Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/schema_salad/tests/cwl-pre.yml @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1 [
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2 {
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3 "name": "https://w3id.org/cwl/cwl#Common Workflow Language, v1.0",
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4 "type": "documentation",
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5 "doc": "\n"
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6 },
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7 {
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8 "name": "https://w3id.org/cwl/salad#PrimitiveType",
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9 "type": "enum",
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10 "symbols": [
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11 "https://w3id.org/cwl/salad#null",
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12 "http://www.w3.org/2001/XMLSchema#boolean",
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13 "http://www.w3.org/2001/XMLSchema#int",
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14 "http://www.w3.org/2001/XMLSchema#long",
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15 "http://www.w3.org/2001/XMLSchema#float",
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16 "http://www.w3.org/2001/XMLSchema#double",
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17 "http://www.w3.org/2001/XMLSchema#string"
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18 ],
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19 "doc": [
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20 "Salad data types are based on Avro schema declarations. Refer to the\n[Avro schema declaration documentation](https://avro.apache.org/docs/current/spec.html#schemas) for\ndetailed information.\n",
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21 "null: no value",
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22 "boolean: a binary value",
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23 "int: 32-bit signed integer",
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24 "long: 64-bit signed integer",
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25 "float: single precision (32-bit) IEEE 754 floating-point number",
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26 "double: double precision (64-bit) IEEE 754 floating-point number",
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27 "string: Unicode character sequence"
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28 ]
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29 },
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30 {
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31 "name": "https://w3id.org/cwl/salad#Any",
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32 "type": "enum",
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33 "symbols": [
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34 "https://w3id.org/cwl/salad#Any"
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35 ],
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36 "doc": "The **Any** type validates for any non-null value.\n"
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37 },
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38 {
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39 "name": "https://w3id.org/cwl/salad#RecordField",
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40 "type": "record",
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41 "doc": "A field of a record.",
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42 "fields": [
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43 {
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44 "name": "https://w3id.org/cwl/salad#RecordField/name",
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45 "type": "string",
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46 "jsonldPredicate": "@id",
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47 "doc": "The name of the field\n"
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48 },
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49 {
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50 "name": "https://w3id.org/cwl/salad#RecordField/doc",
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51 "type": [
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52 "null",
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53 "string"
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54 ],
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55 "doc": "A documentation string for this field\n",
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56 "jsonldPredicate": "rdfs:comment"
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57 },
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58 {
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59 "name": "https://w3id.org/cwl/salad#RecordField/type",
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60 "type": [
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61 "PrimitiveType",
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62 "RecordSchema",
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63 "EnumSchema",
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64 "ArraySchema",
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65 "string",
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66 {
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67 "type": "array",
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68 "items": [
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69 "PrimitiveType",
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70 "RecordSchema",
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71 "EnumSchema",
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72 "ArraySchema",
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73 "string"
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74 ]
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75 }
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76 ],
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77 "jsonldPredicate": {
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78 "_id": "https://w3id.org/cwl/salad#type",
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79 "_type": "@vocab",
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80 "typeDSL": true,
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81 "refScope": 2
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82 },
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83 "doc": "The field type\n"
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84 }
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85 ]
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86 },
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87 {
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88 "name": "https://w3id.org/cwl/salad#RecordSchema",
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89 "type": "record",
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90 "fields": [
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91 {
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92 "type": [
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93 "null",
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94 {
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95 "type": "array",
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96 "items": "RecordField"
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97 }
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98 ],
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99 "jsonldPredicate": {
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100 "_id": "https://w3id.org/cwl/salad#fields",
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101 "mapSubject": "name",
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102 "mapPredicate": "type"
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103 },
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104 "doc": "Defines the fields of the record.",
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105 "name": "https://w3id.org/cwl/salad#RecordSchema/fields"
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106 },
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107 {
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108 "doc": "Must be `record`",
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109 "type": {
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110 "type": "enum",
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111 "symbols": [
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112 "https://w3id.org/cwl/salad#record"
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113 ]
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114 },
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115 "jsonldPredicate": {
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116 "_id": "https://w3id.org/cwl/salad#type",
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117 "_type": "@vocab",
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118 "typeDSL": true,
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119 "refScope": 2
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120 },
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121 "name": "https://w3id.org/cwl/salad#RecordSchema/type"
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122 }
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123 ]
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124 },
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125 {
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126 "name": "https://w3id.org/cwl/salad#EnumSchema",
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127 "type": "record",
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128 "doc": "Define an enumerated type.\n",
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129 "fields": [
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130 {
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131 "type": {
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132 "type": "array",
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133 "items": "string"
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134 },
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135 "jsonldPredicate": {
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136 "_id": "https://w3id.org/cwl/salad#symbols",
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137 "_type": "@id",
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138 "identity": true
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139 },
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140 "doc": "Defines the set of valid symbols.",
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141 "name": "https://w3id.org/cwl/salad#EnumSchema/symbols"
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142 },
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143 {
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144 "doc": "Must be `enum`",
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145 "type": {
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146 "type": "enum",
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147 "symbols": [
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148 "https://w3id.org/cwl/salad#enum"
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149 ]
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150 },
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151 "jsonldPredicate": {
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152 "_id": "https://w3id.org/cwl/salad#type",
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153 "_type": "@vocab",
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154 "typeDSL": true,
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155 "refScope": 2
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156 },
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157 "name": "https://w3id.org/cwl/salad#EnumSchema/type"
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158 }
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159 ]
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160 },
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161 {
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162 "name": "https://w3id.org/cwl/salad#ArraySchema",
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163 "type": "record",
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164 "fields": [
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165 {
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166 "type": [
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167 "PrimitiveType",
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168 "RecordSchema",
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169 "EnumSchema",
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170 "ArraySchema",
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171 "string",
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172 {
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173 "type": "array",
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174 "items": [
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175 "PrimitiveType",
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176 "RecordSchema",
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177 "EnumSchema",
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178 "ArraySchema",
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179 "string"
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180 ]
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181 }
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182 ],
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183 "jsonldPredicate": {
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184 "_id": "https://w3id.org/cwl/salad#items",
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185 "_type": "@vocab",
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186 "refScope": 2
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187 },
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188 "doc": "Defines the type of the array elements.",
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189 "name": "https://w3id.org/cwl/salad#ArraySchema/items"
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190 },
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191 {
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192 "doc": "Must be `array`",
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193 "type": {
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194 "type": "enum",
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195 "symbols": [
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196 "https://w3id.org/cwl/salad#array"
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197 ]
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198 },
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199 "jsonldPredicate": {
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200 "_id": "https://w3id.org/cwl/salad#type",
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201 "_type": "@vocab",
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202 "typeDSL": true,
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203 "refScope": 2
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204 },
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205 "name": "https://w3id.org/cwl/salad#ArraySchema/type"
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206 }
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207 ]
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208 },
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209 {
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210 "name": "https://w3id.org/cwl/cwl#BaseTypesDoc",
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211 "type": "documentation",
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212 "doc": "## Base types\n",
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213 "docChild": [
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214 "https://w3id.org/cwl/cwl#CWLType",
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215 "https://w3id.org/cwl/cwl#Process"
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216 ]
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217 },
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218 {
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219 "type": "enum",
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220 "name": "https://w3id.org/cwl/cwl#CWLVersion",
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221 "doc": "Version symbols for published CWL document versions.",
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222 "symbols": [
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223 "https://w3id.org/cwl/cwl#draft-2",
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224 "https://w3id.org/cwl/cwl#draft-3.dev1",
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225 "https://w3id.org/cwl/cwl#draft-3.dev2",
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226 "https://w3id.org/cwl/cwl#draft-3.dev3",
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227 "https://w3id.org/cwl/cwl#draft-3.dev4",
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228 "https://w3id.org/cwl/cwl#draft-3.dev5",
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229 "https://w3id.org/cwl/cwl#draft-3",
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230 "https://w3id.org/cwl/cwl#draft-4.dev1",
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231 "https://w3id.org/cwl/cwl#draft-4.dev2",
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232 "https://w3id.org/cwl/cwl#draft-4.dev3",
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233 "https://w3id.org/cwl/cwl#v1.0.dev4",
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234 "https://w3id.org/cwl/cwl#v1.0"
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235 ]
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236 },
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237 {
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238 "name": "https://w3id.org/cwl/cwl#CWLType",
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239 "type": "enum",
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240 "extends": "https://w3id.org/cwl/salad#PrimitiveType",
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241 "symbols": [
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242 "https://w3id.org/cwl/cwl#File",
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243 "https://w3id.org/cwl/cwl#Directory"
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244 ],
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245 "doc": [
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246 "Extends primitive types with the concept of a file and directory as a builtin type.",
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247 "File: A File object",
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248 "Directory: A Directory object"
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249 ]
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250 },
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251 {
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252 "name": "https://w3id.org/cwl/cwl#File",
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253 "type": "record",
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254 "docParent": "https://w3id.org/cwl/cwl#CWLType",
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255 "doc": "Represents a file (or group of files if `secondaryFiles` is specified) that\nmust be accessible by tools using standard POSIX file system call API such as\nopen(2) and read(2).\n",
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256 "fields": [
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257 {
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258 "name": "https://w3id.org/cwl/cwl#File/class",
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259 "type": {
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260 "type": "enum",
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parents:
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261 "symbols": [
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262 "https://w3id.org/cwl/cwl#File"
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263 ]
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264 },
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265 "jsonldPredicate": {
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266 "_id": "@type",
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parents:
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267 "_type": "@vocab"
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268 },
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269 "doc": "Must be `File` to indicate this object describes a file."
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270 },
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271 {
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272 "name": "https://w3id.org/cwl/cwl#File/location",
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273 "type": [
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274 "null",
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guerler
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275 "string"
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guerler
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276 ],
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277 "doc": "An IRI that identifies the file resource. This may be a relative\nreference, in which case it must be resolved using the base IRI of the\ndocument. The location may refer to a local or remote resource; the\nimplementation must use the IRI to retrieve file content. If an\nimplementation is unable to retrieve the file content stored at a\nremote resource (due to unsupported protocol, access denied, or other\nissue) it must signal an error.\n\nIf the `location` field is not provided, the `contents` field must be\nprovided. The implementation must assign a unique identifier for\nthe `location` field.\n\nIf the `path` field is provided but the `location` field is not, an\nimplementation may assign the value of the `path` field to `location`,\nthen follow the rules above.\n",
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278 "jsonldPredicate": {
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279 "_id": "@id",
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280 "_type": "@id"
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281 }
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282 },
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283 {
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284 "name": "https://w3id.org/cwl/cwl#File/path",
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285 "type": [
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286 "null",
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287 "string"
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guerler
parents:
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288 ],
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289 "doc": "The local host path where the File is available when a CommandLineTool is\nexecuted. This field must be set by the implementation. The final\npath component must match the value of `basename`. This field\nmust not be used in any other context. The command line tool being\nexecuted must be able to to access the file at `path` using the POSIX\n`open(2)` syscall.\n\nAs a special case, if the `path` field is provided but the `location`\nfield is not, an implementation may assign the value of the `path`\nfield to `location`, and remove the `path` field.\n\nIf the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)\n(`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\\`, `\"`, `'`,\n`<space>`, `<tab>`, and `<newline>`) or characters\n[not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)\nfor [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)\nthen implementations may terminate the process with a\n`permanentFailure`.\n",
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290 "jsonldPredicate": {
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291 "_id": "https://w3id.org/cwl/cwl#path",
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292 "_type": "@id"
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293 }
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294 },
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295 {
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296 "name": "https://w3id.org/cwl/cwl#File/basename",
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297 "type": [
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298 "null",
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299 "string"
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guerler
parents:
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300 ],
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301 "doc": "The base name of the file, that is, the name of the file without any\nleading directory path. The base name must not contain a slash `/`.\n\nIf not provided, the implementation must set this field based on the\n`location` field by taking the final path component after parsing\n`location` as an IRI. If `basename` is provided, it is not required to\nmatch the value from `location`.\n\nWhen this file is made available to a CommandLineTool, it must be named\nwith `basename`, i.e. the final component of the `path` field must match\n`basename`.\n",
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302 "jsonldPredicate": "cwl:basename"
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303 },
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304 {
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305 "name": "https://w3id.org/cwl/cwl#File/dirname",
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parents:
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306 "type": [
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307 "null",
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guerler
parents:
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308 "string"
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309 ],
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310 "doc": "The name of the directory containing file, that is, the path leading up\nto the final slash in the path such that `dirname + '/' + basename ==\npath`.\n\nThe implementation must set this field based on the value of `path`\nprior to evaluating parameter references or expressions in a\nCommandLineTool document. This field must not be used in any other\ncontext.\n"
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311 },
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312 {
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313 "name": "https://w3id.org/cwl/cwl#File/nameroot",
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parents:
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314 "type": [
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315 "null",
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316 "string"
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317 ],
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318 "doc": "The basename root such that `nameroot + nameext == basename`, and\n`nameext` is empty or begins with a period and contains at most one\nperiod. For the purposess of path splitting leading periods on the\nbasename are ignored; a basename of `.cshrc` will have a nameroot of\n`.cshrc`.\n\nThe implementation must set this field automatically based on the value\nof `basename` prior to evaluating parameter references or expressions.\n"
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319 },
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320 {
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321 "name": "https://w3id.org/cwl/cwl#File/nameext",
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322 "type": [
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323 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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324 "string"
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parents:
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325 ],
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326 "doc": "The basename extension such that `nameroot + nameext == basename`, and\n`nameext` is empty or begins with a period and contains at most one\nperiod. Leading periods on the basename are ignored; a basename of\n`.cshrc` will have an empty `nameext`.\n\nThe implementation must set this field automatically based on the value\nof `basename` prior to evaluating parameter references or expressions.\n"
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327 },
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328 {
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329 "name": "https://w3id.org/cwl/cwl#File/checksum",
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330 "type": [
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331 "null",
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332 "string"
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333 ],
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334 "doc": "Optional hash code for validating file integrity. Currently must be in the form\n\"sha1$ + hexadecimal string\" using the SHA-1 algorithm.\n"
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335 },
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336 {
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337 "name": "https://w3id.org/cwl/cwl#File/size",
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338 "type": [
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339 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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340 "long"
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341 ],
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342 "doc": "Optional file size"
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343 },
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344 {
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345 "name": "https://w3id.org/cwl/cwl#File/secondaryFiles",
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346 "type": [
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347 "null",
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348 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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349 "type": "array",
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350 "items": [
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351 "https://w3id.org/cwl/cwl#File",
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352 "https://w3id.org/cwl/cwl#Directory"
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353 ]
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354 }
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355 ],
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356 "jsonldPredicate": "cwl:secondaryFiles",
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357 "doc": "A list of additional files that are associated with the primary file\nand must be transferred alongside the primary file. Examples include\nindexes of the primary file, or external references which must be\nincluded when loading primary document. A file object listed in\n`secondaryFiles` may itself include `secondaryFiles` for which the same\nrules apply.\n"
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358 },
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359 {
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360 "name": "https://w3id.org/cwl/cwl#File/format",
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361 "type": [
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362 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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363 "string"
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guerler
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364 ],
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365 "jsonldPredicate": {
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366 "_id": "https://w3id.org/cwl/cwl#format",
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367 "_type": "@id",
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368 "identity": true
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369 },
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370 "doc": "The format of the file: this must be an IRI of a concept node that\nrepresents the file format, preferrably defined within an ontology.\nIf no ontology is available, file formats may be tested by exact match.\n\nReasoning about format compatability must be done by checking that an\ninput file format is the same, `owl:equivalentClass` or\n`rdfs:subClassOf` the format required by the input parameter.\n`owl:equivalentClass` is transitive with `rdfs:subClassOf`, e.g. if\n`<B> owl:equivalentClass <C>` and `<B> owl:subclassOf <A>` then infer\n`<C> owl:subclassOf <A>`.\n\nFile format ontologies may be provided in the \"$schema\" metadata at the\nroot of the document. If no ontologies are specified in `$schema`, the\nruntime may perform exact file format matches.\n"
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371 },
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372 {
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373 "name": "https://w3id.org/cwl/cwl#File/contents",
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parents:
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374 "type": [
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375 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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376 "string"
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377 ],
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378 "doc": "File contents literal. Maximum of 64 KiB.\n\nIf neither `location` nor `path` is provided, `contents` must be\nnon-null. The implementation must assign a unique identifier for the\n`location` field. When the file is staged as input to CommandLineTool,\nthe value of `contents` must be written to a file.\n\nIf `loadContents` of `inputBinding` or `outputBinding` is true and\n`location` is valid, the implementation must read up to the first 64\nKiB of text from the file and place it in the \"contents\" field.\n"
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379 }
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380 ]
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381 },
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382 {
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383 "name": "https://w3id.org/cwl/cwl#Directory",
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384 "type": "record",
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385 "docAfter": "https://w3id.org/cwl/cwl#File",
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386 "doc": "Represents a directory to present to a command line tool.\n",
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387 "fields": [
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388 {
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389 "name": "https://w3id.org/cwl/cwl#Directory/class",
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390 "type": {
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391 "type": "enum",
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392 "symbols": [
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393 "https://w3id.org/cwl/cwl#Directory"
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394 ]
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395 },
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396 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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397 "_id": "@type",
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parents:
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398 "_type": "@vocab"
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399 },
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400 "doc": "Must be `Directory` to indicate this object describes a Directory."
