Mercurial > repos > tduigou > genetic_design_workflow
comparison Genetic_Design_Workflow.ga @ 0:0cf30759d085 draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Tue, 21 Dec 2021 13:15:48 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:0cf30759d085 |
|---|---|
| 1 { | |
| 2 "a_galaxy_workflow": "true", | |
| 3 "annotation": "", | |
| 4 "format-version": "0.1", | |
| 5 "name": "Genetic_Design_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 Pathway" | |
| 17 } | |
| 18 ], | |
| 19 "label": "SBML Pathway", | |
| 20 "name": "Input dataset", | |
| 21 "outputs": [], | |
| 22 "position": { | |
| 23 "bottom": 393.8000030517578, | |
| 24 "height": 61.80000305175781, | |
| 25 "left": -68, | |
| 26 "right": 132, | |
| 27 "top": 332, | |
| 28 "width": 200, | |
| 29 "x": -68, | |
| 30 "y": 332 | |
| 31 }, | |
| 32 "tool_id": null, | |
| 33 "tool_state": "{\"optional\": false}", | |
| 34 "tool_version": null, | |
| 35 "type": "data_input", | |
| 36 "uuid": "e0c30803-3cb9-41f0-9474-f5f9d1d1e5ad", | |
| 37 "workflow_outputs": [ | |
| 38 { | |
| 39 "label": null, | |
| 40 "output_name": "output", | |
| 41 "uuid": "c6ae200e-5f3c-43d0-a3c0-2a13a1649b32" | |
| 42 } | |
| 43 ] | |
| 44 }, | |
| 45 "1": { | |
| 46 "annotation": "", | |
| 47 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.1.0", | |
| 48 "errors": null, | |
| 49 "id": 1, | |
| 50 "input_connections": { | |
| 51 "pathway": { | |
| 52 "id": 0, | |
| 53 "output_name": "output" | |
| 54 } | |
| 55 }, | |
| 56 "inputs": [], | |
| 57 "label": null, | |
| 58 "name": "Selenzyme", | |
| 59 "outputs": [ | |
| 60 { | |
| 61 "name": "uniprot_ids", | |
| 62 "type": "xml" | |
| 63 }, | |
| 64 { | |
| 65 "name": "uniprot_ids_csv", | |
| 66 "type": "csv" | |
| 67 } | |
| 68 ], | |
| 69 "position": { | |
| 70 "bottom": 611.6000061035156, | |
| 71 "height": 123.60000610351562, | |
| 72 "left": 152.25, | |
| 73 "right": 352.25, | |
| 74 "top": 488, | |
| 75 "width": 200, | |
| 76 "x": 152.25, | |
| 77 "y": 488 | |
| 78 }, | |
| 79 "post_job_actions": {}, | |
| 80 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/selenzy/selenzy-wrapper/0.1.0", | |
| 81 "tool_shed_repository": { | |
| 82 "changeset_revision": "481f7c35323d", | |
| 83 "name": "selenzy", | |
| 84 "owner": "tduigou", | |
| 85 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 86 }, | |
| 87 "tool_state": "{\"adv\": {\"nb_ids\": \"-1\", \"nb_targets\": \"500\", \"direction\": \"0.0\", \"NoMSA\": \"true\", \"taxonIDs\": \"83333\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
| 88 "tool_version": "0.1.0", | |
| 89 "type": "tool", | |
| 90 "uuid": "14aad2ec-173e-4d6b-9a4e-6a377c01eb47", | |
| 91 "workflow_outputs": [ | |
| 92 { | |
| 93 "label": "Uniprot IDs", | |
| 94 "output_name": "uniprot_ids", | |
| 95 "uuid": "dd39886f-4a0a-4b19-ab49-ce78fd6c3e78" | |
| 96 }, | |
| 97 { | |
| 98 "label": "Uniprot IDs", | |
| 99 "output_name": "uniprot_ids_csv", | |
| 100 "uuid": "eb5292b9-77e2-48f6-9f7a-c9f99c94c5f0" | |
