies the file name to use. |
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605 |
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606 If `stdout` is an expression, the expression is evaluated and must |
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607 return a string with the file name to use to capture stdout. If the |
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608 return value is not a string, or the resulting path contains illegal |
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609 characters (such as the path separator `/`) it is an error. |
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610 - name: successCodes |
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611 type: int[]? |
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612 doc: | |
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613 Exit codes that indicate the process completed successfully. |
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614 |
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615 - name: temporaryFailCodes |
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616 type: int[]? |
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617 doc: | |
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618 Exit codes that indicate the process failed due to a possibly |
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619 temporary condition, where executing the process with the same |
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620 runtime environment and inputs may produce different results. |
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621 |
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622 - name: permanentFailCodes |
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623 type: int[]? |
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624 doc: |
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625 Exit codes that indicate the process failed due to a permanent logic |
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626 error, where executing the process with the same runtime environment and |
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627 same inputs is expected to always fail. |
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628 |
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629 |
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630 - type: record |
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631 name: DockerRequirement |
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632 extends: ProcessRequirement |
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633 doc: | |
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634 Indicates that a workflow component should be run in a |
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635 [Docker](http://docker.com) container, and specifies how to fetch or build |
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636 the image. |
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637 |
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638 If a CommandLineTool lists `DockerRequirement` under |
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639 `hints` (or `requirements`), it may (or must) be run in the specified Docker |
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640 container. |
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641 |
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642 The platform must first acquire or install the correct Docker image as |
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643 specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`. |
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644 |
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645 The platform must execute the tool in the container using `docker run` with |
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646 the appropriate Docker image and tool command line. |
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647 |
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648 The workflow platform may provide input files and the designated output |
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649 directory through the use of volume bind mounts. The platform may rewrite |
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650 file paths in the input object to correspond to the Docker bind mounted |
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651 locations. |
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652 |
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653 When running a tool contained in Docker, the workflow platform must not |
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654 assume anything about the contents of the Docker container, such as the |
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655 presence or absence of specific software, except to assume that the |
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656 generated command line represents a valid command within the runtime |
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657 environment of the container. |
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658 |
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659 ## Interaction with other requirements |
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660 |
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661 If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a |
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662 DockerRequirement, the environment variables must be provided to Docker |
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663 using `--env` or `--env-file` and interact with the container's preexisting |
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664 environment as defined by Docker. |
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665 |
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666 fields: |
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667 - name: class |
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668 type: string |
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669 doc: "Always 'DockerRequirement'" |
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670 jsonldPredicate: |
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671 "_id": "@type" |
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672 "_type": "@vocab" |
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673 - name: dockerPull |
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674 type: string? |
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675 doc: "Specify a Docker image to retrieve using `docker pull`." |
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676 - name: dockerLoad |
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677 type: string? |
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678 doc: "Specify a HTTP URL from which to download a Docker image using `docker load`." |
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679 - name: dockerFile |
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680 type: string? |
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681 doc: "Supply the contents of a Dockerfile which will be built using `docker build`." |
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682 - name: dockerImport |
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683 type: string? |
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684 doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import." |
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685 - name: dockerImageId |
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686 type: string? |
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687 doc: | |
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688 The image id that will be used for `docker run`. May be a |
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689 human-readable image name or the image identifier hash. May be skipped |
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690 if `dockerPull` is specified, in which case the `dockerPull` image id |
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691 must be used. |
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692 - name: dockerOutputDirectory |
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693 type: string? |
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|
694 doc: | |
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695 Set the designated output directory to a specific location inside the |
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696 Docker container. |
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|
697 |
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|
698 |
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699 - type: record |
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700 name: SoftwareRequirement |
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|
701 extends: ProcessRequirement |
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|
702 doc: | |
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|
703 A list of software packages that should be configured in the environment of |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
704 the defined process. |
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|
705 fields: |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
706 - name: class |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
707 type: string |
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diff
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|
708 doc: "Always 'SoftwareRequirement'" |
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|
709 jsonldPredicate: |
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|
710 "_id": "@type" |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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711 "_type": "@vocab" |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
712 - name: packages |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
713 type: SoftwarePackage[] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
714 doc: "The list of software to be configured." |
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|
715 jsonldPredicate: |
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|
716 mapSubject: package |
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|
717 mapPredicate: specs |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
718 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
719 - name: SoftwarePackage |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
720 type: record |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff
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|
721 fields: |
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|
722 - name: package |
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|
723 type: string |
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|
724 doc: | |
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|
725 The name of the software to be made available. If the name is |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
726 common, inconsistent, or otherwise ambiguous it should be combined with |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
727 one or more identifiers in the `specs` field. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
728 - name: version |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
729 type: string[]? |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
730 doc: | |
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|
731 The (optional) versions of the software that are known to be |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
732 compatible. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
733 - name: specs |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
734 type: string[]? |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
735 doc: | |
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|
736 One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
737 identifying resources for installing or enabling the software named in |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
738 the `package` field. Implementations may provide resolvers which map |
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parents:
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|
739 these software identifer IRIs to some configuration action; or they can |
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|
740 use only the name from the `package` field on a best effort basis. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
741 |
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|
742 For example, the IRI https://packages.debian.org/bowtie could |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
