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comparison Docking-preparation.ga @ 1:e047a2629ecf

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author marcel
date Thu, 19 Jan 2012 11:33:05 -0500
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0:b17805005cc8 1:e047a2629ecf
1 {
2 "a_galaxy_workflow": "true",
3 "annotation": "Water finding, contraints generation, pocket detection and grid building",
4 "format-version": "0.1",
5 "name": "Docking-preparation: constraints, water, pocket-detection",
6 "steps": {
7 "0": {
8 "annotation": "",
9 "id": 0,
10 "input_connections": {},
11 "inputs": [
12 {
13 "description": "",
14 "name": "Receptor"
15 }
16 ],
17 "name": "Input dataset",
18 "outputs": [],
19 "position": {
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21 "top": 251.5
22 },
23 "tool_errors": null,
24 "tool_id": null,
25 "tool_state": "{\"name\": \"Receptor\"}",
26 "tool_version": null,
27 "type": "data_input",
28 "user_outputs": []
29 },
30 "1": {
31 "annotation": "",
32 "id": 1,
33 "input_connections": {},
34 "inputs": [
35 {
36 "description": "",
37 "name": "pdb-file w/ water molecules"
38 }
39 ],
40 "name": "Input dataset",
41 "outputs": [],
42 "position": {
43 "left": 198,
44 "top": 325
45 },
46 "tool_errors": null,
47 "tool_id": null,
48 "tool_state": "{\"name\": \"pdb-file w/ water molecules\"}",
49 "tool_version": null,
50 "type": "data_input",
51 "user_outputs": []
52 },
53 "2": {
54 "annotation": "",
55 "id": 2,
56 "input_connections": {},
57 "inputs": [
58 {
59 "description": "",
60 "name": "Reference ligand"
61 }
62 ],
63 "name": "Input dataset",
64 "outputs": [],
65 "position": {
66 "left": 254.5,
67 "top": 491
68 },
69 "tool_errors": null,
70 "tool_id": null,
71 "tool_state": "{\"name\": \"Reference ligand\"}",
72 "tool_version": null,
73 "type": "data_input",
74 "user_outputs": []
75 },
76 "3": {
77 "annotation": "",
78 "id": 3,
79 "input_connections": {
80 "i": {
81 "id": 0,
82 "output_name": "output"
83 }
84 },
85 "inputs": [],
86 "name": "ProteinProtonator",
87 "outputs": [
88 {
89 "name": "o",
90 "type": "pdb"
91 }
92 ],
93 "position": {
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95 "top": 255
96 },
97 "tool_errors": null,
98 "tool_id": "proteinprotonator",
99 "tool_state": "{\"i\": \"null\", \"input\": \"null\", \"ph\": \"\\\"7.0\\\"\", \"__page__\": 0}",
100 "tool_version": "1.0",
101 "type": "tool",
102 "user_outputs": []
103 },
104 "4": {
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106 "id": 4,
107 "input_connections": {
108 "rec": {
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110 "output_name": "o"
111 },
112 "rl": {
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114 "output_name": "output"
115 },
116 "wat": {
117 "id": 1,
118 "output_name": "output"
119 }
120 },
121 "inputs": [],
122 "name": "WaterFinder",
123 "outputs": [
124 {
125 "name": "o",
126 "type": "pdb"
127 }
128 ],
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131 "top": 212
132 },
133 "tool_errors": null,
134 "tool_id": "waterfinder",
135 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"ai\": \"\\\"False\\\"\", \"ini\": \"null\", \"water_pdb\": \"null\", \"rl\": \"null\", \"rec\": \"null\", \"wat\": \"null\"}",
136 "tool_version": "1.0",
137 "type": "tool",
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139 },
140 "5": {
141 "annotation": "",
142 "id": 5,
143 "input_connections": {
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146 "output_name": "o"
147 },
148 "rl": {
149 "id": 2,
150 "output_name": "output"
151 }
152 },
153 "inputs": [],
154 "name": "ConstraintsFinder",
155 "outputs": [
156 {
157 "name": "o",
158 "type": "ini"
159 }
160 ],
161 "position": {
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163 "top": 425
164 },
165 "tool_errors": null,
166 "tool_id": "constraintsfinder",
167 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"ini\": \"null\", \"rec\": \"null\", \"rl\": \"null\", \"configfile_input\": \"null\"}",
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169 "type": "tool",
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172 "6": {
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174 "id": 6,
175 "input_connections": {
176 "i": {
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178 "output_name": "o"
179 }
180 },
181 "inputs": [],
182 "name": "ProteinCheck",
183 "outputs": [
184 {
185 "name": "o",
186 "type": "pdf"
187 }
188 ],
189 "position": {
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191 "top": 244
192 },
193 "tool_errors": null,
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195 "tool_state": "{\"i\": \"null\", \"ignorebrokenchains\": \"\\\"False\\\"\", \"__page__\": 0, \"input\": \"null\", \"bc\": \"\\\"False\\\"\"}",
196 "tool_version": "1.0",
197 "type": "tool",
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199 },
200 "7": {
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203 "input_connections": {
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206 "output_name": "o"
207 },
208 "rec": {
209 "id": 4,
210 "output_name": "o"
211 },
212 "rl": {
213 "id": 2,
214 "output_name": "output"
215 }
216 },
217 "inputs": [],
218 "name": "PocketDetector",
219 "outputs": [
220 {
221 "name": "o",
222 "type": "ini"
223 }
224 ],
225 "position": {
226 "left": 773,
227 "top": 420
228 },
229 "tool_errors": null,
230 "tool_id": "pocketdetector",
231 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"ini\": \"null\", \"rec\": \"null\", \"rl\": \"null\", \"configfile_input\": \"null\"}",
232 "tool_version": "1.0",
233 "type": "tool",
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235 },
236 "8": {
237 "annotation": "",
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239 "input_connections": {
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243 },
244 "rec": {
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246 "output_name": "o"
247 },
248 "rl": {
249 "id": 2,
250 "output_name": "output"
251 }
252 },
253 "inputs": [],
254 "name": "GridBuilder",
255 "outputs": [
256 {
257 "name": "grd",
258 "type": "grd.gz"
259 }
260 ],
261 "position": {
262 "left": 982.5,
263 "top": 425
264 },
265 "tool_errors": null,
266 "tool_id": "gridbuilder",
267 "tool_state": "{\"input2\": \"null\", \"__page__\": 0, \"input1\": \"null\", \"configfile\": \"null\", \"ini\": \"null\", \"rl\": \"null\", \"rec\": \"null\"}",
268 "tool_version": "1.0",
269 "type": "tool",
270 "user_outputs": []
271 }
272 }
273 }