Mercurial > repos > tduigou > retrosynthesis_workflow
comparison retrosynthesis_workflow.ga @ 0:5aa8c015b750 draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Thu, 02 Dec 2021 14:11:13 +0000 |
| parents | |
| children | e5803ef59eb6 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:5aa8c015b750 |
|---|---|
| 1 { | |
| 2 "a_galaxy_workflow": "true", | |
| 3 "annotation": "", | |
| 4 "format-version": "0.1", | |
| 5 "name": "RetroSynthesis_workflow", | |
| 6 "steps": { | |
| 7 "0": { | |
| 8 "annotation": "", | |
| 9 "content_id": null, | |
| 10 "errors": null, | |
| 11 "id": 0, | |
| 12 "input_connections": {}, | |
| 13 "inputs": [ | |
| 14 { | |
| 15 "description": "", | |
| 16 "name": "sbml model" | |
| 17 } | |
| 18 ], | |
| 19 "label": "sbml model", | |
| 20 "name": "Input dataset", | |
| 21 "outputs": [], | |
| 22 "position": { | |
| 23 "bottom": 335.3000030517578, | |
| 24 "height": 61.80000305175781, | |
| 25 "left": 278.5, | |
| 26 "right": 478.5, | |
| 27 "top": 273.5, | |
| 28 "width": 200, | |
| 29 "x": 278.5, | |
| 30 "y": 273.5 | |
| 31 }, | |
| 32 "tool_id": null, | |
| 33 "tool_state": "{\"optional\": false}", | |
| 34 "tool_version": null, | |
| 35 "type": "data_input", | |
| 36 "uuid": "8bb11d3f-e915-4ec1-b9c0-f564ab2e0eee", | |
| 37 "workflow_outputs": [ | |
| 38 { | |
| 39 "label": null, | |
| 40 "output_name": "output", | |
| 41 "uuid": "1fa2a565-bbb4-4817-a142-cb6614aeba85" | |
| 42 } | |
| 43 ] | |
| 44 }, | |
| 45 "1": { | |
| 46 "annotation": "", | |
| 47 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.5", | |
| 48 "errors": null, | |
| 49 "id": 1, | |
| 50 "input_connections": {}, | |
| 51 "inputs": [], | |
| 52 "label": null, | |
| 53 "name": "RRules Parser", | |
| 54 "outputs": [ | |
| 55 { | |
| 56 "name": "out_rules", | |
| 57 "type": "csv" | |
| 58 } | |
| 59 ], | |
| 60 "position": { | |
| 61 "bottom": 281.1000061035156, | |
| 62 "height": 102.60000610351562, | |
| 63 "left": 530.5, | |
| 64 "right": 730.5, | |
| 65 "top": 178.5, | |
| 66 "width": 200, | |
| 67 "x": 530.5, | |
| 68 "y": 178.5 | |
| 69 }, | |
| 70 "post_job_actions": {}, | |
| 71 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.5", | |
| 72 "tool_shed_repository": { | |
| 73 "changeset_revision": "024dcd6421db", | |
| 74 "name": "rrparser", | |
| 75 "owner": "tduigou", | |
| 76 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 77 }, | |
| 78 "tool_state": "{\"compress\": \"false\", \"diameters\": [\"2\", \"4\", \"6\", \"8\", \"10\", \"12\", \"14\", \"16\"], \"rules\": {\"type\": \"retro\", \"__current_case__\": 2}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
| 79 "tool_version": null, | |
| 80 "type": "tool", | |
| 81 "uuid": "e7a835df-5172-4fdf-a2a3-81c41a73bc00", | |
| 82 "workflow_outputs": [ | |
| 83 { | |
| 84 "label": "RRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])", | |
| 85 "output_name": "out_rules", | |
| 86 "uuid": "938b8abf-ce03-476e-b92a-39dd14cbd643" | |
| 87 } | |
| 88 ] | |
| 89 }, | |
| 90 "2": { | |
| 91 "annotation": "", | |
| 92 "content_id": null, | |
| 93 "errors": null, | |
| 94 "id": 2, | |
| 95 "input_connections": {}, | |
| 96 "inputs": [ | |
| 97 { | |
| 98 "description": "", | |
| 99 "name": "InChI of target to produce" | |
| 100 } | |
| 101 ], | |
| 102 "label": "InChI of target to produce", | |
| 103 "name": "Input parameter", | |
| 104 "outputs": [], | |
| 105 "position": { | |
| 106 "bottom": 440.6999969482422, | |
| 107 "height": 82.19999694824219, | |
| 108 "left": 518, | |
| 109 "right": 718, | |
| 110 "top": 358.5, | |
| 111 "width": 200, | |
| 112 "x": 518, | |
| 113 "y": 358.5 | |
| 114 }, | |
| 115 "tool_id": null, | |
| 116 "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", | |
| 117 "tool_version": null, | |
| 118 "type": "parameter_input", | |
| 119 "uuid": "95271805-5e3f-40d4-b262-f162cbb790eb", | |