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401 },
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402 {
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403 "name": "https://w3id.org/cwl/cwl#Directory/location",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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404 "type": [
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405 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
406 "string"
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407 ],
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408 "doc": "An IRI that identifies the directory resource. This may be a relative\nreference, in which case it must be resolved using the base IRI of the\ndocument. The location may refer to a local or remote resource. If\nthe `listing` field is not set, the implementation must use the\nlocation IRI to retrieve directory listing. If an implementation is\nunable to retrieve the directory listing stored at a remote resource (due to\nunsupported protocol, access denied, or other issue) it must signal an\nerror.\n\nIf the `location` field is not provided, the `listing` field must be\nprovided. The implementation must assign a unique identifier for\nthe `location` field.\n\nIf the `path` field is provided but the `location` field is not, an\nimplementation may assign the value of the `path` field to `location`,\nthen follow the rules above.\n",
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409 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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410 "_id": "@id",
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411 "_type": "@id"
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412 }
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413 },
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414 {
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diff changeset
415 "name": "https://w3id.org/cwl/cwl#Directory/path",
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416 "type": [
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417 "null",
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418 "string"
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419 ],
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420 "doc": "The local path where the Directory is made available prior to executing a\nCommandLineTool. This must be set by the implementation. This field\nmust not be used in any other context. The command line tool being\nexecuted must be able to to access the directory at `path` using the POSIX\n`opendir(2)` syscall.\n\nIf the `path` contains [POSIX shell metacharacters](http://pubs.opengroup.org/onlinepubs/9699919799/utilities/V3_chap02.html#tag_18_02)\n(`|`,`&`, `;`, `<`, `>`, `(`,`)`, `$`,`` ` ``, `\\`, `\"`, `'`,\n`<space>`, `<tab>`, and `<newline>`) or characters\n[not allowed](http://www.iana.org/assignments/idna-tables-6.3.0/idna-tables-6.3.0.xhtml)\nfor [Internationalized Domain Names for Applications](https://tools.ietf.org/html/rfc6452)\nthen implementations may terminate the process with a\n`permanentFailure`.\n",
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421 "jsonldPredicate": {
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422 "_id": "https://w3id.org/cwl/cwl#path",
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423 "_type": "@id"
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424 }
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425 },
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426 {
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427 "name": "https://w3id.org/cwl/cwl#Directory/basename",
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428 "type": [
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429 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
430 "string"
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431 ],
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432 "doc": "The base name of the directory, that is, the name of the file without any\nleading directory path. The base name must not contain a slash `/`.\n\nIf not provided, the implementation must set this field based on the\n`location` field by taking the final path component after parsing\n`location` as an IRI. If `basename` is provided, it is not required to\nmatch the value from `location`.\n\nWhen this file is made available to a CommandLineTool, it must be named\nwith `basename`, i.e. the final component of the `path` field must match\n`basename`.\n",
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433 "jsonldPredicate": "cwl:basename"
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434 },
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435 {
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diff changeset
436 "name": "https://w3id.org/cwl/cwl#Directory/listing",
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diff changeset
437 "type": [
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438 "null",
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439 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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440 "type": "array",
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441 "items": [
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442 "https://w3id.org/cwl/cwl#File",
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443 "https://w3id.org/cwl/cwl#Directory"
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444 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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445 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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446 ],
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447 "doc": "List of files or subdirectories contained in this directory. The name\nof each file or subdirectory is determined by the `basename` field of\neach `File` or `Directory` object. It is an error if a `File` shares a\n`basename` with any other entry in `listing`. If two or more\n`Directory` object share the same `basename`, this must be treated as\nequivalent to a single subdirectory with the listings recursively\nmerged.\n",
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448 "jsonldPredicate": {
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449 "_id": "https://w3id.org/cwl/cwl#listing"
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450 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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451 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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452 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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453 },
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454 {
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455 "name": "https://w3id.org/cwl/cwl#SchemaBase",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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456 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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457 "abstract": true,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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458 "fields": [
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459 {
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460 "name": "https://w3id.org/cwl/cwl#SchemaBase/label",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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461 "type": [
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462 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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463 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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464 ],
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465 "jsonldPredicate": "rdfs:label",
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466 "doc": "A short, human-readable label of this object."
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467 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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468 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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469 },
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470 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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471 "name": "https://w3id.org/cwl/cwl#Parameter",
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472 "type": "record",
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473 "extends": "https://w3id.org/cwl/cwl#SchemaBase",
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474 "abstract": true,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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475 "doc": "Define an input or output parameter to a process.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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476 "fields": [
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477 {
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478 "name": "https://w3id.org/cwl/cwl#Parameter/secondaryFiles",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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479 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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480 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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481 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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482 "https://w3id.org/cwl/cwl#Expression",
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483 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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484 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
485 "items": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
486 "string",
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guerler
parents:
diff changeset
487 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
488 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
489 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
490 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
491 "jsonldPredicate": "cwl:secondaryFiles",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
492 "doc": "Only valid when `type: File` or is an array of `items: File`.\n\nDescribes files that must be included alongside the primary file(s).\n\nIf the value is an expression, the value of `self` in the expression\nmust be the primary input or output File to which this binding applies.\n\nIf the value is a string, it specifies that the following pattern\nshould be applied to the primary file:\n\n 1. If string begins with one or more caret `^` characters, for each\n caret, remove the last file extension from the path (the last\n period `.` and all following characters). If there are no file\n extensions, the path is unchanged.\n 2. Append the remainder of the string to the end of the file path.\n"
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parents:
diff changeset
493 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
494 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
495 "name": "https://w3id.org/cwl/cwl#Parameter/format",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
496 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
497 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
498 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
499 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
500 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
501 "items": "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
502 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
503 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
504 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
505 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
506 "_id": "https://w3id.org/cwl/cwl#format",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
507 "_type": "@id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
508 "identity": true
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
509 },
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parents:
diff changeset
510 "doc": "Only valid when `type: File` or is an array of `items: File`.\n\nFor input parameters, this must be one or more IRIs of concept nodes\nthat represents file formats which are allowed as input to this\nparameter, preferrably defined within an ontology. If no ontology is\navailable, file formats may be tested by exact match.\n\nFor output parameters, this is the file format that will be assigned to\nthe output parameter.\n"
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parents:
diff changeset
511 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
512 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
513 "name": "https://w3id.org/cwl/cwl#Parameter/streamable",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
514 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
515 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
516 "boolean"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
517 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
518 "doc": "Only valid when `type: File` or is an array of `items: File`.\n\nA value of `true` indicates that the file is read or written\nsequentially without seeking. An implementation may use this flag to\nindicate whether it is valid to stream file contents using a named\npipe. Default: `false`.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
519 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
520 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
521 "name": "https://w3id.org/cwl/cwl#Parameter/doc",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
522 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
523 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
524 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
525 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
526 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
527 "items": "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
528 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
529 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
530 "doc": "A documentation string for this type, or an array of strings which should be concatenated.",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
531 "jsonldPredicate": "rdfs:comment"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
532 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
533 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
534 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
535 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
536 "type": "enum",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
537 "name": "https://w3id.org/cwl/cwl#Expression",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
538 "doc": "'Expression' is not a real type. It indicates that a field must allow\nruntime parameter references. If [InlineJavascriptRequirement](#InlineJavascriptRequirement)\nis declared and supported by the platform, the field must also allow\nJavascript expressions.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
539 "symbols": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
540 "https://w3id.org/cwl/cwl#ExpressionPlaceholder"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
541 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
542 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
543 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
544 "name": "https://w3id.org/cwl/cwl#InputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
545 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
546 "abstract": true,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
547 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
548 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
549 "name": "https://w3id.org/cwl/cwl#InputBinding/loadContents",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
550 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
551 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
552 "boolean"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
553 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
554 "jsonldPredicate": "cwl:loadContents",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
555 "doc": "Only valid when `type: File` or is an array of `items: File`.\n\nRead up to the first 64 KiB of text from the file and place it in the\n\"contents\" field of the file object for use by expressions.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
556 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
557 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
558 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
559 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
560 "name": "https://w3id.org/cwl/cwl#OutputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
561 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
562 "abstract": true
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
563 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
564 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
565 "name": "https://w3id.org/cwl/cwl#InputSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
566 "extends": "https://w3id.org/cwl/cwl#SchemaBase",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
567 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
568 "abstract": true
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
569 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
570 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
571 "name": "https://w3id.org/cwl/cwl#OutputSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
572 "extends": "https://w3id.org/cwl/cwl#SchemaBase",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
573 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
574 "abstract": true
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
575 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
576 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
577 "name": "https://w3id.org/cwl/cwl#InputRecordField",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
578 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
579 "extends": "https://w3id.org/cwl/salad#RecordField",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
580 "specialize": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
581 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
582 "specializeFrom": "https://w3id.org/cwl/salad#RecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
583 "specializeTo": "https://w3id.org/cwl/cwl#InputRecordSchema"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
584 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
585 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
586 "specializeFrom": "https://w3id.org/cwl/salad#EnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
587 "specializeTo": "https://w3id.org/cwl/cwl#InputEnumSchema"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
588 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
589 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
590 "specializeFrom": "https://w3id.org/cwl/salad#ArraySchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
591 "specializeTo": "https://w3id.org/cwl/cwl#InputArraySchema"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
592 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
593 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
594 "specializeFrom": "https://w3id.org/cwl/salad#PrimitiveType",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
595 "specializeTo": "https://w3id.org/cwl/cwl#CWLType"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
596 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
597 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
598 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
599 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
600 "name": "https://w3id.org/cwl/cwl#InputRecordField/inputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
601 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
602 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
603 "https://w3id.org/cwl/cwl#InputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
604 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
605 "jsonldPredicate": "cwl:inputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
606 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
607 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
608 "name": "https://w3id.org/cwl/cwl#InputRecordField/label",
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609 "type": [
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610 "null",
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611 "string"
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612 ],
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614 "doc": "A short, human-readable label of this process object."
