Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/extensions.yml @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1 $base: http://commonwl.org/cwltool#
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2 $namespaces:
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3 cwl: "https://w3id.org/cwl/cwl#"
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4 $graph:
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5 - $import: https://w3id.org/cwl/CommonWorkflowLanguage.yml
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6
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7 - name: LoadListingRequirement
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8 type: record
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9 extends: cwl:ProcessRequirement
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10 inVocab: false
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11 fields:
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12 class:
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13 type: string
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14 doc: "Always 'LoadListingRequirement'"
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15 jsonldPredicate:
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16 "_id": "@type"
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17 "_type": "@vocab"
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18 loadListing:
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19 type:
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20 - type: enum
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21 name: LoadListingEnum
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22 symbols: [no_listing, shallow_listing, deep_listing]
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23
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24 - name: InplaceUpdateRequirement
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25 type: record
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26 inVocab: false
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27 extends: cwl:ProcessRequirement
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28 fields:
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29 class:
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30 type: string
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31 doc: "Always 'InplaceUpdateRequirement'"
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32 jsonldPredicate:
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33 "_id": "@type"
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34 "_type": "@vocab"
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35 inplaceUpdate:
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36 type: boolean
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37
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38 - name: Secrets
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39 type: record
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40 inVocab: false
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41 extends: cwl:ProcessRequirement
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42 fields:
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43 class:
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44 type: string
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45 doc: "Always 'Secrets'"
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46 jsonldPredicate:
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47 "_id": "@type"
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48 "_type": "@vocab"
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49 secrets:
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50 type: string[]
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51 doc: |
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52 List one or more input parameters that are sensitive (such as passwords)
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53 which will be deliberately obscured from logging.
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54 jsonldPredicate:
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55 "_type": "@id"
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56 refScope: 0
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57
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58
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59 - name: TimeLimit
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60 type: record
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61 inVocab: false
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62 extends: cwl:ProcessRequirement
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63 doc: |
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64 Set an upper limit on the execution time of a CommandLineTool or
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65 ExpressionTool. A tool execution which exceeds the time limit may
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66 be preemptively terminated and considered failed. May also be
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67 used by batch systems to make scheduling decisions.
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68 fields:
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69 - name: class
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70 type: string
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71 doc: "Always 'TimeLimit'"
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72 jsonldPredicate:
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73 "_id": "@type"
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74 "_type": "@vocab"
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75 - name: timelimit
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76 type: [long, string]
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77 doc: |
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78 The time limit, in seconds. A time limit of zero means no
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79 time limit. Negative time limits are an error.
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80
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81
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82 - name: WorkReuse
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83 type: record
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84 inVocab: false
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85 extends: cwl:ProcessRequirement
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86 doc: |
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87 For implementations that support reusing output from past work (on
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88 the assumption that same code and same input produce same
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89 results), control whether to enable or disable the reuse behavior
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90 for a particular tool or step (to accomodate situations where that
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91 assumption is incorrect). A reused step is not executed but
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92 instead returns the same output as the original execution.
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93
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94 If `enableReuse` is not specified, correct tools should assume it
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95 is enabled by default.
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96 fields:
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97 - name: class
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98 type: string
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99 doc: "Always 'WorkReuse'"
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100 jsonldPredicate:
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101 "_id": "@type"
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102 "_type": "@vocab"
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103 - name: enableReuse
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104 type: [boolean, string]
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105 #default: true
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106
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107
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108 - name: NetworkAccess
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109 type: record
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110 inVocab: false
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111 extends: cwl:ProcessRequirement
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112 doc: |
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113 Indicate whether a process requires outgoing IPv4/IPv6 network
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114 access. Choice of IPv4 or IPv6 is implementation and site
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115 specific, correct tools must support both.
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116
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117 If `networkAccess` is false or not specified, tools must not
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118 assume network access, except for localhost (the loopback device).
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119
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120 If `networkAccess` is true, the tool must be able to make outgoing
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121 connections to network resources. Resources may be on a private
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122 subnet or the public Internet. However, implementations and sites
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123 may apply their own security policies to restrict what is
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124 accessible by the tool.
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125
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126 Enabling network access does not imply a publically routable IP
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127 address or the ability to accept inbound connections.
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128
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129 fields:
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130 - name: class
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131 type: string
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132 doc: "Always 'NetworkAccess'"
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133 jsonldPredicate:
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134 "_id": "@type"
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135 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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136 - name: networkAccess
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137 type: [boolean, string]
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138
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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139 - name: ProcessGenerator
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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140 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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141 inVocab: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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142 extends: cwl:Process
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143 documentRoot: true
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144 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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145 - name: class
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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146 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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147 "_id": "@type"
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148 "_type": "@vocab"
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149 type: string
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150 - name: run
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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151 type: [string, cwl:Process]
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152 jsonldPredicate:
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153 _id: "cwl:run"
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154 _type: "@id"
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155 doc: |
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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156 Specifies the process to run.