Mercurial > repos > tduigou > retrosynthesis_workflow
annotate retrosynthesis_workflow.ga @ 1:e5803ef59eb6 draft default tip
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author | tduigou |
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date | Thu, 10 Feb 2022 11:07:28 +0000 |
parents | 5aa8c015b750 |
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rev | line source |
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1 { |
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2 "a_galaxy_workflow": "true", |
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3 "annotation": "", |
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4 "format-version": "0.1", |
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5 "name": "Copy of RetroSynthesis_workflow", |
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19 "label": "sbml model", |
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20 "name": "Input dataset", |
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33 "tool_state": "{\"optional\": false}", |
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35 "type": "data_input", |
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37 "workflow_outputs": [ |
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40 "output_name": "output", |
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47 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6", |
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53 "name": "RRules Parser", |
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56 "name": "out_rules", |
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70 "post_job_actions": {}, |
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71 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6", |
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72 "tool_shed_repository": { |
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73 "changeset_revision": "ea590c609fec", |
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74 "name": "rrparser", |
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75 "owner": "tduigou", |
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76 "tool_shed": "toolshed.g2.bx.psu.edu" |
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78 "tool_state": "{\"compress\": \"false\", \"diameters\": [\"2\", \"4\", \"6\", \"8\", \"10\", \"12\", \"14\", \"16\"], \"rules\": {\"type\": \"retro\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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79 "tool_version": "2.4.6", |
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81 "uuid": "39cbe6d0-bd77-4b16-9154-39228a68c875", |
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82 "workflow_outputs": [ |
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83 { |
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84 "label": "RRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])", |
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85 "output_name": "out_rules", |
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87 } |
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88 ] |
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89 }, |
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90 "2": { |
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91 "annotation": "", |
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95 "input_connections": {}, |
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96 "inputs": [ |
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97 { |
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99 "name": "InChI of target to produce" |
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100 } |
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101 ], |
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102 "label": "InChI of target to produce", |
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103 "name": "Input parameter", |
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104 "outputs": [], |
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105 "position": { |
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106 "bottom": 544.1000061035156, |
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107 "height": 102.60000610351562, |
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108 "left": 601.5, |
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109 "right": 801.5, |
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110 "top": 441.5, |
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111 "width": 200, |
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112 "x": 601.5, |
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113 "y": 441.5 |
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114 }, |
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115 "tool_id": null, |
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116 "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", |
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117 "tool_version": null, |
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118 "type": "parameter_input", |
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119 "uuid": "9e4e8764-1433-4bd8-afc0-698fa591ce6d", |
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120 "workflow_outputs": [ |
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121 { |
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122 "label": null, |
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123 "output_name": "output", |
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124 "uuid": "12fa5134-5f52-4ebf-9616-1692e7c2f016" |
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125 } |
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126 ] |
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127 }, |
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128 "3": { |
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129 "annotation": "", |
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130 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1", |
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131 "errors": null, |
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132 "id": 3, |
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133 "input_connections": { |
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134 "input": { |
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135 "id": 0, |
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136 "output_name": "output" |
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137 } |
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138 }, |
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139 "inputs": [], |
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140 "label": null, |
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141 "name": "Sink from SBML", |
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142 "outputs": [ |
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143 { |
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144 "name": "sink", |
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145 "type": "csv" |
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146 } |
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147 ], |
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148 "position": { |
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149 "bottom": 655.1999969482422, |
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150 "height": 93.19999694824219, |
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151 "left": 603.5, |
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152 "right": 803.5, |
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153 "top": 562, |
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154 "width": 200, |
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155 "x": 603.5, |
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156 "y": 562 |
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157 }, |
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158 "post_job_actions": {}, |
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159 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1", |
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160 "tool_shed_repository": { |