| 101 } | |
| 102 ] | |
| 103 }, | |
| 104 "2": { | |
| 105 "annotation": "", | |
| 106 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/sbml2sbol/sbml2sbol/0.1.12", | |
| 107 "errors": null, | |
| 108 "id": 2, | |
| 109 "input_connections": { | |
| 110 "sbml_single_input": { | |
| 111 "id": 1, | |
| 112 "output_name": "uniprot_ids" | |
| 113 } | |
| 114 }, | |
| 115 "inputs": [], | |
| 116 "label": null, | |
| 117 "name": "SbmlToSbol", | |
| 118 "outputs": [ | |
| 119 { | |
| 120 "name": "sbol_outfile", | |
| 121 "type": "xml" | |
| 122 } | |
| 123 ], | |
| 124 "position": { | |
| 125 "bottom": 536.6000061035156, | |
| 126 "height": 113.60000610351562, | |
| 127 "left": 433.5, | |
| 128 "right": 633.5, | |
| 129 "top": 423, | |
| 130 "width": 200, | |
| 131 "x": 433.5, | |
| 132 "y": 423 | |
| 133 }, | |
| 134 "post_job_actions": {}, | |
| 135 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/sbml2sbol/sbml2sbol/0.1.12", | |
| 136 "tool_shed_repository": { | |
| 137 "changeset_revision": "f0a06f526c7f", | |
| 138 "name": "sbml2sbol", | |
| 139 "owner": "tduigou", | |
| 140 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 141 }, | |
| 142 "tool_state": "{\"adv\": {\"rbs\": \"true\", \"max_prot_per_react\": \"3\", \"tirs\": \"\", \"pathway_id\": \"rp_pathway\", \"uniprotID_key\": \"selenzy\"}, \"sbml_single_input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
| 143 "tool_version": "0.1.12", | |
| 144 "type": "tool", | |
| 145 "uuid": "585d5a08-f0c2-4a87-b3ca-ce9e809ad7bb", | |
| 146 "workflow_outputs": [ | |
| 147 { | |
| 148 "label": "SbmlToSbol: sbol outfile", | |
| 149 "output_name": "sbol_outfile", | |
| 150 "uuid": "0ab3c9d1-82fb-4295-89ad-02e8c5dc0e64" | |
| 151 } | |
| 152 ] | |
| 153 }, | |
| 154 "3": { | |
| 155 "annotation": "", | |
| 156 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/partsgenie/PartsGenie/1.0.1", | |
| 157 "errors": null, | |
| 158 "id": 3, | |
| 159 "input_connections": { | |
| 160 "enzymes_file": { | |
| 161 "id": 2, | |
| 162 "output_name": "sbol_outfile" | |
| 163 } | |
| 164 }, | |
| 165 "inputs": [ | |
| 166 { | |
| 167 "description": "runtime parameter for tool PartsGenie", | |
| 168 "name": "enzymes_file" | |
| 169 } | |
| 170 ], | |
| 171 "label": null, | |
| 172 "name": "PartsGenie", | |
| 173 "outputs": [ | |
| 174 { | |
| 175 "name": "parts", | |
| 176 "type": "xml" | |
| 177 } | |
| 178 ], | |
| 179 "position": { | |
| 180 "bottom": 484.1999969482422, | |
| 181 "height": 93.19999694824219, | |
| 182 "left": 692, | |
| 183 "right": 892, | |
| 184 "top": 391, | |
| 185 "width": 200, | |
| 186 "x": 692, | |
| 187 "y": 391 | |
| 188 }, | |
| 189 "post_job_actions": {}, | |
| 190 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/partsgenie/PartsGenie/1.0.1", | |
| 191 "tool_shed_repository": { | |
| 192 "changeset_revision": "295a21fc55d0", | |
| 193 "name": "partsgenie", | |
| 194 "owner": "tduigou", | |
| 195 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 196 }, | |
