Mercurial > repos > tduigou > pathway_analysis_workflow
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 } |