743 be resolved with `apt-get install bowtie`. The IRI |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
744 https://anaconda.org/bioconda/bowtie could be resolved with `conda |
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|
745 install -c bioconda bowtie`. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
746 |
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|
747 IRIs can also be system independent and used to map to a specific |
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|
748 software installation or selection mechanism. |
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|
749 Using [RRID](https://www.identifiers.org/rrid/) as an example: |
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parents:
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|
750 https://identifiers.org/rrid/RRID:SCR_005476 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
751 could be fulfilled using the above mentioned Debian or bioconda |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
752 package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/), |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
753 or any other mechanism the platform chooses. IRIs can also be from |
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|
754 identifer sources that are discipline specific yet still system |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
755 independent. As an example, the equivalent [ELIXIR Tools and Data |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
756 Service Registry](https://bio.tools) IRI to the previous RRID example is |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
757 https://bio.tools/tool/bowtie2/version/2.2.8. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
758 If supported by a given registry, implementations are encouraged to |
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parents:
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|
759 query these system independent sofware identifier IRIs directly for |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
760 links to packaging systems. |
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|
761 |
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|
762 A site specific IRI can be listed as well. For example, an academic |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
763 computing cluster using Environement Modules could list the IRI |
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parents:
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|
764 `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that |
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parents:
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|
765 `module load bowtie-tbb/1.1.2` should be executed to make available |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
766 `bowtie` version 1.1.2 compiled with the TBB library prior to running |
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parents:
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|
767 the accompanying Workflow or CommandLineTool. Note that the example IRI |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
768 is specific to a particular institution and computing environment as |
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parents:
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|
769 the Environment Modules system does not have a common namespace or |
26e78fe6e8c4
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shellac
parents:
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|
770 standardized naming convention. |
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|
771 |
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parents:
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|
772 This last example is the least portable and should only be used if |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
773 mechanisms based off of the `package` field or more generic IRIs are |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
774 unavailable or unsuitable. While harmless to other sites, site specific |
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shellac
parents:
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|
775 software IRIs should be left out of shared CWL descriptions to avoid |
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parents:
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|
776 clutter. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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changeset
|
777 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
778 - name: Dirent |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
779 type: record |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
780 doc: | |
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parents:
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|
781 Define a file or subdirectory that must be placed in the designated output |
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parents:
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|
782 directory prior to executing the command line tool. May be the result of |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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783 executing an expression, such as building a configuration file from a |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
784 template. |
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parents:
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|
785 fields: |
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parents:
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786 - name: entryname |
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|
787 type: ["null", string, Expression] |
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788 jsonldPredicate: |
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|
789 _id: cwl:entryname |
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|
790 doc: | |
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parents:
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791 The name of the file or subdirectory to create in the output directory. |
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792 If `entry` is a File or Directory, the `entryname` field overrides the value |
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793 of `basename` of the File or Directory object. Optional. |
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|
794 - name: entry |
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|
795 type: [string, Expression] |
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796 jsonldPredicate: |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
797 _id: cwl:entry |
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parents:
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|
798 doc: | |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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799 If the value is a string literal or an expression which evaluates to a |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
800 string, a new file must be created with the string as the file contents. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
801 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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802 If the value is an expression that evaluates to a `File` object, this |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
803 indicates the referenced file should be added to the designated output |
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shellac
parents:
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|
804 directory prior to executing the tool. |
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parents:
diff
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|
805 |
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|
806 If the value is an expression that evaluates to a `Dirent` object, this |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
807 indicates that the File or Directory in `entry` should be added to the |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
808 designated output directory with the name in `entryname`. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
809 |
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parents:
diff
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|
810 If `writable` is false, the file may be made available using a bind |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
811 mount or file system link to avoid unnecessary copying of the input |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
812 file. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
813 - name: writable |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
814 type: boolean? |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
815 doc: | |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
816 If true, the file or directory must be writable by the tool. Changes |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
817 to the file or directory must be isolated and not visible by any other |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
818 CommandLineTool process. This may be implemented by making a copy of |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
819 the original file or directory. Default false (files and directories |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
820 read-only by default). |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff
changeset
|
821 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
822 A directory marked as `writable: true` implies that all files and |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
823 subdirectories are recursively writable as well. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
824 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
825 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
826 - name: InitialWorkDirRequirement |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
827 type: record |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff
changeset
|
828 extends: ProcessRequirement |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
829 doc: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
830 Define a list of files and subdirectories that must be created by the |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff
changeset
|
831 workflow platform in the designated output directory prior to executing the |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
832 command line tool. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
833 fields: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff
changeset
|
834 - name: class |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
835 type: string |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
836 doc: InitialWorkDirRequirement |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
837 jsonldPredicate: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
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|
838 "_id": "@type" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff
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|
839 "_type": "@vocab" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
840 - name: listing |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
841 type: |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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changeset
|
842 - type: array |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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changeset
|
843 items: [File, Directory, Dirent, string, Expression] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
844 - string |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
845 - Expression |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
846 jsonldPredicate: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
847 _id: "cwl:listing" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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848 doc: | |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
849 The list of files or subdirectories that must be placed in the |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
850 designated output directory prior to executing the command line tool. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
851 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
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|
852 May be an expression. If so, the expression return value must validate |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
853 as `{type: array, items: [File, Directory]}`. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