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161 "changeset_revision": "47bb93e7832b", |
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162 "name": "rpextractsink", |
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163 "owner": "tduigou", |
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164 "tool_shed": "toolshed.g2.bx.psu.edu" |
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165 }, |
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166 "tool_state": "{\"adv\": {\"remove_dead_end\": \"true\"}, \"compartment_id\": \"c\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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167 "tool_version": "5.12.1", |
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168 "type": "tool", |
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169 "uuid": "65ddba64-bea5-466a-ab26-ba1859009cde", |
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170 "workflow_outputs": [ |
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171 { |
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172 "label": null, |
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173 "output_name": "sink", |
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174 "uuid": "c1f1add8-2a31-4849-9aea-312db78d9414" |
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175 } |
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176 ] |
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177 }, |
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178 "4": { |
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179 "annotation": "", |
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180 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0", |
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181 "errors": null, |
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182 "id": 4, |
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183 "input_connections": { |
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184 "rulesfile": { |
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185 "id": 1, |
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186 "output_name": "out_rules" |
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187 }, |
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188 "sinkfile": { |
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189 "id": 3, |
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190 "output_name": "sink" |
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191 }, |
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192 "source_inchi_type|source_inchi": { |
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193 "id": 2, |
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194 "output_name": "output" |
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195 } |
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196 }, |
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197 "inputs": [], |
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198 "label": null, |
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199 "name": "RetroPath2.0", |
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200 "outputs": [ |
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201 { |
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202 "name": "Reaction_Network", |
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203 "type": "csv" |
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204 } |
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205 ], |
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206 "position": { |
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207 "bottom": 569, |
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208 "height": 154, |
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209 "left": 900.5, |
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210 "right": 1100.5, |
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211 "top": 415, |
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212 "width": 200, |
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213 "x": 900.5, |
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214 "y": 415 |
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215 }, |
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216 "post_job_actions": {}, |
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217 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0", |
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218 "tool_shed_repository": { |
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219 "changeset_revision": "9c8ac9980bd6", |
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220 "name": "retropath2", |
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221 "owner": "tduigou", |
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222 "tool_shed": "toolshed.g2.bx.psu.edu" |
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223 }, |
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224 "tool_state": "{\"adv\": {\"version\": \"r20220104\", \"topx\": \"100\", \"dmin\": \"0\", \"dmax\": \"1000\", \"mwmax_source\": \"1000\", \"timeout\": \"60\"}, \"max_steps\": \"3\", \"rulesfile\": {\"__class__\": \"ConnectedValue\"}, \"sinkfile\": {\"__class__\": \"ConnectedValue\"}, \"source_inchi_type\": {\"inchi_type\": \"string\", \"__current_case__\": 0, \"source_inchi\": {\"__class__\": \"ConnectedValue\"}}, \"source_name\": \"target\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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225 "tool_version": "2.3.0", |
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226 "type": "tool", |
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227 "uuid": "7dd663f6-6633-41f0-b9cd-4bf575f72b90", |
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228 "workflow_outputs": [ |
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229 { |
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230 "label": "RetroPath2.0", |
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231 "output_name": "Reaction_Network", |
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232 "uuid": "48e8b7d2-f341-4cff-b410-30652e68dab4" |
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233 } |
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234 ] |
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235 }, |
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236 "5": { |
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237 "annotation": "", |
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238 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.4.3", |
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239 "errors": null, |
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240 "id": 5, |
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241 "input_connections": { |
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242 "rp2_pathways": { |
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243 "id": 4, |
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244 "output_name": "Reaction_Network" |
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245 } |
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246 }, |
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247 "inputs": [], |
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248 "label": null, |
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249 "name": "RP2paths", |
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250 "outputs": [ |
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251 { |
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252 "name": "master_pathways", |
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253 "type": "csv" |
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254 }, |
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255 { |
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256 "name": "compounds", |
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257 "type": "tsv" |
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258 } |
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259 ], |
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260 "position": { |