| 120 "workflow_outputs": [ | |
| 121 { | |
| 122 "label": null, | |
| 123 "output_name": "output", | |
| 124 "uuid": "ce569b93-19c3-4ea7-bbeb-824d8416bd80" | |
| 125 } | |
| 126 ] | |
| 127 }, | |
| 128 "3": { | |
| 129 "annotation": "", | |
| 130 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpExtractSink/5.9.2", | |
| 131 "errors": null, | |
| 132 "id": 3, | |
| 133 "input_connections": { | |
| 134 "input": { | |
| 135 "id": 0, | |
| 136 "output_name": "output" | |
| 137 } | |
| 138 }, | |
| 139 "inputs": [], | |
| 140 "label": null, | |
| 141 "name": "Sink from SBML", | |
| 142 "outputs": [ | |
| 143 { | |
| 144 "name": "sink", | |
| 145 "type": "csv" | |
| 146 } | |
| 147 ], | |
| 148 "position": { | |
| 149 "bottom": 570.6999969482422, | |
| 150 "height": 93.19999694824219, | |
| 151 "left": 516.5, | |
| 152 "right": 716.5, | |
| 153 "top": 477.5, | |
| 154 "width": 200, | |
| 155 "x": 516.5, | |
| 156 "y": 477.5 | |
| 157 }, | |
| 158 "post_job_actions": {}, | |
| 159 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpExtractSink/5.9.2", | |
| 160 "tool_shed_repository": { | |
| 161 "changeset_revision": "f664f3c3aca8", | |
| 162 "name": "rpextractsink", | |
| 163 "owner": "tduigou", | |
| 164 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 165 }, | |
| 166 "tool_state": "{\"adv\": {\"compartment_id\": \"MNXC3\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"remove_dead_end\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
| 167 "tool_version": null, | |
| 168 "type": "tool", | |
| 169 "uuid": "b8c49635-e74d-41d6-b1ee-7881087039c9", | |
| 170 "workflow_outputs": [ | |
| 171 { | |
| 172 "label": null, | |
| 173 "output_name": "sink", | |
| 174 "uuid": "9398d924-57ce-4b29-924c-db2baec7f913" | |
| 175 } | |
| 176 ] | |
| 177 }, | |
| 178 "4": { | |
| 179 "annotation": "", | |
| 180 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.0.4", | |
| 181 "errors": null, | |
| 182 "id": 4, | |
| 183 "input_connections": { | |
| 184 "rulesfile": { | |
| 185 "id": 1, | |
| 186 "output_name": "out_rules" | |
| 187 }, | |
| 188 "sinkfile": { | |
| 189 "id": 3, | |
| 190 "output_name": "sink" | |
| 191 }, | |
| 192 "source_inchi": { | |
| 193 "id": 2, | |
| 194 "output_name": "output" | |
| 195 } | |
| 196 }, | |
| 197 "inputs": [ | |
| 198 { | |
| 199 "description": "runtime parameter for tool RetroPath2.0", | |
| 200 "name": "rulesfile" | |
| 201 }, | |
| 202 { | |
| 203 "description": "runtime parameter for tool RetroPath2.0", | |
| 204 "name": "sinkfile" | |
| 205 } | |
| 206 ], | |
| 207 "label": null, | |
| 208 "name": "RetroPath2.0", | |
| 209 "outputs": [ | |
| 210 { | |
| 211 "name": "Reaction_Network", | |
| 212 "type": "csv" | |
| 213 } | |
| 214 ], | |
| 215 "position": { | |
| 216 "bottom": 504.5, | |
| 217 "height": 154, | |
| 218 "left": 794.5, | |
| 219 "right": 994.5, | |
| 220 "top": 350.5, | |
| 221 "width": 200, | |
| 222 "x": 794.5, | |
| 223 "y": 350.5 | |
| 224 }, | |
| 225 "post_job_actions": {}, | |
| 226 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.0.4", | |
| 227 "tool_shed_repository": { | |
| 228 "changeset_revision": "6cdbb534cbca", | |
| 229 "name": "retropath2", | |
| 230 "owner": "tduigou", | |
| 231 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 232 }, | |
| 233 "tool_state": "{\"adv\": {\"max_steps\": \"3\", \"topx\": \"100\", \"dmin\": \"0\", \"dmax\": \"1000\", \"mwmax_source\": \"1000\", \"mwmax_cof\": \"1000\", \"timeout\": \"60\"}, \"rulesfile\": {\"__class__\": \"RuntimeValue\"}, \"sinkfile\": {\"__class__\": \"RuntimeValue\"}, \"source_inchi\": {\"__class__\": \"ConnectedValue\"}, \"source_name\": \"target\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
| 234 "tool_version": null, | |
| 235 "type": "tool", | |
| 236 "uuid": "e705e614-950a-436a-96a8-f8e9bcc4bb64", | |
| 237 "workflow_outputs": [ | |
| 238 { | |
| 239 "label": "RetroPath2.0", | |
