Mercurial > repos > tduigou > retrosynthesis_workflow

comparison retrosynthesis_workflow.ga @ 1:e5803ef59eb6 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Thu, 10 Feb 2022 11:07:28 +0000
parents 5aa8c015b750
children
comparison
equal deleted inserted replaced
0:5aa8c015b750 1:e5803ef59eb6
1 { 1 {
2 "a_galaxy_workflow": "true", 2 "a_galaxy_workflow": "true",
3 "annotation": "", 3 "annotation": "",
4 "format-version": "0.1", 4 "format-version": "0.1",
5 "name": "RetroSynthesis_workflow", 5 "name": "Copy of RetroSynthesis_workflow",
6 "steps": { 6 "steps": {
7 "0": { 7 "0": {
8 "annotation": "", 8 "annotation": "",
9 "content_id": null, 9 "content_id": null,
10 "errors": null, 10 "errors": null,
18 ], 18 ],
19 "label": "sbml model", 19 "label": "sbml model",
20 "name": "Input dataset", 20 "name": "Input dataset",
21 "outputs": [], 21 "outputs": [],
22 "position": { 22 "position": {
23 "bottom": 335.3000030517578, 23 "bottom": 495.3000030517578,
24 "height": 61.80000305175781, 24 "height": 61.80000305175781,
25 "left": 278.5, 25 "left": 339,
26 "right": 478.5, 26 "right": 539,
27 "top": 273.5, 27 "top": 433.5,
28 "width": 200, 28 "width": 200,
29 "x": 278.5, 29 "x": 339,
30 "y": 273.5 30 "y": 433.5
31 }, 31 },
32 "tool_id": null, 32 "tool_id": null,
33 "tool_state": "{\"optional\": false}", 33 "tool_state": "{\"optional\": false}",
34 "tool_version": null, 34 "tool_version": null,
35 "type": "data_input", 35 "type": "data_input",
36 "uuid": "8bb11d3f-e915-4ec1-b9c0-f564ab2e0eee", 36 "uuid": "8bb11d3f-e915-4ec1-b9c0-f564ab2e0eee",
37 "workflow_outputs": [ 37 "workflow_outputs": [
38 { 38 {
39 "label": null, 39 "label": null,
40 "output_name": "output", 40 "output_name": "output",
41 "uuid": "1fa2a565-bbb4-4817-a142-cb6614aeba85" 41 "uuid": "0d8c01b5-de3b-4f6c-816e-f3d50dc39f81"
42 } 42 }
43 ] 43 ]
44 }, 44 },
45 "1": { 45 "1": {
46 "annotation": "", 46 "annotation": "",
47 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.5", 47 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6",
48 "errors": null, 48 "errors": null,
49 "id": 1, 49 "id": 1,
50 "input_connections": {}, 50 "input_connections": {},
51 "inputs": [], 51 "inputs": [],
52 "label": null, 52 "label": null,
56 "name": "out_rules", 56 "name": "out_rules",
57 "type": "csv" 57 "type": "csv"
58 } 58 }
59 ], 59 ],
60 "position": { 60 "position": {
61 "bottom": 281.1000061035156, 61 "bottom": 412.6000061035156,
62 "height": 102.60000610351562, 62 "height": 102.60000610351562,
63 "left": 530.5, 63 "left": 588.5,
64 "right": 730.5, 64 "right": 788.5,
65 "top": 178.5, 65 "top": 310,
66 "width": 200, 66 "width": 200,
67 "x": 530.5, 67 "x": 588.5,
68 "y": 178.5 68 "y": 310
69 }, 69 },
70 "post_job_actions": {}, 70 "post_job_actions": {},
71 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.5", 71 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rrparser/rrparser/2.4.6",
72 "tool_shed_repository": { 72 "tool_shed_repository": {
73 "changeset_revision": "024dcd6421db", 73 "changeset_revision": "ea590c609fec",
74 "name": "rrparser", 74 "name": "rrparser",
75 "owner": "tduigou", 75 "owner": "tduigou",
76 "tool_shed": "toolshed.g2.bx.psu.edu" 76 "tool_shed": "toolshed.g2.bx.psu.edu"
77 }, 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}", 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}",
79 "tool_version": null, 79 "tool_version": "2.4.6",
80 "type": "tool", 80 "type": "tool",
81 "uuid": "e7a835df-5172-4fdf-a2a3-81c41a73bc00", 81 "uuid": "39cbe6d0-bd77-4b16-9154-39228a68c875",
82 "workflow_outputs": [ 82 "workflow_outputs": [
83 { 83 {