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615 }
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618 {
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640 {
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643 "null",
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645 ],
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647 }
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658 {
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683 }
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725 ],
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735 "name": "https://w3id.org/cwl/cwl#OutputEnumSchema",
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parents:
diff changeset
736 "type": "record",
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parents:
diff changeset
737 "extends": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
738 "https://w3id.org/cwl/salad#EnumSchema",
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guerler
parents:
diff changeset
739 "https://w3id.org/cwl/cwl#OutputSchema"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
740 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
741 "docParent": "https://w3id.org/cwl/cwl#OutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
742 "fields": [
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parents:
diff changeset
743 {
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parents:
diff changeset
744 "name": "https://w3id.org/cwl/cwl#OutputEnumSchema/outputBinding",
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parents:
diff changeset
745 "type": [
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parents:
diff changeset
746 "null",
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parents:
diff changeset
747 "https://w3id.org/cwl/cwl#OutputBinding"
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parents:
diff changeset
748 ],
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parents:
diff changeset
749 "jsonldPredicate": "cwl:outputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
750 }
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parents:
diff changeset
751 ]
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parents:
diff changeset
752 },
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parents:
diff changeset
753 {
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guerler
parents:
diff changeset
754 "name": "https://w3id.org/cwl/cwl#OutputArraySchema",
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parents:
diff changeset
755 "type": "record",
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parents:
diff changeset
756 "extends": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
757 "https://w3id.org/cwl/salad#ArraySchema",
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guerler
parents:
diff changeset
758 "https://w3id.org/cwl/cwl#OutputSchema"
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parents:
diff changeset
759 ],
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guerler
parents:
diff changeset
760 "docParent": "https://w3id.org/cwl/cwl#OutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
761 "specialize": [
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parents:
diff changeset
762 {
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parents:
diff changeset
763 "specializeFrom": "https://w3id.org/cwl/salad#RecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
764 "specializeTo": "https://w3id.org/cwl/cwl#OutputRecordSchema"
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parents:
diff changeset
765 },
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parents:
diff changeset
766 {
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parents:
diff changeset
767 "specializeFrom": "https://w3id.org/cwl/salad#EnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
768 "specializeTo": "https://w3id.org/cwl/cwl#OutputEnumSchema"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
769 },
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parents:
diff changeset
770 {
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guerler
parents:
diff changeset
771 "specializeFrom": "https://w3id.org/cwl/salad#ArraySchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
772 "specializeTo": "https://w3id.org/cwl/cwl#OutputArraySchema"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
773 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
774 {
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guerler
parents:
diff changeset
775 "specializeFrom": "https://w3id.org/cwl/salad#PrimitiveType",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
776 "specializeTo": "https://w3id.org/cwl/cwl#CWLType"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
777 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
778 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
779 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
780 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
781 "name": "https://w3id.org/cwl/cwl#OutputArraySchema/outputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
782 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
783 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
784 "https://w3id.org/cwl/cwl#OutputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
785 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
786 "jsonldPredicate": "cwl:outputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
787 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
788 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
789 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
790 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
791 "name": "https://w3id.org/cwl/cwl#InputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
792 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
793 "extends": "https://w3id.org/cwl/cwl#Parameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
794 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
795 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
796 "name": "https://w3id.org/cwl/cwl#InputParameter/id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
797 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
798 "jsonldPredicate": "@id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
799 "doc": "The unique identifier for this parameter object."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
800 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
801 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
802 "name": "https://w3id.org/cwl/cwl#InputParameter/inputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
803 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
804 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
805 "https://w3id.org/cwl/cwl#InputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
806 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
807 "jsonldPredicate": "cwl:inputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
808 "doc": "Describes how to handle the inputs of a process and convert them\ninto a concrete form for execution, such as command line parameters.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
809 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
810 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
811 "name": "https://w3id.org/cwl/cwl#InputParameter/default",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
812 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
813 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
814 "Any"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
815 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
816 "jsonldPredicate": "cwl:default",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
817 "doc": "The default value for this parameter if not provided in the input\nobject.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
818 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
819 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
820 "name": "https://w3id.org/cwl/cwl#InputParameter/type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
821 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
822 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
823 "https://w3id.org/cwl/cwl#CWLType",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
824 "https://w3id.org/cwl/cwl#InputRecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
825 "https://w3id.org/cwl/cwl#InputEnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
826 "https://w3id.org/cwl/cwl#InputArraySchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
827 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
828 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
829 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
830 "items": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
831 "https://w3id.org/cwl/cwl#CWLType",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
832 "https://w3id.org/cwl/cwl#InputRecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
833 "https://w3id.org/cwl/cwl#InputEnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
834 "https://w3id.org/cwl/cwl#InputArraySchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
835 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
836 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
837 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
838 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
839 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
840 "_id": "https://w3id.org/cwl/salad#type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
841 "_type": "@vocab",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
842 "refScope": 2,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
843 "typeDSL": true
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
844 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
845 "doc": "Specify valid types of data that may be assigned to this parameter.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
846 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
847 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
848 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
849 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
850 "name": "https://w3id.org/cwl/cwl#OutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
851 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
852 "extends": "https://w3id.org/cwl/cwl#Parameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
853 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
854 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
855 "name": "https://w3id.org/cwl/cwl#OutputParameter/id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
856 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
857 "jsonldPredicate": "@id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
858 "doc": "The unique identifier for this parameter object."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
859 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
860 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
861 "name": "https://w3id.org/cwl/cwl#OutputParameter/outputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
862 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
863 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
864 "https://w3id.org/cwl/cwl#OutputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
865 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
866 "jsonldPredicate": "cwl:outputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
867 "doc": "Describes how to handle the outputs of a process.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
868 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
869 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
870 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
871 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
872 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
873 "name": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
874 "abstract": true,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
875 "doc": "A process requirement declares a prerequisite that may or must be fulfilled\nbefore executing a process. See [`Process.hints`](#process) and\n[`Process.requirements`](#process).\n\nProcess requirements are the primary mechanism for specifying extensions to\nthe CWL core specification.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
876 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
877 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
878 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
879 "name": "https://w3id.org/cwl/cwl#Process",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
880 "abstract": true,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
881 "doc": "\nThe base executable type in CWL is the `Process` object defined by the\ndocument. Note that the `Process` object is abstract and cannot be\ndirectly executed.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
882 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
883 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
884 "name": "https://w3id.org/cwl/cwl#Process/id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
885 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
886 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
887 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
888 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
889 "jsonldPredicate": "@id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
890 "doc": "The unique identifier for this process object."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
891 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
892 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
893 "name": "https://w3id.org/cwl/cwl#Process/inputs",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
894 "type": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
895 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
896 "items": "https://w3id.org/cwl/cwl#InputParameter"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
897 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
898 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
899 "_id": "https://w3id.org/cwl/cwl#inputs",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
900 "mapSubject": "id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
901 "mapPredicate": "type"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
902 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
903 "doc": "Defines the input parameters of the process. The process is ready to\nrun when all required input parameters are associated with concrete\nvalues. Input parameters include a schema for each parameter which is\nused to validate the input object. It may also be used to build a user\ninterface for constructing the input object.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
904 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
905 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
906 "name": "https://w3id.org/cwl/cwl#Process/outputs",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
907 "type": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
908 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
909 "items": "https://w3id.org/cwl/cwl#OutputParameter"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
910 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
911 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
912 "_id": "https://w3id.org/cwl/cwl#outputs",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
913 "mapSubject": "id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
914 "mapPredicate": "type"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
915 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
916 "doc": "Defines the parameters representing the output of the process. May be\nused to generate and/or validate the output object.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
917 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
918 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
919 "name": "https://w3id.org/cwl/cwl#Process/requirements",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
920 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
921 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
922 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
923 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
924 "items": "https://w3id.org/cwl/cwl#ProcessRequirement"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
925 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
926 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
927 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
928 "_id": "https://w3id.org/cwl/cwl#requirements",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
929 "mapSubject": "class"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
930 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
931 "doc": "Declares requirements that apply to either the runtime environment or the\nworkflow engine that must be met in order to execute this process. If\nan implementation cannot satisfy all requirements, or a requirement is\nlisted which is not recognized by the implementation, it is a fatal\nerror and the implementation must not attempt to run the process,\nunless overridden at user option.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
932 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
933 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
934 "name": "https://w3id.org/cwl/cwl#Process/hints",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
935 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
936 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
937 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
938 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
939 "items": "Any"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
940 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
941 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
942 "doc": "Declares hints applying to either the runtime environment or the\nworkflow engine that may be helpful in executing this process. It is\nnot an error if an implementation cannot satisfy all hints, however\nthe implementation may report a warning.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
943 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
944 "_id": "https://w3id.org/cwl/cwl#hints",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
945 "noLinkCheck": true,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
946 "mapSubject": "class"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
947 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
948 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
949 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
950 "name": "https://w3id.org/cwl/cwl#Process/label",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
951 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
952 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
953 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
954 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
955 "jsonldPredicate": "rdfs:label",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
956 "doc": "A short, human-readable label of this process object."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
957 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
958 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
959 "name": "https://w3id.org/cwl/cwl#Process/doc",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
960 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
961 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
962 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
963 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
964 "jsonldPredicate": "rdfs:comment",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
965 "doc": "A long, human-readable description of this process object."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
966 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
967 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
968 "name": "https://w3id.org/cwl/cwl#Process/cwlVersion",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
969 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
970 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
971 "https://w3id.org/cwl/cwl#CWLVersion"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
972 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
973 "doc": "CWL document version. Always required at the document root. Not\nrequired for a Process embedded inside another Process.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
974 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
975 "_id": "https://w3id.org/cwl/cwl#cwlVersion",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
976 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
977 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
978 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
979 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
980 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
981 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
982 "name": "https://w3id.org/cwl/cwl#InlineJavascriptRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
983 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
984 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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985 "doc": "Indicates that the workflow platform must support inline Javascript expressions.\nIf this requirement is not present, the workflow platform must not perform expression\ninterpolatation.\n",
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986 "fields": [
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987 {
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988 "name": "https://w3id.org/cwl/cwl#InlineJavascriptRequirement/class",
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989 "type": "string",
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990 "doc": "Always 'InlineJavascriptRequirement'",
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991 "jsonldPredicate": {
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992 "_id": "@type",
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993 "_type": "@vocab"
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994 }
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995 },
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996 {
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997 "name": "https://w3id.org/cwl/cwl#InlineJavascriptRequirement/expressionLib",
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998 "type": [
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999 "null",
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1000 {
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1001 "type": "array",
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1002 "items": "string"
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1003 }
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1004 ],
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1005 "doc": "Additional code fragments that will also be inserted\nbefore executing the expression code. Allows for function definitions that may\nbe called from CWL expressions.\n"
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1006 }
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1007 ]
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1008 },
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1009 {
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1010 "name": "https://w3id.org/cwl/cwl#SchemaDefRequirement",
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1011 "type": "record",
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1012 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
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1013 "doc": "This field consists of an array of type definitions which must be used when\ninterpreting the `inputs` and `outputs` fields. When a `type` field\ncontain a IRI, the implementation must check if the type is defined in\n`schemaDefs` and use that definition. If the type is not found in\n`schemaDefs`, it is an error. The entries in `schemaDefs` must be\nprocessed in the order listed such that later schema definitions may refer\nto earlier schema definitions.\n",
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1014 "fields": [
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1015 {
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1016 "name": "https://w3id.org/cwl/cwl#SchemaDefRequirement/class",
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1017 "type": "string",
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1018 "doc": "Always 'SchemaDefRequirement'",
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1019 "jsonldPredicate": {
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1020 "_id": "@type",
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1021 "_type": "@vocab"
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1022 }
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1023 },
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1024 {
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1025 "name": "https://w3id.org/cwl/cwl#SchemaDefRequirement/types",
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1026 "type": {
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1027 "type": "array",
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1028 "items": "https://w3id.org/cwl/cwl#InputSchema"
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1029 },
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1030 "doc": "The list of type definitions."
