comparison Pathway_Analysis_workflow.ga @ 0:8fb4e270be9f draft default tip

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Mon, 13 Dec 2021 19:02:39 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:8fb4e270be9f
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "",
4 "format-version": "0.1",
5 "name": "Pathway_Analysis_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": "rpbsml_pathways"
17 }
18 ],
19 "label": "rpbsml_pathways",
20 "name": "Input dataset collection",
21 "outputs": [],
22 "position": {
23 "bottom": 522.8000030517578,
24 "height": 61.80000305175781,
25 "left": -138,
26 "right": 62,
27 "top": 461,
28 "width": 200,
29 "x": -138,
30 "y": 461
31 },
32 "tool_id": null,
33 "tool_state": "{\"optional\": false, \"collection_type\": \"list\"}",
34 "tool_version": null,
35 "type": "data_collection_input",
36 "uuid": "40022f70-14b3-4291-aa3b-8f2693d6752c",
37 "workflow_outputs": [
38 {
39 "label": null,
40 "output_name": "output",
41 "uuid": "760719ed-d2e1-47d5-9f46-d6dd876f6b6c"
42 }
43 ]
44 },
45 "1": {
46 "annotation": "",
47 "content_id": null,
48 "errors": null,
49 "id": 1,
50 "input_connections": {},
51 "inputs": [
52 {
53 "description": "",
54 "name": "sbml_model"
55 }
56 ],
57 "label": "sbml_model",
58 "name": "Input dataset",
59 "outputs": [],
60 "position": {
61 "bottom": 632.8000030517578,
62 "height": 61.80000305175781,
63 "left": -137,
64 "right": 63,
65 "top": 571,
66 "width": 200,
67 "x": -137,
68 "y": 571
69 },
70 "tool_id": null,
71 "tool_state": "{\"optional\": false}",
72 "tool_version": null,
73 "type": "data_input",
74 "uuid": "715f8537-ff4b-4b00-86a2-0c358576ddd8",
75 "workflow_outputs": [
76 {
77 "label": null,
78 "output_name": "output",
79 "uuid": "80fd34b8-0b64-4bd7-8860-4354ecc86f78"
80 }
81 ]
82 },
83 "2": {
84 "annotation": "",
85 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpfba/rpFBA/5.9.2",
86 "errors": null,
87 "id": 2,
88 "input_connections": {
89 "model": {
90 "id": 1,
91 "output_name": "output"
92 },
93 "pathway": {
94 "id": 0,
95 "output_name": "output"
96 }
97 },
98 "inputs": [],
99 "label": null,
100 "name": "FBA",
101 "outputs": [
102 {
103 "name": "pathway_with_fba",
104 "type": "xml"
105 }
106 ],
107 "position": {
108 "bottom": 612.6000061035156,
109 "height": 123.60000610351562,
110 "left": 157,
111 "right": 357,
112 "top": 489,
113 "width": 200,
114 "x": 157,
115 "y": 489
116 },
117 "post_job_actions": {},
118 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpfba/rpFBA/5.9.2",
119 "tool_shed_repository": {
120 "changeset_revision": "fb5efc456dcc",
121 "name": "rpfba",
122 "owner": "tduigou",
123 "tool_shed": "toolshed.g2.bx.psu.edu"
124 },
125 "tool_state": "{\"adv\": {\"merge\": \"false\", \"ignore_orphan_species\": \"true\", \"log_level\": \"error\"}, \"compartment_id\": \"MNXC3\", \"input_sim_type\": {\"sim_type\": \"fraction\", \"__current_case__\": 0, \"fraction_of\": \"0.75\", \"objective_rxn_id\": \"rxn_target\", \"biomass_rxn_id\": \"biomass\"}, \"model\": {\"__class__\": \"ConnectedValue\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
126 "tool_version": "5.9.2",
127 "type": "tool",
128 "uuid": "219ff424-7956-43bc-adaf-ebbb4341af01",
129 "workflow_outputs": [
130 {
131 "label": null,
132 "output_name": "pathway_with_fba",
133 "uuid": "91b6f335-54fa-42bd-a6bb-2ff71f2fd50b"
134 }
135 ]
136 },
137 "3": {
138 "annotation": "",
139 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpThermo/5.9.2",
140 "errors": null,
141 "id": 3,
142 "input_connections": {
143 "input": {
144 "id": 2,
145 "output_name": "pathway_with_fba"
146 }
147 },
148 "inputs": [],
149 "label": null,
150 "name": "Thermodynamics",
151 "outputs": [
152 {