84 "label": "RRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])", 84 "label": "RRules Parser(retro, d=['2', '4', '6', '8', '10', '12', '14', '16'])",
85 "output_name": "out_rules", 85 "output_name": "out_rules",
86 "uuid": "938b8abf-ce03-476e-b92a-39dd14cbd643" 86 "uuid": "2fb329ce-971d-4158-9ec7-9b82c1b39be2"
87 } 87 }
88 ] 88 ]
89 }, 89 },
90 "2": { 90 "2": {
91 "annotation": "", 91 "annotation": "",
101 ], 101 ],
102 "label": "InChI of target to produce", 102 "label": "InChI of target to produce",
103 "name": "Input parameter", 103 "name": "Input parameter",
104 "outputs": [], 104 "outputs": [],
105 "position": { 105 "position": {
106 "bottom": 440.6999969482422, 106 "bottom": 544.1000061035156,
107 "height": 82.19999694824219, 107 "height": 102.60000610351562,
108 "left": 518, 108 "left": 601.5,
109 "right": 718, 109 "right": 801.5,
110 "top": 358.5, 110 "top": 441.5,
111 "width": 200, 111 "width": 200,
112 "x": 518, 112 "x": 601.5,
113 "y": 358.5 113 "y": 441.5
114 }, 114 },
115 "tool_id": null, 115 "tool_id": null,
116 "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", 116 "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
117 "tool_version": null, 117 "tool_version": null,
118 "type": "parameter_input", 118 "type": "parameter_input",
119 "uuid": "95271805-5e3f-40d4-b262-f162cbb790eb", 119 "uuid": "9e4e8764-1433-4bd8-afc0-698fa591ce6d",
120 "workflow_outputs": [ 120 "workflow_outputs": [
121 { 121 {
122 "label": null, 122 "label": null,
123 "output_name": "output", 123 "output_name": "output",
124 "uuid": "ce569b93-19c3-4ea7-bbeb-824d8416bd80" 124 "uuid": "12fa5134-5f52-4ebf-9616-1692e7c2f016"
125 } 125 }
126 ] 126 ]
127 }, 127 },
128 "3": { 128 "3": {
129 "annotation": "", 129 "annotation": "",
130 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpExtractSink/5.9.2", 130 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1",
131 "errors": null, 131 "errors": null,
132 "id": 3, 132 "id": 3,
133 "input_connections": { 133 "input_connections": {
134 "input": { 134 "input": {
135 "id": 0, 135 "id": 0,
144 "name": "sink", 144 "name": "sink",
145 "type": "csv" 145 "type": "csv"
146 } 146 }
147 ], 147 ],
148 "position": { 148 "position": {
149 "bottom": 570.6999969482422, 149 "bottom": 655.1999969482422,
150 "height": 93.19999694824219, 150 "height": 93.19999694824219,
151 "left": 516.5, 151 "left": 603.5,
152 "right": 716.5, 152 "right": 803.5,
153 "top": 477.5, 153 "top": 562,
154 "width": 200, 154 "width": 200,
155 "x": 516.5, 155 "x": 603.5,
156 "y": 477.5 156 "y": 562
157 }, 157 },
158 "post_job_actions": {}, 158 "post_job_actions": {},
159 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpExtractSink/5.9.2", 159 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpextractsink/rpextractsink/5.12.1",
160 "tool_shed_repository": { 160 "tool_shed_repository": {
161 "changeset_revision": "f664f3c3aca8", 161 "changeset_revision": "47bb93e7832b",
162 "name": "rpextractsink", 162 "name": "rpextractsink",
163 "owner": "tduigou", 163 "owner": "tduigou",
164 "tool_shed": "toolshed.g2.bx.psu.edu" 164 "tool_shed": "toolshed.g2.bx.psu.edu"
165 }, 165 },
166 "tool_state": "{\"adv\": {\"compartment_id\": \"MNXC3\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"remove_dead_end\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", 166 "tool_state": "{\"adv\": {\"remove_dead_end\": \"true\"}, \"compartment_id\": \"c\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
167 "tool_version": null, 167 "tool_version": "5.12.1",
168 "type": "tool", 168 "type": "tool",
169 "uuid": "b8c49635-e74d-41d6-b1ee-7881087039c9", 169 "uuid": "65ddba64-bea5-466a-ab26-ba1859009cde",
170 "workflow_outputs": [ 170 "workflow_outputs": [