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1031 }
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1032 ]
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1033 },
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1034 {
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1035 "name": "https://w3id.org/cwl/cwl#CommandLineToolDoc",
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1036 "type": "documentation",
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1037 "doc": [
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1038 "# Common Workflow Language (CWL) Command Line Tool Description, v1.0\n\nThis version:\n * https://w3id.org/cwl/v1.0/\n\nCurrent version:\n * https://w3id.org/cwl/\n",
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1039 "\n\n",
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1040 "\n",
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1041 "\n\n",
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1042 "# Abstract\n\nA Command Line Tool is a non-interactive executable program that reads\nsome input, performs a computation, and terminates after producing some\noutput. Command line programs are a flexible unit of code sharing and\nreuse, unfortunately the syntax and input/output semantics among command\nline programs is extremely heterogeneous. A common layer for describing\nthe syntax and semantics of programs can reduce this incidental\ncomplexity by providing a consistent way to connect programs together.\nThis specification defines the Common Workflow Language (CWL) Command\nLine Tool Description, a vendor-neutral standard for describing the\nsyntax and input/output semantics of command line programs.\n",
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1043 "\n",
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1044 "## Introduction to v1.0\n\nThis specification represents the first full release from the CWL group.\nSince draft-3, version 1.0 introduces the following changes and additions:\n\n * The [Directory](#Directory) type.\n * Syntax simplifcations: denoted by the `map<>` syntax. Example: inputs\n contains a list of items, each with an id. Now one can specify\n a mapping of that identifier to the corresponding\n `CommandInputParamater`.\n ```\n inputs:\n - id: one\n type: string\n doc: First input parameter\n - id: two\n type: int\n doc: Second input parameter\n ```\n can be\n ```\n inputs:\n one:\n type: string\n doc: First input parameter\n two:\n type: int\n doc: Second input parameter\n ```\n * [InitialWorkDirRequirement](#InitialWorkDirRequirement): list of\n files and subdirectories to be present in the output directory prior\n to execution.\n * Shortcuts for specifying the standard [output](#stdout) and/or\n [error](#stderr) streams as a (streamable) File output.\n * [SoftwareRequirement](#SoftwareRequirement) for describing software\n dependencies of a tool.\n * The common `description` field has been renamed to `doc`.\n\n## Errata\n\nPost v1.0 release changes to the spec.\n\n * 13 July 2016: Mark `baseCommand` as optional and update descriptive text.\n\n## Purpose\n\nStandalone programs are a flexible and interoperable form of code reuse.\nUnlike monolithic applications, applications and analysis workflows which\nare composed of multiple separate programs can be written in multiple\nlanguages and execute concurrently on multiple hosts. However, POSIX\ndoes not dictate computer-readable grammar or semantics for program input\nand output, resulting in extremely heterogeneous command line grammar and\ninput/output semantics among program. This is a particular problem in\ndistributed computing (multi-node compute clusters) and virtualized\nenvironments (such as Docker containers) where it is often necessary to\nprovision resources such as input files before executing the program.\n\nOften this gap is filled by hard coding program invocation and\nimplicitly assuming requirements will be met, or abstracting program\ninvocation with wrapper scripts or descriptor documents. Unfortunately,\nwhere these approaches are application or platform specific it creates a\nsignificant barrier to reproducibility and portability, as methods\ndeveloped for one platform must be manually ported to be used on new\nplatforms. Similarly it creates redundant work, as wrappers for popular\ntools must be rewritten for each application or platform in use.\n\nThe Common Workflow Language Command Line Tool Description is designed to\nprovide a common standard description of grammar and semantics for\ninvoking programs used in data-intensive fields such as Bioinformatics,\nChemistry, Physics, Astronomy, and Statistics. This specification\ndefines a precise data and execution model for Command Line Tools that\ncan be implemented on a variety of computing platforms, ranging from a\nsingle workstation to cluster, grid, cloud, and high performance\ncomputing platforms.\n",
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1045 "\n",
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1046 "\n"
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1047 ]
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1048 },
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1049 {
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1050 "type": "record",
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1051 "name": "https://w3id.org/cwl/cwl#EnvironmentDef",
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1052 "doc": "Define an environment variable that will be set in the runtime environment\nby the workflow platform when executing the command line tool. May be the\nresult of executing an expression, such as getting a parameter from input.\n",
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1053 "fields": [
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1054 {
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1055 "name": "https://w3id.org/cwl/cwl#EnvironmentDef/envName",
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1056 "type": "string",
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1057 "doc": "The environment variable name"
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1058 },
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1059 {
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1060 "name": "https://w3id.org/cwl/cwl#EnvironmentDef/envValue",
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1061 "type": [
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1062 "string",
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1063 "https://w3id.org/cwl/cwl#Expression"
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1064 ],
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1065 "doc": "The environment variable value"
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1066 }
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1067 ]
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1068 },
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1069 {
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1070 "type": "record",
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1071 "name": "https://w3id.org/cwl/cwl#CommandLineBinding",
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1072 "extends": "https://w3id.org/cwl/cwl#InputBinding",
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1073 "doc": "\nWhen listed under `inputBinding` in the input schema, the term\n\"value\" refers to the the corresponding value in the input object. For\nbinding objects listed in `CommandLineTool.arguments`, the term \"value\"\nrefers to the effective value after evaluating `valueFrom`.\n\nThe binding behavior when building the command line depends on the data\ntype of the value. If there is a mismatch between the type described by\nthe input schema and the effective value, such as resulting from an\nexpression evaluation, an implementation must use the data type of the\neffective value.\n\n - **string**: Add `prefix` and the string to the command line.\n\n - **number**: Add `prefix` and decimal representation to command line.\n\n - **boolean**: If true, add `prefix` to the command line. If false, add\n nothing.\n\n - **File**: Add `prefix` and the value of\n [`File.path`](#File) to the command line.\n\n - **array**: If `itemSeparator` is specified, add `prefix` and the join\n the array into a single string with `itemSeparator` separating the\n items. Otherwise first add `prefix`, then recursively process\n individual elements.\n\n - **object**: Add `prefix` only, and recursively add object fields for\n which `inputBinding` is specified.\n\n - **null**: Add nothing.\n",
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1074 "fields": [
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1075 {
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1076 "name": "https://w3id.org/cwl/cwl#CommandLineBinding/position",
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1077 "type": [
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1078 "null",
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1079 "int"
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1080 ],
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1081 "doc": "The sorting key. Default position is 0."
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1082 },
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1083 {
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1084 "name": "https://w3id.org/cwl/cwl#CommandLineBinding/prefix",
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1085 "type": [
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1086 "null",
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1087 "string"
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1088 ],
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1089 "doc": "Command line prefix to add before the value."
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1090 },
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1091 {
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1092 "name": "https://w3id.org/cwl/cwl#CommandLineBinding/separate",
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parents:
diff changeset
1093 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1094 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1095 "boolean"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1096 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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1097 "doc": "If true (default), then the prefix and value must be added as separate\ncommand line arguments; if false, prefix and value must be concatenated\ninto a single command line argument.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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1098 },
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guerler
parents:
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1099 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1100 "name": "https://w3id.org/cwl/cwl#CommandLineBinding/itemSeparator",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1101 "type": [
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parents:
diff changeset
1102 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1103 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1104 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1105 "doc": "Join the array elements into a single string with the elements\nseparated by by `itemSeparator`.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1106 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1107 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1108 "name": "https://w3id.org/cwl/cwl#CommandLineBinding/valueFrom",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1109 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1110 "null",
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guerler
parents:
diff changeset
1111 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1112 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1113 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1114 "jsonldPredicate": "cwl:valueFrom",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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1115 "doc": "If `valueFrom` is a constant string value, use this as the value and\napply the binding rules above.\n\nIf `valueFrom` is an expression, evaluate the expression to yield the\nactual value to use to build the command line and apply the binding\nrules above. If the inputBinding is associated with an input\nparameter, the value of `self` in the expression will be the value of the\ninput parameter.\n\nWhen a binding is part of the `CommandLineTool.arguments` field,\nthe `valueFrom` field is required.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1116 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1117 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1118 "name": "https://w3id.org/cwl/cwl#CommandLineBinding/shellQuote",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1119 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1120 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1121 "boolean"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1122 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1123 "doc": "If `ShellCommandRequirement` is in the requirements for the current command,\nthis controls whether the value is quoted on the command line (default is true).\nUse `shellQuote: false` to inject metacharacters for operations such as pipes.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1124 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1125 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1126 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1127 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1128 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1129 "name": "https://w3id.org/cwl/cwl#CommandOutputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1130 "extends": "https://w3id.org/cwl/cwl#OutputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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1131 "doc": "Describes how to generate an output parameter based on the files produced\nby a CommandLineTool.\n\nThe output parameter is generated by applying these operations in\nthe following order:\n\n - glob\n - loadContents\n - outputEval\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1132 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1133 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1134 "name": "https://w3id.org/cwl/cwl#CommandOutputBinding/glob",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1135 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1136 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1137 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1138 "https://w3id.org/cwl/cwl#Expression",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1139 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1140 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1141 "items": "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1142 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1143 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1144 "doc": "Find files relative to the output directory, using POSIX glob(3)\npathname matching. If an array is provided, find files that match any\npattern in the array. If an expression is provided, the expression must\nreturn a string or an array of strings, which will then be evaluated as\none or more glob patterns. Must only match and return files which\nactually exist.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1145 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1146 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1147 "name": "https://w3id.org/cwl/cwl#CommandOutputBinding/loadContents",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1148 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1149 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1150 "boolean"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1151 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1152 "jsonldPredicate": "cwl:loadContents",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1153 "doc": "For each file matched in `glob`, read up to\nthe first 64 KiB of text from the file and place it in the `contents`\nfield of the file object for manipulation by `outputEval`.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1154 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1155 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1156 "name": "https://w3id.org/cwl/cwl#CommandOutputBinding/outputEval",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1157 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1158 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1159 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1160 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1161 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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1162 "doc": "Evaluate an expression to generate the output value. If `glob` was\nspecified, the value of `self` must be an array containing file objects\nthat were matched. If no files were matched, `self` must be a zero\nlength array; if a single file was matched, the value of `self` is an\narray of a single element. Additionally, if `loadContents` is `true`,\nthe File objects must include up to the first 64 KiB of file contents\nin the `contents` field.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1163 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1164 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1165 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1166 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1167 "name": "https://w3id.org/cwl/cwl#CommandInputRecordField",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1168 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1169 "extends": "https://w3id.org/cwl/cwl#InputRecordField",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1170 "specialize": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1171 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1172 "specializeFrom": "https://w3id.org/cwl/cwl#InputRecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1173 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputRecordSchema"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1174 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1175 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1176 "specializeFrom": "https://w3id.org/cwl/cwl#InputEnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1177 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputEnumSchema"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1178 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1179 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1180 "specializeFrom": "https://w3id.org/cwl/cwl#InputArraySchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1181 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputArraySchema"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1182 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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1183 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1184 "specializeFrom": "https://w3id.org/cwl/cwl#InputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1185 "specializeTo": "https://w3id.org/cwl/cwl#CommandLineBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1186 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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1187 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1188 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1189 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1190 "name": "https://w3id.org/cwl/cwl#CommandInputRecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1191 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1192 "extends": "https://w3id.org/cwl/cwl#InputRecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1193 "specialize": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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1194 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1195 "specializeFrom": "https://w3id.org/cwl/cwl#InputRecordField",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1196 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputRecordField"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1197 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1198 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1199 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1200 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1201 "name": "https://w3id.org/cwl/cwl#CommandInputEnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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1202 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1203 "extends": "https://w3id.org/cwl/cwl#InputEnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1204 "specialize": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1205 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1206 "specializeFrom": "https://w3id.org/cwl/cwl#InputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1207 "specializeTo": "https://w3id.org/cwl/cwl#CommandLineBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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1208 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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1209 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1210 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1211 {
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diff changeset
1212 "name": "https://w3id.org/cwl/cwl#CommandInputArraySchema",
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diff changeset
1213 "type": "record",
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diff changeset
1214 "extends": "https://w3id.org/cwl/cwl#InputArraySchema",
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diff changeset
1215 "specialize": [
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diff changeset
1216 {
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diff changeset
1217 "specializeFrom": "https://w3id.org/cwl/cwl#InputRecordSchema",
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diff changeset
1218 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputRecordSchema"
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diff changeset
1219 },
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1220 {
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diff changeset
1221 "specializeFrom": "https://w3id.org/cwl/cwl#InputEnumSchema",
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diff changeset
1222 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputEnumSchema"
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1223 },
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1224 {
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diff changeset
1225 "specializeFrom": "https://w3id.org/cwl/cwl#InputArraySchema",
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diff changeset
1226 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputArraySchema"
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diff changeset
1227 },
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diff changeset
1228 {
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diff changeset
1229 "specializeFrom": "https://w3id.org/cwl/cwl#InputBinding",
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diff changeset
1230 "specializeTo": "https://w3id.org/cwl/cwl#CommandLineBinding"
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diff changeset
1231 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1232 ]
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1233 },
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diff changeset
1234 {
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diff changeset
1235 "name": "https://w3id.org/cwl/cwl#CommandOutputRecordField",
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diff changeset
1236 "type": "record",
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diff changeset
1237 "extends": "https://w3id.org/cwl/cwl#OutputRecordField",
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diff changeset
1238 "specialize": [
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diff changeset
1239 {
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diff changeset
1240 "specializeFrom": "https://w3id.org/cwl/cwl#OutputRecordSchema",
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1241 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputRecordSchema"
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1242 },
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1243 {
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diff changeset
1244 "specializeFrom": "https://w3id.org/cwl/cwl#OutputEnumSchema",
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diff changeset
1245 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputEnumSchema"
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1246 },
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1247 {
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diff changeset
1248 "specializeFrom": "https://w3id.org/cwl/cwl#OutputArraySchema",
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diff changeset
1249 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputArraySchema"
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diff changeset
1250 },
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1251 {
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diff changeset
1252 "specializeFrom": "https://w3id.org/cwl/cwl#OutputBinding",
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diff changeset
1253 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1254 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1255 ]
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1256 },
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1257 {
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diff changeset
1258 "name": "https://w3id.org/cwl/cwl#CommandOutputRecordSchema",
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diff changeset
1259 "type": "record",
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diff changeset
1260 "extends": "https://w3id.org/cwl/cwl#OutputRecordSchema",
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diff changeset
1261 "specialize": [
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diff changeset
1262 {
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diff changeset
1263 "specializeFrom": "https://w3id.org/cwl/cwl#OutputRecordField",
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diff changeset
1264 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputRecordField"
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diff changeset
1265 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1266 ]
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1267 },
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1268 {
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diff changeset
1269 "name": "https://w3id.org/cwl/cwl#CommandOutputEnumSchema",
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1270 "type": "record",
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diff changeset
1271 "extends": "https://w3id.org/cwl/cwl#OutputEnumSchema",
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diff changeset
1272 "specialize": [
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diff changeset
1273 {
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diff changeset
1274 "specializeFrom": "https://w3id.org/cwl/cwl#OutputRecordSchema",
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1275 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputRecordSchema"
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1276 },
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1277 {
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diff changeset
1278 "specializeFrom": "https://w3id.org/cwl/cwl#OutputEnumSchema",
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diff changeset
1279 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputEnumSchema"
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diff changeset
1280 },
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1281 {
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diff changeset
1282 "specializeFrom": "https://w3id.org/cwl/cwl#OutputArraySchema",
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diff changeset
1283 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputArraySchema"
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diff changeset
1284 },
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diff changeset
1285 {
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diff changeset
1286 "specializeFrom": "https://w3id.org/cwl/cwl#OutputBinding",
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diff changeset
1287 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1288 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1289 ]
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diff changeset
1290 },
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diff changeset
1291 {
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diff changeset
1292 "name": "https://w3id.org/cwl/cwl#CommandOutputArraySchema",
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diff changeset
1293 "type": "record",
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diff changeset
1294 "extends": "https://w3id.org/cwl/cwl#OutputArraySchema",
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diff changeset
1295 "specialize": [
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diff changeset
1296 {
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diff changeset
1297 "specializeFrom": "https://w3id.org/cwl/cwl#OutputRecordSchema",
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diff changeset
1298 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputRecordSchema"
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diff changeset
1299 },
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diff changeset
1300 {
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diff changeset
1301 "specializeFrom": "https://w3id.org/cwl/cwl#OutputEnumSchema",
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diff changeset
1302 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputEnumSchema"
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diff changeset
1303 },
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diff changeset
1304 {
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diff changeset
1305 "specializeFrom": "https://w3id.org/cwl/cwl#OutputArraySchema",
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diff changeset
1306 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputArraySchema"
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diff changeset
1307 },
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diff changeset
1308 {
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diff changeset
1309 "specializeFrom": "https://w3id.org/cwl/cwl#OutputBinding",
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diff changeset