854 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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changeset
|
855 Files or Directories which are listed in the input parameters and |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
856 appear in the `InitialWorkDirRequirement` listing must have their |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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changeset
|
857 `path` set to their staged location in the designated output directory. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
858 If the same File or Directory appears more than once in the |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
859 `InitialWorkDirRequirement` listing, the implementation must choose |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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changeset
|
860 exactly one value for `path`; how this value is chosen is undefined. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
861 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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changeset
|
862 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
863 - name: EnvVarRequirement |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
864 type: record |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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changeset
|
865 extends: ProcessRequirement |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
866 doc: | |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
867 Define a list of environment variables which will be set in the |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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|
868 execution environment of the tool. See `EnvironmentDef` for details. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
869 fields: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
870 - name: class |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
871 type: string |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
872 doc: "Always 'EnvVarRequirement'" |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
873 jsonldPredicate: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
874 "_id": "@type" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
875 "_type": "@vocab" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
876 - name: envDef |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
877 type: EnvironmentDef[] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
878 doc: The list of environment variables. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
879 jsonldPredicate: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
880 mapSubject: envName |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff
changeset
|
881 mapPredicate: envValue |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
882 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
883 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
884 - type: record |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
885 name: ShellCommandRequirement |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
changeset
|
886 extends: ProcessRequirement |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
887 doc: | |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
888 Modify the behavior of CommandLineTool to generate a single string |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
889 containing a shell command line. Each item in the argument list must be |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
890 joined into a string separated by single spaces and quoted to prevent |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
891 intepretation by the shell, unless `CommandLineBinding` for that argument |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
892 contains `shellQuote: false`. If `shellQuote: false` is specified, the |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
893 argument is joined into the command string without quoting, which allows |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
894 the use of shell metacharacters such as `|` for pipes. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
895 fields: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
896 - name: class |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
897 type: string |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
898 doc: "Always 'ShellCommandRequirement'" |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
899 jsonldPredicate: |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
900 "_id": "@type" |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
901 "_type": "@vocab" |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
902 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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changeset
|
903 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
904 - type: record |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
905 name: ResourceRequirement |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
906 extends: ProcessRequirement |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff
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|
907 doc: | |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
908 Specify basic hardware resource requirements. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
909 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
910 "min" is the minimum amount of a resource that must be reserved to schedule |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
911 a job. If "min" cannot be satisfied, the job should not be run. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
912 |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
913 "max" is the maximum amount of a resource that the job shall be permitted |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
914 to use. If a node has sufficient resources, multiple jobs may be scheduled |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
915 on a single node provided each job's "max" resource requirements are |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
916 met. If a job attempts to exceed its "max" resource allocation, an |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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917 implementation may deny additional resources, which may result in job |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
918 failure. |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff
changeset
|
919 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
920 If "min" is specified but "max" is not, then "max" == "min" |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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921 If "max" is specified by "min" is not, then "min" == "max". |
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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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|
922 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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923 It is an error if max < min. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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|
924 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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925 It is an error if the value of any of these fields is negative. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
926 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
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927 If neither "min" nor "max" is specified for a resource, an implementation may provide a default. |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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|
928 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff
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|
929 fields: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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|
930 - name: class |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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931 type: string |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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|
932 doc: "Always 'ResourceRequirement'" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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changeset
|
933 jsonldPredicate: |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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|
934 "_id": "@type" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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935 "_type": "@vocab" |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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936 - name: coresMin |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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937 type: ["null", long, string, Expression] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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938 doc: Minimum reserved number of CPU cores |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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939 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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940 - name: coresMax |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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941 type: ["null", int, string, Expression] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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942 doc: Maximum reserved number of CPU cores |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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943 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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944 - name: ramMin |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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945 type: ["null", long, string, Expression] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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946 doc: Minimum reserved RAM in mebibytes (2**20) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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947 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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948 - name: ramMax |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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949 type: ["null", long, string, Expression] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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950 doc: Maximum reserved RAM in mebibytes (2**20) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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951 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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952 - name: tmpdirMin |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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953 type: ["null", long, string, Expression] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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954 doc: Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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955 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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956 - name: tmpdirMax |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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957 type: ["null", long, string, Expression] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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958 doc: Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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959 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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960 - name: outdirMin |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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961 type: ["null", long, string, Expression] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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962 doc: Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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963 |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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964 - name: outdirMax |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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965 type: ["null", long, string, Expression] |
26e78fe6e8c4
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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966 doc: Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20) |