171 { 171 {
172 "label": null, 172 "label": null,
173 "output_name": "sink", 173 "output_name": "sink",
174 "uuid": "9398d924-57ce-4b29-924c-db2baec7f913" 174 "uuid": "c1f1add8-2a31-4849-9aea-312db78d9414"
175 } 175 }
176 ] 176 ]
177 }, 177 },
178 "4": { 178 "4": {
179 "annotation": "", 179 "annotation": "",
180 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.0.4", 180 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0",
181 "errors": null, 181 "errors": null,
182 "id": 4, 182 "id": 4,
183 "input_connections": { 183 "input_connections": {
184 "rulesfile": { 184 "rulesfile": {
185 "id": 1, 185 "id": 1,
187 }, 187 },
188 "sinkfile": { 188 "sinkfile": {
189 "id": 3, 189 "id": 3,
190 "output_name": "sink" 190 "output_name": "sink"
191 }, 191 },
192 "source_inchi": { 192 "source_inchi_type|source_inchi": {
193 "id": 2, 193 "id": 2,
194 "output_name": "output" 194 "output_name": "output"
195 } 195 }
196 }, 196 },
197 "inputs": [ 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, 198 "label": null,
208 "name": "RetroPath2.0", 199 "name": "RetroPath2.0",
209 "outputs": [ 200 "outputs": [
210 { 201 {
211 "name": "Reaction_Network", 202 "name": "Reaction_Network",
212 "type": "csv" 203 "type": "csv"
213 } 204 }
214 ], 205 ],
215 "position": { 206 "position": {
216 "bottom": 504.5, 207 "bottom": 569,
217 "height": 154, 208 "height": 154,
218 "left": 794.5, 209 "left": 900.5,
219 "right": 994.5, 210 "right": 1100.5,
220 "top": 350.5, 211 "top": 415,
221 "width": 200, 212 "width": 200,
222 "x": 794.5, 213 "x": 900.5,
223 "y": 350.5 214 "y": 415
224 }, 215 },
225 "post_job_actions": {}, 216 "post_job_actions": {},
226 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.0.4", 217 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/2.3.0",
227 "tool_shed_repository": { 218 "tool_shed_repository": {
228 "changeset_revision": "6cdbb534cbca", 219 "changeset_revision": "9c8ac9980bd6",
229 "name": "retropath2", 220 "name": "retropath2",
230 "owner": "tduigou", 221 "owner": "tduigou",
231 "tool_shed": "toolshed.g2.bx.psu.edu" 222 "tool_shed": "toolshed.g2.bx.psu.edu"
232 }, 223 },
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}", 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}",
234 "tool_version": null, 225 "tool_version": "2.3.0",
235 "type": "tool", 226 "type": "tool",
236 "uuid": "e705e614-950a-436a-96a8-f8e9bcc4bb64", 227 "uuid": "7dd663f6-6633-41f0-b9cd-4bf575f72b90",
237 "workflow_outputs": [ 228 "workflow_outputs": [
238 { 229 {
239 "label": "RetroPath2.0", 230 "label": "RetroPath2.0",
240 "output_name": "Reaction_Network", 231 "output_name": "Reaction_Network",
241 "uuid": "31cac3f6-2f12-48c4-b265-9d745d5ba36d" 232 "uuid": "48e8b7d2-f341-4cff-b410-30652e68dab4"
242 } 233 }
243 ] 234 ]
244 }, 235 },
245 "5": { 236 "5": {
246 "annotation": "", 237 "annotation": "",
265 "name": "compounds", 256 "name": "compounds",
266 "type": "tsv" 257 "type": "tsv"
267 } 258 }
268 ], 259 ],
269 "position": { 260 "position": {
270 "bottom": 437.8999938964844, 261 "bottom": 526.3999938964844,
271 "height": 164.39999389648438, 262 "height": 164.39999389648438,
272 "left": 1050.5, 263 "left": 1193.5,
273 "right": 1250.5, 264 "right": 1393.5,
274 "top": 273.5, 265 "top": 362,
275 "width": 200, 266 "width": 200,
276 "x": 1050.5, 267 "x": 1193.5,
277 "y": 273.5 268 "y": 362
278 }, 269 },
279 "post_job_actions": {}, 270 "post_job_actions": {},
280 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.4.3", 271 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rp2paths/rp2paths/1.4.3",
281 "tool_shed_repository": { 272 "tool_shed_repository": {