1310 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1311 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1312 ]
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diff changeset
1313 },
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diff changeset
1314 {
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diff changeset
1315 "type": "record",
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diff changeset
1316 "name": "https://w3id.org/cwl/cwl#CommandInputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1317 "extends": "https://w3id.org/cwl/cwl#InputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1318 "doc": "An input parameter for a CommandLineTool.",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1319 "specialize": [
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diff changeset
1320 {
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diff changeset
1321 "specializeFrom": "https://w3id.org/cwl/cwl#InputRecordSchema",
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diff changeset
1322 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputRecordSchema"
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diff changeset
1323 },
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diff changeset
1324 {
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diff changeset
1325 "specializeFrom": "https://w3id.org/cwl/cwl#InputEnumSchema",
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diff changeset
1326 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputEnumSchema"
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diff changeset
1327 },
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diff changeset
1328 {
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diff changeset
1329 "specializeFrom": "https://w3id.org/cwl/cwl#InputArraySchema",
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parents:
diff changeset
1330 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputArraySchema"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1331 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1332 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1333 "specializeFrom": "https://w3id.org/cwl/cwl#InputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1334 "specializeTo": "https://w3id.org/cwl/cwl#CommandLineBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1335 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1336 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1337 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1338 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1339 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1340 "name": "https://w3id.org/cwl/cwl#CommandOutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1341 "extends": "https://w3id.org/cwl/cwl#OutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1342 "doc": "An output parameter for a CommandLineTool.",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1343 "specialize": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1344 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1345 "specializeFrom": "https://w3id.org/cwl/cwl#OutputBinding",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1346 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputBinding"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1347 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1348 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1349 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1350 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1351 "name": "https://w3id.org/cwl/cwl#CommandOutputParameter/type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1352 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1353 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1354 "https://w3id.org/cwl/cwl#CWLType",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1355 "https://w3id.org/cwl/cwl#stdout",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1356 "https://w3id.org/cwl/cwl#stderr",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1357 "https://w3id.org/cwl/cwl#CommandOutputRecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1358 "https://w3id.org/cwl/cwl#CommandOutputEnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1359 "https://w3id.org/cwl/cwl#CommandOutputArraySchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1360 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1361 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1362 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1363 "items": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1364 "https://w3id.org/cwl/cwl#CWLType",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1365 "https://w3id.org/cwl/cwl#CommandOutputRecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1366 "https://w3id.org/cwl/cwl#CommandOutputEnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1367 "https://w3id.org/cwl/cwl#CommandOutputArraySchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1368 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1369 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1370 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1371 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1372 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1373 "_id": "https://w3id.org/cwl/salad#type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1374 "_type": "@vocab",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1375 "refScope": 2,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1376 "typeDSL": true
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1377 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1378 "doc": "Specify valid types of data that may be assigned to this parameter.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1379 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1380 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1381 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1382 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1383 "name": "https://w3id.org/cwl/cwl#stdout",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1384 "type": "enum",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1385 "symbols": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1386 "https://w3id.org/cwl/cwl#stdout"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1387 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1388 "docParent": "https://w3id.org/cwl/cwl#CommandOutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1389 "doc": "Only valid as a `type` for a `CommandLineTool` output with no\n`outputBinding` set.\n\nThe following\n```\noutputs:\n an_output_name:\n type: stdout\n\nstdout: a_stdout_file\n```\nis equivalent to\n```\noutputs:\n an_output_name:\n type: File\n streamable: true\n outputBinding:\n glob: a_stdout_file\n\nstdout: a_stdout_file\n```\n\nIf there is no `stdout` name provided, a random filename will be created.\nFor example, the following\n```\noutputs:\n an_output_name:\n type: stdout\n```\nis equivalent to\n```\noutputs:\n an_output_name:\n type: File\n streamable: true\n outputBinding:\n glob: random_stdout_filenameABCDEFG\n\nstdout: random_stdout_filenameABCDEFG\n```\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1390 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1391 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1392 "name": "https://w3id.org/cwl/cwl#stderr",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1393 "type": "enum",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1394 "symbols": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1395 "https://w3id.org/cwl/cwl#stderr"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1396 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1397 "docParent": "https://w3id.org/cwl/cwl#CommandOutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1398 "doc": "Only valid as a `type` for a `CommandLineTool` output with no\n`outputBinding` set.\n\nThe following\n```\noutputs:\n an_output_name:\n type: stderr\n\nstderr: a_stderr_file\n```\nis equivalent to\n```\noutputs:\n an_output_name:\n type: File\n streamable: true\n outputBinding:\n glob: a_stderr_file\n\nstderr: a_stderr_file\n```\n\nIf there is no `stderr` name provided, a random filename will be created.\nFor example, the following\n```\noutputs:\n an_output_name:\n type: stderr\n```\nis equivalent to\n```\noutputs:\n an_output_name:\n type: File\n streamable: true\n outputBinding:\n glob: random_stderr_filenameABCDEFG\n\nstderr: random_stderr_filenameABCDEFG\n```\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1399 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1400 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1401 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1402 "name": "https://w3id.org/cwl/cwl#CommandLineTool",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1403 "extends": "https://w3id.org/cwl/cwl#Process",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1404 "documentRoot": true,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1405 "specialize": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1406 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1407 "specializeFrom": "https://w3id.org/cwl/cwl#InputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1408 "specializeTo": "https://w3id.org/cwl/cwl#CommandInputParameter"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1409 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1410 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1411 "specializeFrom": "https://w3id.org/cwl/cwl#OutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1412 "specializeTo": "https://w3id.org/cwl/cwl#CommandOutputParameter"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1413 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1414 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1415 "doc": "This defines the schema of the CWL Command Line Tool Description document.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1416 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1417 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1418 "name": "https://w3id.org/cwl/cwl#CommandLineTool/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1419 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1420 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1421 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1422 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1423 "type": "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1424 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1425 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1426 "name": "https://w3id.org/cwl/cwl#CommandLineTool/baseCommand",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1427 "doc": "Specifies the program to execute. If an array, the first element of\nthe array is the command to execute, and subsequent elements are\nmandatory command line arguments. The elements in `baseCommand` must\nappear before any command line bindings from `inputBinding` or\n`arguments`.\n\nIf `baseCommand` is not provided or is an empty array, the first\nelement of the command line produced after processing `inputBinding` or\n`arguments` must be used as the program to execute.\n\nIf the program includes a path separator character it must\nbe an absolute path, otherwise it is an error. If the program does not\ninclude a path separator, search the `$PATH` variable in the runtime\nenvironment of the workflow runner find the absolute path of the\nexecutable.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1428 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1429 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1430 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1431 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1432 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1433 "items": "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1434 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1435 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1436 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1437 "_id": "https://w3id.org/cwl/cwl#baseCommand",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1438 "_container": "@list"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1439 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1440 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1441 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1442 "name": "https://w3id.org/cwl/cwl#CommandLineTool/arguments",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1443 "doc": "Command line bindings which are not directly associated with input parameters.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1444 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1445 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1446 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1447 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1448 "items": [
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parents:
diff changeset
1449 "string",
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parents:
diff changeset
1450 "https://w3id.org/cwl/cwl#Expression",
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guerler
parents:
diff changeset
1451 "https://w3id.org/cwl/cwl#CommandLineBinding"
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parents:
diff changeset
1452 ]
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parents:
diff changeset
1453 }
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parents:
diff changeset
1454 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1455 "jsonldPredicate": {
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parents:
diff changeset
1456 "_id": "https://w3id.org/cwl/cwl#arguments",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1457 "_container": "@list"
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parents:
diff changeset
1458 }
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parents:
diff changeset
1459 },
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guerler
parents:
diff changeset
1460 {
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guerler
parents:
diff changeset
1461 "name": "https://w3id.org/cwl/cwl#CommandLineTool/stdin",
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guerler
parents:
diff changeset
1462 "type": [
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parents:
diff changeset
1463 "null",
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guerler
parents:
diff changeset
1464 "string",
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guerler
parents:
diff changeset
1465 "https://w3id.org/cwl/cwl#Expression"
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parents:
diff changeset
1466 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1467 "doc": "A path to a file whose contents must be piped into the command's\nstandard input stream.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1468 },
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parents:
diff changeset
1469 {
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guerler
parents:
diff changeset
1470 "name": "https://w3id.org/cwl/cwl#CommandLineTool/stderr",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1471 "type": [
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guerler
parents:
diff changeset
1472 "null",
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guerler
parents:
diff changeset
1473 "string",
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guerler
parents:
diff changeset
1474 "https://w3id.org/cwl/cwl#Expression"
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guerler
parents:
diff changeset
1475 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1476 "jsonldPredicate": "https://w3id.org/cwl/cwl#stderr",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1477 "doc": "Capture the command's standard error stream to a file written to\nthe designated output directory.\n\nIf `stderr` is a string, it specifies the file name to use.\n\nIf `stderr` is an expression, the expression is evaluated and must\nreturn a string with the file name to use to capture stderr. If the\nreturn value is not a string, or the resulting path contains illegal\ncharacters (such as the path separator `/`) it is an error.\n"
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parents:
diff changeset
1478 },
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parents:
diff changeset
1479 {
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guerler
parents:
diff changeset
1480 "name": "https://w3id.org/cwl/cwl#CommandLineTool/stdout",
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guerler
parents:
diff changeset
1481 "type": [
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parents:
diff changeset
1482 "null",
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guerler
parents:
diff changeset
1483 "string",
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guerler
parents:
diff changeset
1484 "https://w3id.org/cwl/cwl#Expression"
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guerler
parents:
diff changeset
1485 ],
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guerler
parents:
diff changeset
1486 "jsonldPredicate": "https://w3id.org/cwl/cwl#stdout",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1487 "doc": "Capture the command's standard output stream to a file written to\nthe designated output directory.\n\nIf `stdout` is a string, it specifies the file name to use.\n\nIf `stdout` is an expression, the expression is evaluated and must\nreturn a string with the file name to use to capture stdout. If the\nreturn value is not a string, or the resulting path contains illegal\ncharacters (such as the path separator `/`) it is an error.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1488 },
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guerler
parents:
diff changeset
1489 {
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guerler
parents:
diff changeset
1490 "name": "https://w3id.org/cwl/cwl#CommandLineTool/successCodes",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1491 "type": [
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guerler
parents:
diff changeset
1492 "null",
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guerler
parents:
diff changeset
1493 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1494 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1495 "items": "int"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1496 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1497 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1498 "doc": "Exit codes that indicate the process completed successfully.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1499 },
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guerler
parents:
diff changeset
1500 {
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guerler
parents:
diff changeset
1501 "name": "https://w3id.org/cwl/cwl#CommandLineTool/temporaryFailCodes",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1502 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1503 "null",
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guerler
parents:
diff changeset
1504 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1505 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1506 "items": "int"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1507 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1508 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1509 "doc": "Exit codes that indicate the process failed due to a possibly\ntemporary condition, where executing the process with the same\nruntime environment and inputs may produce different results.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1510 },
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guerler
parents:
diff changeset
1511 {
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guerler
parents:
diff changeset
1512 "name": "https://w3id.org/cwl/cwl#CommandLineTool/permanentFailCodes",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1513 "type": [
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parents:
diff changeset
1514 "null",
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guerler
parents:
diff changeset
1515 {
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guerler
parents:
diff changeset
1516 "type": "array",
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guerler
parents:
diff changeset
1517 "items": "int"
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guerler
parents:
diff changeset
1518 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1519 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1520 "doc": "Exit codes that indicate the process failed due to a permanent logic error, where executing the process with the same runtime environment and same inputs is expected to always fail."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1521 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1522 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1523 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1524 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1525 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1526 "name": "https://w3id.org/cwl/cwl#DockerRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1527 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1528 "doc": "Indicates that a workflow component should be run in a\n[Docker](http://docker.com) container, and specifies how to fetch or build\nthe image.\n\nIf a CommandLineTool lists `DockerRequirement` under\n`hints` (or `requirements`), it may (or must) be run in the specified Docker\ncontainer.\n\nThe platform must first acquire or install the correct Docker image as\nspecified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`.\n\nThe platform must execute the tool in the container using `docker run` with\nthe appropriate Docker image and tool command line.\n\nThe workflow platform may provide input files and the designated output\ndirectory through the use of volume bind mounts. The platform may rewrite\nfile paths in the input object to correspond to the Docker bind mounted\nlocations.\n\nWhen running a tool contained in Docker, the workflow platform must not\nassume anything about the contents of the Docker container, such as the\npresence or absence of specific software, except to assume that the\ngenerated command line represents a valid command within the runtime\nenvironment of the container.\n\n## Interaction with other requirements\n\nIf [EnvVarRequirement](#EnvVarRequirement) is specified alongside a\nDockerRequirement, the environment variables must be provided to Docker\nusing `--env` or `--env-file` and interact with the container's preexisting\nenvironment as defined by Docker.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1529 "fields": [
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guerler
parents:
diff changeset
1530 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1531 "name": "https://w3id.org/cwl/cwl#DockerRequirement/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1532 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1533 "doc": "Always 'DockerRequirement'",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1534 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1535 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1536 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1537 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1538 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1539 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1540 "name": "https://w3id.org/cwl/cwl#DockerRequirement/dockerPull",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1541 "type": [
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guerler
parents:
diff changeset
1542 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1543 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1544 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1545 "doc": "Specify a Docker image to retrieve using `docker pull`."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1546 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1547 {
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guerler
parents:
diff changeset
1548 "name": "https://w3id.org/cwl/cwl#DockerRequirement/dockerLoad",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1549 "type": [
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guerler
parents:
diff changeset
1550 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1551 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1552 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1553 "doc": "Specify a HTTP URL from which to download a Docker image using `docker load`."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1554 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1555 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1556 "name": "https://w3id.org/cwl/cwl#DockerRequirement/dockerFile",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1557 "type": [
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guerler
parents:
diff changeset
1558 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1559 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1560 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1561 "doc": "Supply the contents of a Dockerfile which will be built using `docker build`."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1562 },
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guerler
parents:
diff changeset
1563 {
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guerler
parents:
diff changeset
1564 "name": "https://w3id.org/cwl/cwl#DockerRequirement/dockerImport",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1565 "type": [
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guerler
parents:
diff changeset
1566 "null",
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guerler
parents:
diff changeset
1567 "string"
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guerler
parents:
diff changeset
1568 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1569 "doc": "Provide HTTP URL to download and gunzip a Docker images using `docker import."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1570 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1571 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1572 "name": "https://w3id.org/cwl/cwl#DockerRequirement/dockerImageId",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1573 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1574 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1575 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1576 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1577 "doc": "The image id that will be used for `docker run`. May be a\nhuman-readable image name or the image identifier hash. May be skipped\nif `dockerPull` is specified, in which case the `dockerPull` image id\nmust be used.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1578 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1579 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1580 "name": "https://w3id.org/cwl/cwl#DockerRequirement/dockerOutputDirectory",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1581 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1582 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1583 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1584 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1585 "doc": "Set the designated output directory to a specific location inside the\nDocker container.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1586 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1587 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1588 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1589 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1590 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1591 "name": "https://w3id.org/cwl/cwl#SoftwareRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1592 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1593 "doc": "A list of software packages that should be configured in the environment of\nthe defined process.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1594 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1595 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1596 "name": "https://w3id.org/cwl/cwl#SoftwareRequirement/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1597 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1598 "doc": "Always 'SoftwareRequirement'",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1599 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1600 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1601 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1602 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1603 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1604 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1605 "name": "https://w3id.org/cwl/cwl#SoftwareRequirement/packages",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1606 "type": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1607 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1608 "items": "https://w3id.org/cwl/cwl#SoftwarePackage"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1609 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1610 "doc": "The list of software to be configured.",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1611 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1612 "mapSubject": "package",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1613 "mapPredicate": "specs"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1614 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1615 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1616 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1617 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1618 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1619 "name": "https://w3id.org/cwl/cwl#SoftwarePackage",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1620 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1621 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1622 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1623 "name": "https://w3id.org/cwl/cwl#SoftwarePackage/package",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1624 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1625 "doc": "The common name of the software to be configured."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1626 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1627 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1628 "name": "https://w3id.org/cwl/cwl#SoftwarePackage/version",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1629 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1630 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1631 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1632 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1633 "items": "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1634 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1635 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1636 "doc": "The (optional) version of the software to configured."