| 197 "tool_state": "{\"adv\": {\"url\": \"https://partsgenie.micalis.inrae.fr\"}, \"enzymes_file\": {\"__class__\": \"RuntimeValue\"}, \"taxonomy_id\": \"83333\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
| 198 "tool_version": "1.0.1", | |
| 199 "type": "tool", | |
| 200 "uuid": "a6dd01a2-6def-4872-89d0-c762b7e6e1ca", | |
| 201 "workflow_outputs": [ | |
| 202 { | |
| 203 "label": "Parts", | |
| 204 "output_name": "parts", | |
| 205 "uuid": "73bc4334-9596-47f8-9fc3-a6e4767e97bb" | |
| 206 } | |
| 207 ] | |
| 208 }, | |
| 209 "4": { | |
| 210 "annotation": "", | |
| 211 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/optdoe/OptDoE/2.0.1", | |
| 212 "errors": null, | |
| 213 "id": 4, | |
| 214 "input_connections": { | |
| 215 "adv|genes_sbol_file": { | |
| 216 "id": 3, | |
| 217 "output_name": "parts" | |
| 218 }, | |
| 219 "genes_file": { | |
| 220 "id": 1, | |
| 221 "output_name": "uniprot_ids_csv" | |
| 222 } | |
| 223 }, | |
| 224 "inputs": [ | |
| 225 { | |
| 226 "description": "runtime parameter for tool Design of Experiment", | |
| 227 "name": "adv" | |
| 228 } | |
| 229 ], | |
| 230 "label": null, | |
| 231 "name": "Design of Experiment", | |
| 232 "outputs": [ | |
| 233 { | |
| 234 "name": "constructs", | |
| 235 "type": "xml" | |
| 236 } | |
| 237 ], | |
| 238 "position": { | |
| 239 "bottom": 693.8999938964844, | |
| 240 "height": 174.39999389648438, | |
| 241 "left": 939.5, | |
| 242 "right": 1139.5, | |
| 243 "top": 519.5, | |
| 244 "width": 200, | |
| 245 "x": 939.5, | |
| 246 "y": 519.5 | |
| 247 }, | |
| 248 "post_job_actions": {}, | |
| 249 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/optdoe/OptDoE/2.0.1", | |
| 250 "tool_shed_repository": { | |
| 251 "changeset_revision": "7f13e58f1532", | |
| 252 "name": "optdoe", | |
| 253 "owner": "tduigou", | |
| 254 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 255 }, | |
| 256 "tool_state": "{\"adv\": {\"genes_sbol_file\": {\"__class__\": \"ConnectedValue\"}, \"ref_parts_file\": {\"__class__\": \"RuntimeValue\"}, \"libsize\": \"32\", \"get_sequences\": \"true\", \"backtranslate\": \"true\", \"codon_table\": \"Eecoli.cut\"}, \"genes_file\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
| 257 "tool_version": "2.0.1", | |
| 258 "type": "tool", | |
| 259 "uuid": "b9872d59-e433-4e31-8dc2-c00fd03c7a83", | |
| 260 "workflow_outputs": [ | |
| 261 { | |
| 262 "label": "Constructs", | |
| 263 "output_name": "constructs", | |
| 264 "uuid": "d677903a-dd9b-4deb-a09a-7c81b7803dac" | |
| 265 } | |
| 266 ] | |
| 267 }, | |
| 268 "5": { | |
| 269 "annotation": "", | |
| 270 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnaweaver/DNAWeaver/1.0.1", | |
| 271 "errors": null, | |
| 272 "id": 5, | |
| 273 "input_connections": { | |
| 274 "input": { | |
| 275 "id": 4, | |
| 276 "output_name": "constructs" | |
| 277 } | |
| 278 }, | |
| 279 "inputs": [], | |
| 280 "label": null, | |
| 281 "name": "DNA Weaver", | |