153 "name": "pathway_with_thermo",
154 "type": "xml"
155 }
156 ],
157 "position": {
158 "bottom": 604.6000061035156,
159 "height": 113.60000610351562,
160 "left": 439,
161 "right": 639,
162 "top": 491,
163 "width": 200,
164 "x": 439,
165 "y": 491
166 },
167 "post_job_actions": {},
168 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpthermo/rpThermo/5.9.2",
169 "tool_shed_repository": {
170 "changeset_revision": "44e54b56328d",
171 "name": "rpthermo",
172 "owner": "tduigou",
173 "tool_shed": "toolshed.g2.bx.psu.edu"
174 },
175 "tool_state": "{\"adv\": {\"ph\": \"7.5\", \"ionic_strength\": \"200.0\", \"pMg\": \"10.0\", \"temp_k\": \"298.15\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
176 "tool_version": "5.9.2",
177 "type": "tool",
178 "uuid": "24b0f086-293c-45cf-be0e-b17265316a38",
179 "workflow_outputs": [
180 {
181 "label": null,
182 "output_name": "pathway_with_thermo",
183 "uuid": "f0c3c790-65ac-42d9-8793-9ec26327ad74"
184 }
185 ]
186 },
187 "4": {
188 "annotation": "",
189 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.9.2",
190 "errors": null,
191 "id": 4,
192 "input_connections": {
193 "pathway": {
194 "id": 3,
195 "output_name": "pathway_with_thermo"
196 }
197 },
198 "inputs": [],
199 "label": null,
200 "name": "Score Pathway",
201 "outputs": [
202 {
203 "name": "scored_pathway",
204 "type": "xml"
205 }
206 ],
207 "position": {
208 "bottom": 604.1999969482422,
209 "height": 93.19999694824219,
210 "left": 692,
211 "right": 892,
212 "top": 511,
213 "width": 200,
214 "x": 692,
215 "y": 511
216 },
217 "post_job_actions": {},
218 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpscore/rpscore/5.9.2",
219 "tool_shed_repository": {
220 "changeset_revision": "f818d489ca7d",
221 "name": "rpscore",
222 "owner": "tduigou",
223 "tool_shed": "toolshed.g2.bx.psu.edu"
224 },
225 "tool_state": "{\"adv\": {\"no_of_rxns_thres\": \"10\", \"log_level\": \"error\"}, \"pathway\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
226 "tool_version": "5.9.2",
227 "type": "tool",
228 "uuid": "418f937f-5114-4330-9825-42a2c0028b78",
229 "workflow_outputs": [
230 {
231 "label": null,
232 "output_name": "scored_pathway",
233 "uuid": "c99d61ef-cd94-48be-ae0e-fbac6c6b5d5b"
234 }
235 ]
236 },
237 "5": {
238 "annotation": "",
239 "content_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.10.0",
240 "errors": null,
241 "id": 5,
242 "input_connections": {
243 "pathway_collection": {
244 "id": 4,
245 "output_name": "scored_pathway"
246 }
247 },
248 "inputs": [
249 {
250 "description": "runtime parameter for tool Rank Pathways",
251 "name": "pathway_collection"
252 }
253 ],
254 "label": null,
255 "name": "Rank Pathways",
256 "outputs": [
257 {
258 "name": "sorted_pathways",
259 "type": "csv"
260 }
261 ],
262 "position": {
263 "bottom": 635.1999969482422,
264 "height": 93.19999694824219,
265 "left": 933,
266 "right": 1133,
267 "top": 542,
268 "width": 200,
269 "x": 933,
270 "y": 542
271 },
272 "post_job_actions": {},
273 "tool_id": "toolshed.g2.bx.psu.edu/repos/tduigou/rpranker/rpranker/5.10.0",
274 "tool_shed_repository": {
275 "changeset_revision": "e95370d2e5f9",
276 "name": "rpranker",
277 "owner": "tduigou",
278 "tool_shed": "toolshed.g2.bx.psu.edu"
279 },
280 "tool_state": "{\"pathway_collection\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
281 "tool_version": "5.10.0",
282 "type": "tool",
283 "uuid": "2035ac50-9127-4363-90f5-86990ecc4239",
284 "workflow_outputs": [
285 {
286 "label": "Ranked Pathways",
287 "output_name": "sorted_pathways",
288 "uuid": "db1ad6c3-983a-4678-8db0-fe5c59b81025"
289 }
290 ]
291 }
292 },
293 "tags": [],
294 "uuid": "f1092980-8652-4560-bda2-ed95629cad24",
295 "version": 3
296 }