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1637 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1638 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1639 "name": "https://w3id.org/cwl/cwl#SoftwarePackage/specs",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1640 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1641 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1642 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1643 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1644 "items": "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1645 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1646 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1647 "doc": "Must be one or more IRIs identifying resources for installing or\nenabling the software. Implementations may provide resolvers which map\nwell-known software spec IRIs to some configuration action.\n\nFor example, an IRI `https://packages.debian.org/jessie/bowtie` could\nbe resolved with `apt-get install bowtie`. An IRI\n`https://anaconda.org/bioconda/bowtie` could be resolved with `conda\ninstall -c bioconda bowtie`.\n\nTools may also provide IRIs to index entries such as\n[RRID](http://www.identifiers.org/rrid/), such as\n`http://identifiers.org/rrid/RRID:SCR_005476`\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1648 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1649 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1650 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1651 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1652 "name": "https://w3id.org/cwl/cwl#Dirent",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1653 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1654 "doc": "Define a file or subdirectory that must be placed in the designated output\ndirectory prior to executing the command line tool. May be the result of\nexecuting an expression, such as building a configuration file from a\ntemplate.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1655 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1656 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1657 "name": "https://w3id.org/cwl/cwl#Dirent/entryname",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1658 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1659 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1660 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1661 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1662 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1663 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1664 "_id": "https://w3id.org/cwl/cwl#entryname"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1665 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1666 "doc": "The name of the file or subdirectory to create in the output directory.\nIf `entry` is a File or Directory, this overrides `basename`. Optional.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1667 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1668 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1669 "name": "https://w3id.org/cwl/cwl#Dirent/entry",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1670 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1671 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1672 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1673 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1674 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1675 "_id": "https://w3id.org/cwl/cwl#entry"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1676 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1677 "doc": "If the value is a string literal or an expression which evaluates to a\nstring, a new file must be created with the string as the file contents.\n\nIf the value is an expression that evaluates to a `File` object, this\nindicates the referenced file should be added to the designated output\ndirectory prior to executing the tool.\n\nIf the value is an expression that evaluates to a `Dirent` object, this\nindicates that the File or Directory in `entry` should be added to the\ndesignated output directory with the name in `entryname`.\n\nIf `writable` is false, the file may be made available using a bind\nmount or file system link to avoid unnecessary copying of the input\nfile.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1678 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1679 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1680 "name": "https://w3id.org/cwl/cwl#Dirent/writable",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1681 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1682 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1683 "boolean"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1684 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1685 "doc": "If true, the file or directory must be writable by the tool. Changes\nto the file or directory must be isolated and not visible by any other\nCommandLineTool process. This may be implemented by making a copy of\nthe original file or directory. Default false (files and directories\nread-only by default).\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1686 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1687 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1688 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1689 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1690 "name": "https://w3id.org/cwl/cwl#InitialWorkDirRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1691 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1692 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1693 "doc": "Define a list of files and subdirectories that must be created by the workflow platform in the designated output directory prior to executing the command line tool.",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1694 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1695 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1696 "name": "https://w3id.org/cwl/cwl#InitialWorkDirRequirement/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1697 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1698 "doc": "InitialWorkDirRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1699 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1700 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1701 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1702 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1703 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1704 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1705 "name": "https://w3id.org/cwl/cwl#InitialWorkDirRequirement/listing",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1706 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1707 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1708 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1709 "items": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1710 "https://w3id.org/cwl/cwl#File",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1711 "https://w3id.org/cwl/cwl#Directory",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1712 "https://w3id.org/cwl/cwl#Dirent",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1713 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1714 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1715 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1716 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1717 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1718 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1719 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1720 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1721 "_id": "https://w3id.org/cwl/cwl#listing"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1722 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1723 "doc": "The list of files or subdirectories that must be placed in the\ndesignated output directory prior to executing the command line tool.\n\nMay be an expression. If so, the expression return value must validate\nas `{type: array, items: [File, Directory]}`.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1724 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1725 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1726 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1727 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1728 "name": "https://w3id.org/cwl/cwl#EnvVarRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1729 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1730 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1731 "doc": "Define a list of environment variables which will be set in the\nexecution environment of the tool. See `EnvironmentDef` for details.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1732 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1733 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1734 "name": "https://w3id.org/cwl/cwl#EnvVarRequirement/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1735 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1736 "doc": "Always 'EnvVarRequirement'",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1737 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1738 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1739 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1740 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1741 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1742 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1743 "name": "https://w3id.org/cwl/cwl#EnvVarRequirement/envDef",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1744 "type": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1745 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1746 "items": "https://w3id.org/cwl/cwl#EnvironmentDef"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1747 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1748 "doc": "The list of environment variables.",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1749 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1750 "mapSubject": "envName",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1751 "mapPredicate": "envValue"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1752 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1753 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1754 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1755 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1756 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1757 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1758 "name": "https://w3id.org/cwl/cwl#ShellCommandRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1759 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1760 "doc": "Modify the behavior of CommandLineTool to generate a single string\ncontaining a shell command line. Each item in the argument list must be\njoined into a string separated by single spaces and quoted to prevent\nintepretation by the shell, unless `CommandLineBinding` for that argument\ncontains `shellQuote: false`. If `shellQuote: false` is specified, the\nargument is joined into the command string without quoting, which allows\nthe use of shell metacharacters such as `|` for pipes.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1761 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1762 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1763 "name": "https://w3id.org/cwl/cwl#ShellCommandRequirement/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1764 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1765 "doc": "Always 'ShellCommandRequirement'",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1766 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1767 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1768 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1769 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1770 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1771 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1772 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1773 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1774 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1775 "name": "https://w3id.org/cwl/cwl#ResourceRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1776 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1777 "doc": "Specify basic hardware resource requirements.\n\n\"min\" is the minimum amount of a resource that must be reserved to schedule\na job. If \"min\" cannot be satisfied, the job should not be run.\n\n\"max\" is the maximum amount of a resource that the job shall be permitted\nto use. If a node has sufficient resources, multiple jobs may be scheduled\non a single node provided each job's \"max\" resource requirements are\nmet. If a job attempts to exceed its \"max\" resource allocation, an\nimplementation may deny additional resources, which may result in job\nfailure.\n\nIf \"min\" is specified but \"max\" is not, then \"max\" == \"min\"\nIf \"max\" is specified by \"min\" is not, then \"min\" == \"max\".\n\nIt is an error if max < min.\n\nIt is an error if the value of any of these fields is negative.\n\nIf neither \"min\" nor \"max\" is specified for a resource, an implementation may provide a default.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1778 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1779 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1780 "name": "https://w3id.org/cwl/cwl#ResourceRequirement/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1781 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1782 "doc": "Always 'ResourceRequirement'",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1783 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1784 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1785 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1786 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1787 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1788 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1789 "name": "https://w3id.org/cwl/cwl#ResourceRequirement/coresMin",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1790 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1791 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1792 "long",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1793 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1794 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1795 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1796 "doc": "Minimum reserved number of CPU cores"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1797 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1798 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1799 "name": "https://w3id.org/cwl/cwl#ResourceRequirement/coresMax",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1800 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1801 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1802 "int",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1803 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1804 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1805 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1806 "doc": "Maximum reserved number of CPU cores"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1807 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1808 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1809 "name": "https://w3id.org/cwl/cwl#ResourceRequirement/ramMin",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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1810 "type": [
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1811 "null",
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1812 "long",
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1813 "string",
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1814 "https://w3id.org/cwl/cwl#Expression"
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1815 ],
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1816 "doc": "Minimum reserved RAM in mebibytes (2**20)"
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1817 },
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1818 {
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1819 "name": "https://w3id.org/cwl/cwl#ResourceRequirement/ramMax",
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1820 "type": [
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1821 "null",
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1822 "long",
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1823 "string",
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1824 "https://w3id.org/cwl/cwl#Expression"
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1825 ],
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1826 "doc": "Maximum reserved RAM in mebibytes (2**20)"
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1827 },
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1828 {
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1829 "name": "https://w3id.org/cwl/cwl#ResourceRequirement/tmpdirMin",
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diff changeset
1830 "type": [
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1831 "null",
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diff changeset
1832 "long",
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diff changeset
1833 "string",
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diff changeset
1834 "https://w3id.org/cwl/cwl#Expression"
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1835 ],
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1836 "doc": "Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)"
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1837 },
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1838 {
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1839 "name": "https://w3id.org/cwl/cwl#ResourceRequirement/tmpdirMax",
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1840 "type": [
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diff changeset
1841 "null",
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diff changeset
1842 "long",
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diff changeset
1843 "string",
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diff changeset
1844 "https://w3id.org/cwl/cwl#Expression"
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1845 ],
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1846 "doc": "Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)"
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diff changeset
1847 },
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diff changeset
1848 {
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diff changeset
1849 "name": "https://w3id.org/cwl/cwl#ResourceRequirement/outdirMin",
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1850 "type": [
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1851 "null",
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diff changeset
1852 "long",
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diff changeset
1853 "string",
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diff changeset
1854 "https://w3id.org/cwl/cwl#Expression"
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1855 ],
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1856 "doc": "Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)"
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1857 },
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1858 {
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diff changeset
1859 "name": "https://w3id.org/cwl/cwl#ResourceRequirement/outdirMax",
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1860 "type": [
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1861 "null",
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1862 "long",
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diff changeset
1863 "string",
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diff changeset
1864 "https://w3id.org/cwl/cwl#Expression"
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1865 ],
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1866 "doc": "Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)"
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1867 }
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1868 ]
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1869 },
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1870 {
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1871 "name": "https://w3id.org/cwl/cwl#WorkflowDoc",
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1872 "type": "documentation",
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1873 "doc": [
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1874 "# Common Workflow Language (CWL) Workflow Description, v1.0\n\nThis version:\n * https://w3id.org/cwl/v1.0/\n\nCurrent version:\n * https://w3id.org/cwl/\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
1875 "\n\n",
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diff changeset
1876 "\n",
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diff changeset
1877 "\n\n",
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1878 "# Abstract\n\nOne way to define a workflow is: an analysis task represented by a\ndirected graph describing a sequence of operations that transform an\ninput data set to output. This specification defines the Common Workflow\nLanguage (CWL) Workflow description, a vendor-neutral standard for\nrepresenting workflows intended to be portable across a variety of\ncomputing platforms.\n",
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1879 "\n",
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1880 "\n## Introduction to v1.0\n\nThis specification represents the first full release from the CWL group.\nSince draft-3, this draft introduces the following changes and additions:\n\n * The `inputs` and `outputs` fields have been renamed `in` and `out`.\n * Syntax simplifcations: denoted by the `map<>` syntax. Example: `in`\n contains a list of items, each with an id. Now one can specify\n a mapping of that identifier to the corresponding\n `InputParameter`.\n ```\n in:\n - id: one\n type: string\n doc: First input parameter\n - id: two\n type: int\n doc: Second input parameter\n ```\n can be\n ```\n in:\n one:\n type: string\n doc: First input parameter\n two:\n type: int\n doc: Second input parameter\n ```\n * The common field `description` has been renamed to `doc`.\n\n## Purpose\n\nThe Common Workflow Language Command Line Tool Description express\nworkflows for data-intensive science, such as Bioinformatics, Chemistry,\nPhysics, and Astronomy. This specification is intended to define a data\nand execution model for Workflows that can be implemented on top of a\nvariety of computing platforms, ranging from an individual workstation to\ncluster, grid, cloud, and high performance computing systems.\n",
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diff changeset
1881 "\n"
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1882 ]
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1883 },
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1884 {
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1885 "name": "https://w3id.org/cwl/cwl#ExpressionToolOutputParameter",
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1886 "type": "record",
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1887 "extends": "https://w3id.org/cwl/cwl#OutputParameter",
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1888 "fields": [
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1889 {
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1890 "name": "https://w3id.org/cwl/cwl#ExpressionToolOutputParameter/type",
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1891 "type": [
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1892 "null",
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diff changeset
1893 "https://w3id.org/cwl/cwl#CWLType",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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1894 "https://w3id.org/cwl/cwl#OutputRecordSchema",
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1895 "https://w3id.org/cwl/cwl#OutputEnumSchema",