282 "changeset_revision": "2782bee7c5a6", 273 "changeset_revision": "2782bee7c5a6",
283 "name": "rp2paths", 274 "name": "rp2paths",
284 "owner": "tduigou", 275 "owner": "tduigou",
285 "tool_shed": "toolshed.g2.bx.psu.edu" 276 "tool_shed": "toolshed.g2.bx.psu.edu"
286 }, 277 },
287 "tool_state": "{\"adv\": {\"timeout\": \"1800\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", 278 "tool_state": "{\"adv\": {\"timeout\": \"1800\"}, \"rp2_pathways\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
288 "tool_version": null, 279 "tool_version": "1.4.3",
289 "type": "tool", 280 "type": "tool",
290 "uuid": "3ebbcfa4-dd81-4200-b023-dbb445131657", 281 "uuid": "0d9f290f-a11c-4471-ba16-e0c561634be5",
291 "workflow_outputs": [ 282 "workflow_outputs": [
292 { 283 {
293 "label": "RP2paths (Pathways)", 284 "label": "RP2paths (Pathways)",
294 "output_name": "master_pathways", 285 "output_name": "master_pathways",
295 "uuid": "9b5454c6-35e7-4632-96d3-2d75ba8b1afe" 286 "uuid": "2225e9b3-8984-4d53-9878-232b4f773869"
296 }, 287 },
297 { 288 {
298 "label": "RP2paths (Compounds)", 289 "label": "RP2paths (Compounds)",
299 "output_name": "compounds", 290 "output_name": "compounds",
300 "uuid": "fc35e5fb-8556-4c7f-b11f-45b93467f7f6" 291 "uuid": "651afa73-ad92-4296-b788-00bd78f6df32"
301 } 292 }
302 ] 293 ]
303 }, 294 },
304 "6": { 295 "6": {
305 "annotation": "", 296 "annotation": "",
306 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpCompletion/5.9.2", 297 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.1",
307 "errors": null, 298 "errors": null,
308 "id": 6, 299 "id": 6,
309 "input_connections": { 300 "input_connections": {
310 "rp2_pathways": { 301 "rp2_pathways": {
311 "id": 4, 302 "id": 4,
332 "name": "pathways", 323 "name": "pathways",
333 "type": "input" 324 "type": "input"
334 } 325 }
335 ], 326 ],
336 "position": { 327 "position": {
337 "bottom": 646.1000061035156, 328 "bottom": 807.6000061035156,
338 "height": 245.60000610351562, 329 "height": 245.60000610351562,
339 "left": 1323.5, 330 "left": 1447.5,
340 "right": 1523.5, 331 "right": 1647.5,
341 "top": 400.5, 332 "top": 562,
342 "width": 200, 333 "width": 200,
343 "x": 1323.5, 334 "x": 1447.5,
344 "y": 400.5 335 "y": 562
345 }, 336 },
346 "post_job_actions": {}, 337 "post_job_actions": {},
347 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpCompletion/5.9.2", 338 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpcompletion/rpcompletion/5.12.1",
348 "tool_shed_repository": { 339 "tool_shed_repository": {
349 "changeset_revision": "98d925a75257", 340 "changeset_revision": "b8242cf18cc0",
350 "name": "rpcompletion", 341 "name": "rpcompletion",
351 "owner": "tduigou", 342 "owner": "tduigou",
352 "tool_shed": "toolshed.g2.bx.psu.edu" 343 "tool_shed": "toolshed.g2.bx.psu.edu"
353 }, 344 },
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}", 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}",
355 "tool_version": null, 346 "tool_version": "5.12.1",
356 "type": "tool", 347 "type": "tool",
357 "uuid": "bfc32617-1870-4240-8cf6-ea93da840007", 348 "uuid": "9acba2e0-e30c-47a7-8166-a6d694e425f8",
358 "workflow_outputs": [ 349 "workflow_outputs": [
359 { 350 {
360 "label": "Complete Reactions", 351 "label": "Complete Reactions",
361 "output_name": "pathways", 352 "output_name": "pathways",
362 "uuid": "b77df22c-2b09-4787-8762-18f3fd748aea" 353 "uuid": "fd9a697a-6bf9-4b84-88bf-a1c749475e30"
363 } 354 }
364 ] 355 ]
365 } 356 }
366 }, 357 },
367 "tags": [], 358 "tags": [],
368 "uuid": "a8283850-4dcb-4bd9-a11e-507bf58e8b4b", 359 "uuid": "c563c2dc-6f52-45c3-978a-43777561081d",
369 "version": 8 360 "version": 9
370 } 361 }