| 282 "outputs": [ | |
| 283 { | |
| 284 "name": "output", | |
| 285 "type": "xlsx" | |
| 286 } | |
| 287 ], | |
| 288 "position": { | |
| 289 "bottom": 631.9499969482422, | |
| 290 "height": 93.19999694824219, | |
| 291 "left": 1222.25, | |
| 292 "right": 1422.25, | |
| 293 "top": 538.75, | |
| 294 "width": 200, | |
| 295 "x": 1222.25, | |
| 296 "y": 538.75 | |
| 297 }, | |
| 298 "post_job_actions": {}, | |
| 299 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/dnaweaver/DNAWeaver/1.0.1", | |
| 300 "tool_shed_repository": { | |
| 301 "changeset_revision": "90025c4cd50e", | |
| 302 "name": "dnaweaver", | |
| 303 "owner": "tduigou", | |
| 304 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 305 }, | |
| 306 "tool_state": "{\"adv\": {\"max_constructs\": \"-1\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"method\": \"golden_gate\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
| 307 "tool_version": "1.0.1", | |
| 308 "type": "tool", | |
| 309 "uuid": "c045b22d-b1df-4620-80fe-d22c335b7e78", | |
| 310 "workflow_outputs": [ | |
| 311 { | |
| 312 "label": "Assembly Plan", | |
| 313 "output_name": "output", | |
| 314 "uuid": "42769098-1a73-4c65-ac2d-e0a54d9f2ea2" | |
| 315 } | |
| 316 ] | |
| 317 }, | |
| 318 "6": { | |
| 319 "annotation": "", | |
| 320 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/lcrgenie/LCRGenie/1.0.1", | |
| 321 "errors": null, | |
| 322 "id": 6, | |
| 323 "input_connections": { | |
| 324 "LCR_input": { | |
| 325 "id": 4, | |
| 326 "output_name": "constructs" | |
| 327 } | |
| 328 }, | |
| 329 "inputs": [], | |
| 330 "label": null, | |
| 331 "name": "LCR Genie", | |
| 332 "outputs": [ | |
| 333 { | |
| 334 "name": "LCR_output", | |
| 335 "type": "xlsx" | |
| 336 } | |
| 337 ], | |
| 338 "position": { | |
| 339 "bottom": 802.6000061035156, | |
| 340 "height": 113.60000610351562, | |
| 341 "left": 1224.5, | |
| 342 "right": 1424.5, | |
| 343 "top": 689, | |
| 344 "width": 200, | |
| 345 "x": 1224.5, | |
| 346 "y": 689 | |
| 347 }, | |
| 348 "post_job_actions": {}, | |
| 349 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/lcrgenie/LCRGenie/1.0.1", | |
| 350 "tool_shed_repository": { | |
| 351 "changeset_revision": "71568c0c83f4", | |
| 352 "name": "lcrgenie", | |
| 353 "owner": "tduigou", | |
| 354 "tool_shed": "toolshed.g2.bx.psu.edu" | |
| 355 }, | |
| 356 "tool_state": "{\"LCR_input\": {\"__class__\": \"ConnectedValue\"}, \"adv\": {\"melting_temp\": \"60.0\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", | |
| 357 "tool_version": "1.0.1", | |
| 358 "type": "tool", | |
| 359 "uuid": "14974d0a-257e-4cba-8bea-37367638750e", | |
| 360 "workflow_outputs": [ | |
| 361 { | |
| 362 "label": "LCR Genie: Assembly Plan", | |
| 363 "output_name": "LCR_output", | |
| 364 "uuid": "ba05b6d0-a81f-496f-925b-bc2a9e014eac" | |
| 365 } | |
| 366 ] | |
| 367 } | |
| 368 }, | |
| 369 "tags": [], | |
| 370 "uuid": "156b3f3d-9925-48fc-bb22-cfff50584c3e", | |
| 371 "version": 6 | |
| 372 } |