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1896 "https://w3id.org/cwl/cwl#OutputArraySchema",
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guerler
parents:
diff changeset
1897 "string",
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diff changeset
1898 {
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1899 "type": "array",
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1900 "items": [
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diff changeset
1901 "https://w3id.org/cwl/cwl#CWLType",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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1902 "https://w3id.org/cwl/cwl#OutputRecordSchema",
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1903 "https://w3id.org/cwl/cwl#OutputEnumSchema",
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1904 "https://w3id.org/cwl/cwl#OutputArraySchema",
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1905 "string"
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1906 ]
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1907 }
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1908 ],
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1909 "jsonldPredicate": {
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1910 "_id": "https://w3id.org/cwl/salad#type",
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1911 "_type": "@vocab",
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1912 "refScope": 2,
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1913 "typeDSL": true
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1914 },
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1915 "doc": "Specify valid types of data that may be assigned to this parameter.\n"
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1916 }
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1917 ]
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1918 },
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1919 {
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1920 "type": "record",
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1921 "name": "https://w3id.org/cwl/cwl#ExpressionTool",
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1922 "extends": "https://w3id.org/cwl/cwl#Process",
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1923 "specialize": [
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1924 {
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1925 "specializeFrom": "https://w3id.org/cwl/cwl#OutputParameter",
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1926 "specializeTo": "https://w3id.org/cwl/cwl#ExpressionToolOutputParameter"
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1927 }
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1928 ],
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diff changeset
1929 "documentRoot": true,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1930 "doc": "Execute an expression as a Workflow step.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1931 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1932 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1933 "name": "https://w3id.org/cwl/cwl#ExpressionTool/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1934 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1935 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1936 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1937 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1938 "type": "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1939 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1940 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1941 "name": "https://w3id.org/cwl/cwl#ExpressionTool/expression",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1942 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1943 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1944 "https://w3id.org/cwl/cwl#Expression"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1945 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1946 "doc": "The expression to execute. The expression must return a JSON object which\nmatches the output parameters of the ExpressionTool.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1947 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1948 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1949 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1950 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1951 "name": "https://w3id.org/cwl/cwl#LinkMergeMethod",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1952 "type": "enum",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1953 "docParent": "https://w3id.org/cwl/cwl#WorkflowStepInput",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1954 "doc": "The input link merge method, described in [WorkflowStepInput](#WorkflowStepInput).",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1955 "symbols": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1956 "https://w3id.org/cwl/cwl#LinkMergeMethod/merge_nested",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1957 "https://w3id.org/cwl/cwl#LinkMergeMethod/merge_flattened"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1958 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1959 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1960 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1961 "name": "https://w3id.org/cwl/cwl#WorkflowOutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1962 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1963 "extends": "https://w3id.org/cwl/cwl#OutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1964 "docParent": "https://w3id.org/cwl/cwl#Workflow",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1965 "doc": "Describe an output parameter of a workflow. The parameter must be\nconnected to one or more parameters defined in the workflow that will\nprovide the value of the output parameter.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1966 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1967 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1968 "name": "https://w3id.org/cwl/cwl#WorkflowOutputParameter/outputSource",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1969 "doc": "Specifies one or more workflow parameters that supply the value of to\nthe output parameter.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1970 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1971 "_id": "https://w3id.org/cwl/cwl#outputSource",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1972 "_type": "@id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1973 "refScope": 0
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1974 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1975 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1976 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1977 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1978 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1979 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1980 "items": "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1981 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1982 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1983 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1984 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1985 "name": "https://w3id.org/cwl/cwl#WorkflowOutputParameter/linkMerge",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1986 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1987 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1988 "https://w3id.org/cwl/cwl#LinkMergeMethod"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1989 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1990 "jsonldPredicate": "cwl:linkMerge",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1991 "doc": "The method to use to merge multiple sources into a single array.\nIf not specified, the default method is \"merge_nested\".\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1992 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1993 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1994 "name": "https://w3id.org/cwl/cwl#WorkflowOutputParameter/type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1995 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1996 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1997 "https://w3id.org/cwl/cwl#CWLType",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1998 "https://w3id.org/cwl/cwl#OutputRecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1999 "https://w3id.org/cwl/cwl#OutputEnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2000 "https://w3id.org/cwl/cwl#OutputArraySchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2001 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2002 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2003 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2004 "items": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2005 "https://w3id.org/cwl/cwl#CWLType",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2006 "https://w3id.org/cwl/cwl#OutputRecordSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2007 "https://w3id.org/cwl/cwl#OutputEnumSchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2008 "https://w3id.org/cwl/cwl#OutputArraySchema",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2009 "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2010 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2011 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2012 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2013 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2014 "_id": "https://w3id.org/cwl/salad#type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2015 "_type": "@vocab",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2016 "refScope": 2,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2017 "typeDSL": true
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2018 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2019 "doc": "Specify valid types of data that may be assigned to this parameter.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2020 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2021 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2022 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2023 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2024 "name": "https://w3id.org/cwl/cwl#Sink",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2025 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2026 "abstract": true,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2027 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2028 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2029 "name": "https://w3id.org/cwl/cwl#Sink/source",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2030 "doc": "Specifies one or more workflow parameters that will provide input to\nthe underlying step parameter.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2031 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2032 "_id": "https://w3id.org/cwl/cwl#source",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2033 "_type": "@id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2034 "refScope": 2
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2035 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2036 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2037 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2038 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2039 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2040 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2041 "items": "string"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2042 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2043 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2044 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2045 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2046 "name": "https://w3id.org/cwl/cwl#Sink/linkMerge",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2047 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2048 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2049 "https://w3id.org/cwl/cwl#LinkMergeMethod"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2050 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2051 "jsonldPredicate": "cwl:linkMerge",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2052 "doc": "The method to use to merge multiple inbound links into a single array.\nIf not specified, the default method is \"merge_nested\".\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2053 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2054 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2055 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2056 {
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parents:
diff changeset
2057 "type": "record",
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parents:
diff changeset
2058 "name": "https://w3id.org/cwl/cwl#WorkflowStepInput",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2059 "extends": "https://w3id.org/cwl/cwl#Sink",
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parents:
diff changeset
2060 "docParent": "https://w3id.org/cwl/cwl#WorkflowStep",
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2061 "doc": "The input of a workflow step connects an upstream parameter (from the\nworkflow inputs, or the outputs of other workflows steps) with the input\nparameters of the underlying step.\n\n## Input object\n\nA WorkflowStepInput object must contain an `id` field in the form\n`#fieldname` or `#stepname.fieldname`. When the `id` field contains a\nperiod `.` the field name consists of the characters following the final\nperiod. This defines a field of the workflow step input object with the\nvalue of the `source` parameter(s).\n\n## Merging\n\nTo merge multiple inbound data links,\n[MultipleInputFeatureRequirement](#MultipleInputFeatureRequirement) must be specified\nin the workflow or workflow step requirements.\n\nIf the sink parameter is an array, or named in a [workflow\nscatter](#WorkflowStep) operation, there may be multiple inbound data links\nlisted in the `source` field. The values from the input links are merged\ndepending on the method specified in the `linkMerge` field. If not\nspecified, the default method is \"merge_nested\".\n\n* **merge_nested**\n\n The input must be an array consisting of exactly one entry for each\n input link. If \"merge_nested\" is specified with a single link, the value\n from the link must be wrapped in a single-item list.\n\n* **merge_flattened**\n\n 1. The source and sink parameters must be compatible types, or the source\n type must be compatible with single element from the \"items\" type of\n the destination array parameter.\n 2. Source parameters which are arrays are concatenated.\n Source parameters which are single element types are appended as\n single elements.\n",
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parents:
diff changeset
2062 "fields": [
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parents:
diff changeset
2063 {
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parents:
diff changeset
2064 "name": "https://w3id.org/cwl/cwl#WorkflowStepInput/id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2065 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2066 "jsonldPredicate": "@id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2067 "doc": "A unique identifier for this workflow input parameter."
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parents:
diff changeset
2068 },
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guerler
parents:
diff changeset
2069 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2070 "name": "https://w3id.org/cwl/cwl#WorkflowStepInput/default",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2071 "type": [
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guerler
parents:
diff changeset
2072 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2073 "Any"
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guerler
parents:
diff changeset
2074 ],
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parents:
diff changeset
2075 "doc": "The default value for this parameter if there is no `source`\nfield.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2076 "jsonldPredicate": "cwl:default"
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parents:
diff changeset
2077 },
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guerler
parents:
diff changeset
2078 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2079 "name": "https://w3id.org/cwl/cwl#WorkflowStepInput/valueFrom",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2080 "type": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2081 "null",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2082 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2083 "https://w3id.org/cwl/cwl#Expression"
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guerler
parents:
diff changeset
2084 ],
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guerler
parents:
diff changeset
2085 "jsonldPredicate": "cwl:valueFrom",
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2086 "doc": "To use valueFrom, [StepInputExpressionRequirement](#StepInputExpressionRequirement) must\nbe specified in the workflow or workflow step requirements.\n\nIf `valueFrom` is a constant string value, use this as the value for\nthis input parameter.\n\nIf `valueFrom` is a parameter reference or expression, it must be\nevaluated to yield the actual value to be assiged to the input field.\n\nThe `self` value of in the parameter reference or expression must be\nthe value of the parameter(s) specified in the `source` field, or\nnull if there is no `source` field.\n\nThe value of `inputs` in the parameter reference or expression must be\nthe input object to the workflow step after assigning the `source`\nvalues and then scattering. The order of evaluating `valueFrom` among\nstep input parameters is undefined and the result of evaluating\n`valueFrom` on a parameter must not be visible to evaluation of\n`valueFrom` on other parameters.\n"
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parents:
diff changeset
2087 }
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parents:
diff changeset
2088 ]
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parents:
diff changeset
2089 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2090 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2091 "type": "record",
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parents:
diff changeset
2092 "name": "https://w3id.org/cwl/cwl#WorkflowStepOutput",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2093 "docParent": "https://w3id.org/cwl/cwl#WorkflowStep",
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2094 "doc": "Associate an output parameter of the underlying process with a workflow\nparameter. The workflow parameter (given in the `id` field) be may be used\nas a `source` to connect with input parameters of other workflow steps, or\nwith an output parameter of the process.\n",
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parents:
diff changeset
2095 "fields": [
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diff changeset
2096 {
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parents:
diff changeset
2097 "name": "https://w3id.org/cwl/cwl#WorkflowStepOutput/id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2098 "type": "string",
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guerler
parents:
diff changeset
2099 "jsonldPredicate": "@id",
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diff changeset
2100 "doc": "A unique identifier for this workflow output parameter. This is the\nidentifier to use in the `source` field of `WorkflowStepInput` to\nconnect the output value to downstream parameters.\n"
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parents:
diff changeset
2101 }
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parents:
diff changeset
2102 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2103 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2104 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2105 "name": "https://w3id.org/cwl/cwl#ScatterMethod",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2106 "type": "enum",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2107 "docParent": "https://w3id.org/cwl/cwl#WorkflowStep",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2108 "doc": "The scatter method, as described in [workflow step scatter](#WorkflowStep).",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2109 "symbols": [
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parents:
diff changeset
2110 "https://w3id.org/cwl/cwl#ScatterMethod/dotproduct",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2111 "https://w3id.org/cwl/cwl#ScatterMethod/nested_crossproduct",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2112 "https://w3id.org/cwl/cwl#ScatterMethod/flat_crossproduct"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2113 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2114 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2115 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2116 "name": "https://w3id.org/cwl/cwl#WorkflowStep",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2117 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2118 "docParent": "https://w3id.org/cwl/cwl#Workflow",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2119 "doc": "A workflow step is an executable element of a workflow. It specifies the\nunderlying process implementation (such as `CommandLineTool` or another\n`Workflow`) in the `run` field and connects the input and output parameters\nof the underlying process to workflow parameters.\n\n# Scatter/gather\n\nTo use scatter/gather,\n[ScatterFeatureRequirement](#ScatterFeatureRequirement) must be specified\nin the workflow or workflow step requirements.\n\nA \"scatter\" operation specifies that the associated workflow step or\nsubworkflow should execute separately over a list of input elements. Each\njob making up a scatter operation is independent and may be executed\nconcurrently.\n\nThe `scatter` field specifies one or more input parameters which will be\nscattered. An input parameter may be listed more than once. The declared\ntype of each input parameter is implicitly wrapped in an array for each\ntime it appears in the `scatter` field. As a result, upstream parameters\nwhich are connected to scattered parameters may be arrays.\n\nAll output parameter types are also implicitly wrapped in arrays. Each job\nin the scatter results in an entry in the output array.\n\nIf `scatter` declares more than one input parameter, `scatterMethod`\ndescribes how to decompose the input into a discrete set of jobs.\n\n * **dotproduct** specifies that each of the input arrays are aligned and one\n element taken from each array to construct each job. It is an error\n if all input arrays are not the same length.\n\n * **nested_crossproduct** specifies the Cartesian product of the inputs,\n producing a job for every combination of the scattered inputs. The\n output must be nested arrays for each level of scattering, in the\n order that the input arrays are listed in the `scatter` field.\n\n * **flat_crossproduct** specifies the Cartesian product of the inputs,\n producing a job for every combination of the scattered inputs. The\n output arrays must be flattened to a single level, but otherwise listed in the\n order that the input arrays are listed in the `scatter` field.\n\n# Subworkflows\n\nTo specify a nested workflow as part of a workflow step,\n[SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) must be\nspecified in the workflow or workflow step requirements.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2120 "fields": [
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2121 {
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diff changeset
2122 "name": "https://w3id.org/cwl/cwl#WorkflowStep/id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2123 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2124 "jsonldPredicate": "@id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2125 "doc": "The unique identifier for this workflow step."