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261 "bottom": 526.3999938964844, |
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262 "height": 164.39999389648438, |
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263 "left": 1193.5, |
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264 "right": 1393.5, |
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265 "top": 362, |
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266 "width": 200, |
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267 "x": 1193.5, |
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268 "y": 362 |
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269 }, |
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270 "post_job_actions": {}, |
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271 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.4.3", |
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272 "tool_shed_repository": { |
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273 "changeset_revision": "2782bee7c5a6", |
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274 "name": "rp2paths", |
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275 "owner": "tduigou", |
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276 "tool_shed": "toolshed.g2.bx.psu.edu" |
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277 }, |
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278 "tool_state": "{\"adv\": {\"timeout\": \"1800\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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279 "tool_version": "1.4.3", |
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280 "type": "tool", |
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281 "uuid": "0d9f290f-a11c-4471-ba16-e0c561634be5", |
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282 "workflow_outputs": [ |
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283 { |
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284 "label": "RP2paths (Pathways)", |
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285 "output_name": "master_pathways", |
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286 "uuid": "2225e9b3-8984-4d53-9878-232b4f773869" |
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287 }, |
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288 { |
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289 "label": "RP2paths (Compounds)", |
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290 "output_name": "compounds", |
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291 "uuid": "651afa73-ad92-4296-b788-00bd78f6df32" |
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292 } |
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293 ] |
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294 }, |
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295 "6": { |
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296 "annotation": "", |
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297 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.1", |
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298 "errors": null, |
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299 "id": 6, |
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300 "input_connections": { |
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301 "rp2_pathways": { |
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302 "id": 4, |
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303 "output_name": "Reaction_Network" |
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304 }, |
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305 "rp2paths_compounds": { |
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306 "id": 5, |
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307 "output_name": "compounds" |
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308 }, |
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309 "rp2paths_pathways": { |
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310 "id": 5, |
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311 "output_name": "master_pathways" |
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312 }, |
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313 "sink": { |
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314 "id": 3, |
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315 "output_name": "sink" |
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316 } |
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317 }, |
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318 "inputs": [], |
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319 "label": null, |
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320 "name": "Complete Reactions", |
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321 "outputs": [ |
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322 { |
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323 "name": "pathways", |
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324 "type": "input" |
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325 } |
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326 ], |
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327 "position": { |
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328 "bottom": 807.6000061035156, |
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329 "height": 245.60000610351562, |
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330 "left": 1447.5, |
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331 "right": 1647.5, |
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332 "top": 562, |
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333 "width": 200, |
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334 "x": 1447.5, |
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335 "y": 562 |
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336 }, |
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337 "post_job_actions": {}, |
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338 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.1", |
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339 "tool_shed_repository": { |
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340 "changeset_revision": "b8242cf18cc0", |
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341 "name": "rpcompletion", |
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342 "owner": "tduigou", |
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343 "tool_shed": "toolshed.g2.bx.psu.edu" |
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344 }, |
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345 "tool_state": "{\"adv\": {\"max_subpaths_filter\": \"10\", \"upper_flux_bound\": \"999999\", \"lower_flux_bound\": \"0\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"rp2paths_compounds\": {\"__class__\": \"ConnectedValue\"}, \"rp2paths_pathways\": {\"__class__\": \"ConnectedValue\"}, \"sink\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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346 "tool_version": "5.12.1", |
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347 "type": "tool", |
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348 "uuid": "9acba2e0-e30c-47a7-8166-a6d694e425f8", |
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349 "workflow_outputs": [ |
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350 { |
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351 "label": "Complete Reactions", |
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352 "output_name": "pathways", |
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353 "uuid": "fd9a697a-6bf9-4b84-88bf-a1c749475e30" |
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354 } |
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355 ] |
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356 } |
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357 }, |
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358 "tags": [], |
1
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359 "uuid": "c563c2dc-6f52-45c3-978a-43777561081d", |
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360 "version": 9 |
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361 } |