| 240 "output_name": "Reaction_Network", | |
| 241 "uuid": "31cac3f6-2f12-48c4-b265-9d745d5ba36d" | |
| 242 } | |
| 243 ] | |
| 244 }, | |
| 245 "5": { | |
| 246 "annotation": "", | |
| 247 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.4.3", | |
| 248 "errors": null, | |
| 249 "id": 5, | |
| 250 "input_connections": { | |
| 251 "rp2_pathways": { | |
| 252 "id": 4, | |
| 253 "output_name": "Reaction_Network" | |
| 254 } | |
| 255 }, | |
| 256 "inputs": [], | |
| 257 "label": null, | |
| 258 "name": "RP2paths", | |
| 259 "outputs": [ | |
| 260 { | |
| 261 "name": "master_pathways", | |
| 262 "type": "csv" | |
| 263 }, | |
| 264 { | |
| 265 "name": "compounds", | |
| 266 "type": "tsv" | |
| 267 } | |
| 268 ], | |
| 269 "position": { | |
| 270 "bottom": 437.8999938964844, | |
| 271 "height": 164.39999389648438, | |
| 272 "left": 1050.5, | |
| 273 "right": 1250.5, | |
| 274 "top": 273.5, | |
| 275 "width": 200, | |
| 276 "x": 1050.5, | |
| 277 "y": 273.5 | |
| 278 }, | |
| 279 "post_job_actions": {}, | |
| 280 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.4.3", | |
| 281 "tool_shed_repository": { | |
| 282 "changeset_revision": "2782bee7c5a6", | |
| 283 "name": "rp2paths", | |
| 284 "owner": "tduigou", | |
| 285 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 286 }, | |
| 287 "tool_state": "{\"adv\": {\"timeout\": \"1800\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
| 288 "tool_version": null, | |
| 289 "type": "tool", | |
| 290 "uuid": "3ebbcfa4-dd81-4200-b023-dbb445131657", | |
| 291 "workflow_outputs": [ | |
| 292 { | |
| 293 "label": "RP2paths (Pathways)", | |
| 294 "output_name": "master_pathways", | |
| 295 "uuid": "9b5454c6-35e7-4632-96d3-2d75ba8b1afe" | |
| 296 }, | |
| 297 { | |
| 298 "label": "RP2paths (Compounds)", | |
| 299 "output_name": "compounds", | |
| 300 "uuid": "fc35e5fb-8556-4c7f-b11f-45b93467f7f6" | |
| 301 } | |
| 302 ] | |
| 303 }, | |
| 304 "6": { | |
| 305 "annotation": "", | |
| 306 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpCompletion/5.9.2", | |
| 307 "errors": null, | |
| 308 "id": 6, | |
| 309 "input_connections": { | |
| 310 "rp2_pathways": { | |
| 311 "id": 4, | |
| 312 "output_name": "Reaction_Network" | |
| 313 }, | |
| 314 "rp2paths_compounds": { | |
| 315 "id": 5, | |
| 316 "output_name": "compounds" | |
| 317 }, | |
| 318 "rp2paths_pathways": { | |
| 319 "id": 5, | |
| 320 "output_name": "master_pathways" | |
| 321 }, | |
| 322 "sink": { | |
| 323 "id": 3, | |
| 324 "output_name": "sink" | |
| 325 } | |
| 326 }, | |
| 327 "inputs": [], | |
| 328 "label": null, | |
| 329 "name": "Complete Reactions", | |
| 330 "outputs": [ | |
| 331 { | |
| 332 "name": "pathways", | |
| 333 "type": "input" | |
| 334 } | |
| 335 ], | |
| 336 "position": { | |
| 337 "bottom": 646.1000061035156, | |
| 338 "height": 245.60000610351562, | |
| 339 "left": 1323.5, | |
| 340 "right": 1523.5, | |
| 341 "top": 400.5, | |
| 342 "width": 200, | |
| 343 "x": 1323.5, | |
| 344 "y": 400.5 | |
| 345 }, | |
| 346 "post_job_actions": {}, | |
| 347 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpCompletion/5.9.2", | |
| 348 "tool_shed_repository": { | |
| 349 "changeset_revision": "98d925a75257", | |
| 350 "name": "rpcompletion", | |
| 351 "owner": "tduigou", | |
| 352 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 353 }, | |
| 354 "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}", | |
| 355 "tool_version": null, | |
| 356 "type": "tool", | |
| 357 "uuid": "bfc32617-1870-4240-8cf6-ea93da840007", | |
| 358 "workflow_outputs": [ | |
| 359 { | |
| 360 "label": "Complete Reactions", | |
| 361 "output_name": "pathways", | |
| 362 "uuid": "b77df22c-2b09-4787-8762-18f3fd748aea" | |
| 363 } | |
| 364 ] | |
| 365 } | |
| 366 }, | |
| 367 "tags": [], | |
| 368 "uuid": "a8283850-4dcb-4bd9-a11e-507bf58e8b4b", | |
| 369 "version": 8 | |
| 370 } |