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parents:
diff changeset
2126 },
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parents:
diff changeset
2127 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2128 "name": "https://w3id.org/cwl/cwl#WorkflowStep/in",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2129 "type": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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2130 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2131 "items": "https://w3id.org/cwl/cwl#WorkflowStepInput"
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diff changeset
2132 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2133 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2134 "_id": "https://w3id.org/cwl/cwl#in",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2135 "mapSubject": "id",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2136 "mapPredicate": "source"
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parents:
diff changeset
2137 },
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2138 "doc": "Defines the input parameters of the workflow step. The process is ready to\nrun when all required input parameters are associated with concrete\nvalues. Input parameters include a schema for each parameter which is\nused to validate the input object. It may also be used build a user\ninterface for constructing the input object.\n"
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2139 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2140 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2141 "name": "https://w3id.org/cwl/cwl#WorkflowStep/out",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2142 "type": [
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parents:
diff changeset
2143 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2144 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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2145 "items": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2146 "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2147 "https://w3id.org/cwl/cwl#WorkflowStepOutput"
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2148 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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2149 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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2150 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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2151 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2152 "_id": "https://w3id.org/cwl/cwl#out",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2153 "_type": "@id",
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guerler
parents:
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2154 "identity": true
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2155 },
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2156 "doc": "Defines the parameters representing the output of the process. May be\nused to generate and/or validate the output object.\n"
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2157 },
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2158 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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2159 "name": "https://w3id.org/cwl/cwl#WorkflowStep/requirements",
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2160 "type": [
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diff changeset
2161 "null",
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diff changeset
2162 {
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diff changeset
2163 "type": "array",
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diff changeset
2164 "items": "https://w3id.org/cwl/cwl#ProcessRequirement"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2165 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2166 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2167 "jsonldPredicate": {
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parents:
diff changeset
2168 "_id": "https://w3id.org/cwl/cwl#requirements",
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parents:
diff changeset
2169 "mapSubject": "class"
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parents:
diff changeset
2170 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2171 "doc": "Declares requirements that apply to either the runtime environment or the\nworkflow engine that must be met in order to execute this workflow step. If\nan implementation cannot satisfy all requirements, or a requirement is\nlisted which is not recognized by the implementation, it is a fatal\nerror and the implementation must not attempt to run the process,\nunless overridden at user option.\n"
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diff changeset
2172 },
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parents:
diff changeset
2173 {
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parents:
diff changeset
2174 "name": "https://w3id.org/cwl/cwl#WorkflowStep/hints",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2175 "type": [
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parents:
diff changeset
2176 "null",
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parents:
diff changeset
2177 {
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parents:
diff changeset
2178 "type": "array",
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parents:
diff changeset
2179 "items": "Any"
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parents:
diff changeset
2180 }
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parents:
diff changeset
2181 ],
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diff changeset
2182 "jsonldPredicate": {
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diff changeset
2183 "_id": "https://w3id.org/cwl/cwl#hints",
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parents:
diff changeset
2184 "noLinkCheck": true,
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2185 "mapSubject": "class"
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parents:
diff changeset
2186 },
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parents:
diff changeset
2187 "doc": "Declares hints applying to either the runtime environment or the\nworkflow engine that may be helpful in executing this workflow step. It is\nnot an error if an implementation cannot satisfy all hints, however\nthe implementation may report a warning.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2188 },
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diff changeset
2189 {
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parents:
diff changeset
2190 "name": "https://w3id.org/cwl/cwl#WorkflowStep/label",
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parents:
diff changeset
2191 "type": [
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diff changeset
2192 "null",
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parents:
diff changeset
2193 "string"
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parents:
diff changeset
2194 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2195 "jsonldPredicate": "rdfs:label",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2196 "doc": "A short, human-readable label of this process object."
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parents:
diff changeset
2197 },
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parents:
diff changeset
2198 {
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parents:
diff changeset
2199 "name": "https://w3id.org/cwl/cwl#WorkflowStep/doc",
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parents:
diff changeset
2200 "type": [
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parents:
diff changeset
2201 "null",
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parents:
diff changeset
2202 "string"
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diff changeset
2203 ],
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diff changeset
2204 "jsonldPredicate": "rdfs:comment",
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parents:
diff changeset
2205 "doc": "A long, human-readable description of this process object."
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parents:
diff changeset
2206 },
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diff changeset
2207 {
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diff changeset
2208 "name": "https://w3id.org/cwl/cwl#WorkflowStep/run",
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parents:
diff changeset
2209 "type": [
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parents:
diff changeset
2210 "string",
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parents:
diff changeset
2211 "https://w3id.org/cwl/cwl#Process"
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parents:
diff changeset
2212 ],
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parents:
diff changeset
2213 "jsonldPredicate": {
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diff changeset
2214 "_id": "https://w3id.org/cwl/cwl#run",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2215 "_type": "@id"
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parents:
diff changeset
2216 },
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parents:
diff changeset
2217 "doc": "Specifies the process to run.\n"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2218 },
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diff changeset
2219 {
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parents:
diff changeset
2220 "name": "https://w3id.org/cwl/cwl#WorkflowStep/scatter",
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parents:
diff changeset
2221 "type": [
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diff changeset
2222 "null",
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diff changeset
2223 "string",
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parents:
diff changeset
2224 {
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parents:
diff changeset
2225 "type": "array",
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parents:
diff changeset
2226 "items": "string"
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parents:
diff changeset
2227 }
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parents:
diff changeset
2228 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2229 "jsonldPredicate": {
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parents:
diff changeset
2230 "_id": "https://w3id.org/cwl/cwl#scatter",
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guerler
parents:
diff changeset
2231 "_type": "@id",
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parents:
diff changeset
2232 "_container": "@list",
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parents:
diff changeset
2233 "refScope": 0
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parents:
diff changeset
2234 }
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parents:
diff changeset
2235 },
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parents:
diff changeset
2236 {
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parents:
diff changeset
2237 "name": "https://w3id.org/cwl/cwl#WorkflowStep/scatterMethod",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2238 "doc": "Required if `scatter` is an array of more than one element.\n",
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parents:
diff changeset
2239 "type": [
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diff changeset
2240 "null",
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parents:
diff changeset
2241 "https://w3id.org/cwl/cwl#ScatterMethod"
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diff changeset
2242 ],
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diff changeset
2243 "jsonldPredicate": {
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diff changeset
2244 "_id": "https://w3id.org/cwl/cwl#scatterMethod",
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parents:
diff changeset
2245 "_type": "@vocab"
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diff changeset
2246 }
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diff changeset
2247 }
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diff changeset
2248 ]
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diff changeset
2249 },
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parents:
diff changeset
2250 {
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parents:
diff changeset
2251 "name": "https://w3id.org/cwl/cwl#Workflow",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2252 "type": "record",
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parents:
diff changeset
2253 "extends": "https://w3id.org/cwl/cwl#Process",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2254 "documentRoot": true,
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parents:
diff changeset
2255 "specialize": [
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parents:
diff changeset
2256 {
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parents:
diff changeset
2257 "specializeFrom": "https://w3id.org/cwl/cwl#OutputParameter",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2258 "specializeTo": "https://w3id.org/cwl/cwl#WorkflowOutputParameter"
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parents:
diff changeset
2259 }
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parents:
diff changeset
2260 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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2261 "doc": "A workflow describes a set of **steps** and the **dependencies** between\nthose steps. When a step produces output that will be consumed by a\nsecond step, the first step is a dependency of the second step.\n\nWhen there is a dependency, the workflow engine must execute the preceeding\nstep and wait for it to successfully produce output before executing the\ndependent step. If two steps are defined in the workflow graph that\nare not directly or indirectly dependent, these steps are **independent**,\nand may execute in any order or execute concurrently. A workflow is\ncomplete when all steps have been executed.\n\nDependencies between parameters are expressed using the `source` field on\n[workflow step input parameters](#WorkflowStepInput) and [workflow output\nparameters](#WorkflowOutputParameter).\n\nThe `source` field expresses the dependency of one parameter on another\nsuch that when a value is associated with the parameter specified by\n`source`, that value is propagated to the destination parameter. When all\ndata links inbound to a given step are fufilled, the step is ready to\nexecute.\n\n## Workflow success and failure\n\nA completed step must result in one of `success`, `temporaryFailure` or\n`permanentFailure` states. An implementation may choose to retry a step\nexecution which resulted in `temporaryFailure`. An implementation may\nchoose to either continue running other steps of a workflow, or terminate\nimmediately upon `permanentFailure`.\n\n* If any step of a workflow execution results in `permanentFailure`, then\nthe workflow status is `permanentFailure`.\n\n* If one or more steps result in `temporaryFailure` and all other steps\ncomplete `success` or are not executed, then the workflow status is\n`temporaryFailure`.\n\n* If all workflow steps are executed and complete with `success`, then the\nworkflow status is `success`.\n\n# Extensions\n\n[ScatterFeatureRequirement](#ScatterFeatureRequirement) and\n[SubworkflowFeatureRequirement](#SubworkflowFeatureRequirement) are\navailable as standard [extensions](#Extensions_and_Metadata) to core\nworkflow semantics.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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2262 "fields": [
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2263 {
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parents:
diff changeset
2264 "name": "https://w3id.org/cwl/cwl#Workflow/class",
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parents:
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2265 "jsonldPredicate": {
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2266 "_id": "@type",
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parents:
diff changeset
2267 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2268 },
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parents:
diff changeset
2269 "type": "string"
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parents:
diff changeset
2270 },
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2271 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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2272 "name": "https://w3id.org/cwl/cwl#Workflow/steps",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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2273 "doc": "The individual steps that make up the workflow. Each step is executed when all of its\ninput data links are fufilled. An implementation may choose to execute\nthe steps in a different order than listed and/or execute steps\nconcurrently, provided that dependencies between steps are met.\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2274 "type": [
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parents:
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2275 {
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parents:
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2276 "type": "array",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
2277 "items": "https://w3id.org/cwl/cwl#WorkflowStep"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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2278 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
2279 ],
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2280 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2281 "mapSubject": "id"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2282 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2283 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2284 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2285 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2286 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2287 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2288 "name": "https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2289 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2290 "doc": "Indicates that the workflow platform must support nested workflows in\nthe `run` field of [WorkflowStep](#WorkflowStep).\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2291 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2292 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2293 "name": "https://w3id.org/cwl/cwl#SubworkflowFeatureRequirement/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2294 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2295 "doc": "Always 'SubworkflowFeatureRequirement'",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2296 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2297 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2298 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2299 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2300 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2301 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2302 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2303 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2304 "name": "https://w3id.org/cwl/cwl#ScatterFeatureRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2305 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2306 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2307 "doc": "Indicates that the workflow platform must support the `scatter` and\n`scatterMethod` fields of [WorkflowStep](#WorkflowStep).\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2308 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2309 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2310 "name": "https://w3id.org/cwl/cwl#ScatterFeatureRequirement/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2311 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2312 "doc": "Always 'ScatterFeatureRequirement'",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2313 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2314 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2315 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2316 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2317 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2318 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2319 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2320 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2321 "name": "https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2322 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2323 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2324 "doc": "Indicates that the workflow platform must support multiple inbound data links\nlisted in the `source` field of [WorkflowStepInput](#WorkflowStepInput).\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2325 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2326 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2327 "name": "https://w3id.org/cwl/cwl#MultipleInputFeatureRequirement/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2328 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2329 "doc": "Always 'MultipleInputFeatureRequirement'",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2330 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2331 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2332 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2333 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2334 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2335 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2336 },
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2337 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2338 "type": "record",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2339 "name": "https://w3id.org/cwl/cwl#StepInputExpressionRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2340 "extends": "https://w3id.org/cwl/cwl#ProcessRequirement",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2341 "doc": "Indicate that the workflow platform must support the `valueFrom` field\nof [WorkflowStepInput](#WorkflowStepInput).\n",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2342 "fields": [
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2343 {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2344 "name": "https://w3id.org/cwl/cwl#StepInputExpressionRequirement/class",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2345 "type": "string",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2346 "doc": "Always 'StepInputExpressionRequirement'",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2347 "jsonldPredicate": {
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2348 "_id": "@type",
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2349 "_type": "@vocab"
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2350 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2351 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2352 ]
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2353 }
56ad4e20f292 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
2354 ]