Mercurial > repos > iuc > hyphy_conv
comparison test-data/params.json @ 0:9ce3d6d4bd0e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author | iuc |
---|---|
date | Tue, 20 Apr 2021 10:31:50 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:9ce3d6d4bd0e |
---|---|
1 { | |
2 "filepath": "/home/sweaver/datamonkey/datamonkey-js-dev/app/models/../../uploads/msa/5446bc0d355080301f18a8c6.fasta", | |
3 "msa": [ | |
4 { | |
5 "rawsites": 1698, | |
6 "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)", | |
7 "goodtree": 0, | |
8 "sequences": 21, | |
9 "sites": 566, | |
10 "partitions": 1, | |
11 "analysis_type": "1", | |
12 "gencodeid": 0, | |
13 "datatype": 0, | |
14 "_id": "5446bc0d355080301f18a8c7", | |
15 "created": "2014-10-21T20:03:25.803Z", | |
16 "sequence_info": [ | |
17 { | |
18 "seqindex": 0, | |
19 "name": "TREESPARROW_HENAN_1_2004", | |
20 "_id": "5446bc0d355080301f18a8c8" | |
21 }, | |
22 { | |
23 "seqindex": 1, | |
24 "name": "HUMAN_VIETNAM_CL105_2005", | |
25 "_id": "5446bc0d355080301f18a8c9" | |
26 }, | |
27 { | |
28 "seqindex": 2, | |
29 "name": "TREESPARROW_HENAN_4_2004", | |
30 "_id": "5446bc0d355080301f18a8ca" | |
31 }, | |
32 { | |
33 "seqindex": 3, | |
34 "name": "CHICKEN_HEBEI_326_2005", | |
35 "_id": "5446bc0d355080301f18a8cb" | |
36 }, | |
37 { | |
38 "seqindex": 4, | |
39 "name": "CHICKEN_HONGKONG_915_97", | |
40 "_id": "5446bc0d355080301f18a8cc" | |
41 }, | |
42 { | |
43 "seqindex": 5, | |
44 "name": "HUMAN_VIETNAM_3062_2004", | |
45 "_id": "5446bc0d355080301f18a8cd" | |
46 }, | |
47 { | |
48 "seqindex": 6, | |
49 "name": "GOOSE_HONGKONG_W355_97", | |
50 "_id": "5446bc0d355080301f18a8ce" | |
51 }, | |
52 { | |
53 "seqindex": 7, | |
54 "name": "DUCK_HONGKONG_Y283_97", | |
55 "_id": "5446bc0d355080301f18a8cf" | |
56 }, | |
57 { | |
58 "seqindex": 8, | |
59 "name": "DUCK_VIETNAM_376_2005", | |
60 "_id": "5446bc0d355080301f18a8d0" | |
61 }, | |
62 { | |
63 "seqindex": 9, | |
64 "name": "MALLARD_VIETNAM_16_2003", | |
65 "_id": "5446bc0d355080301f18a8d1" | |
66 }, | |
67 { | |
68 "seqindex": 10, | |
69 "name": "CHICKEN_CK_160_2005", | |
70 "_id": "5446bc0d355080301f18a8d2" | |
71 }, | |
72 { | |
73 "seqindex": 11, | |
74 "name": "DUCK_GUANGZHOU_20_2005", | |
75 "_id": "5446bc0d355080301f18a8d3" | |
76 }, | |
77 { | |
78 "seqindex": 12, | |
79 "name": "CK_HK_WF157_2003", | |
80 "_id": "5446bc0d355080301f18a8d4" | |
81 }, | |
82 { | |
83 "seqindex": 13, | |
84 "name": "SWINE_ANHUI_1_2004", | |
85 "_id": "5446bc0d355080301f18a8d5" | |
86 }, | |
87 { | |
88 "seqindex": 14, | |
89 "name": "DUCK_VIETNAM_272_2005", | |
90 "_id": "5446bc0d355080301f18a8d6" | |
91 }, | |
92 { | |
93 "seqindex": 15, | |
94 "name": "HONGKONG_1_97_98", | |
95 "_id": "5446bc0d355080301f18a8d7" | |
96 }, | |
97 { | |
98 "seqindex": 16, | |
99 "name": "GOOSE_SHANTOU_2216_2005", | |
100 "_id": "5446bc0d355080301f18a8d8" | |
101 }, | |
102 { | |
103 "seqindex": 17, | |
104 "name": "TREESPARROW_HENAN_3_2004", | |
105 "_id": "5446bc0d355080301f18a8d9" | |
106 }, | |
107 { | |
108 "seqindex": 18, | |
109 "name": "PEREGRINEFALCON_HK_D0028_2004", | |
110 "_id": "5446bc0d355080301f18a8da" | |
111 }, | |
112 { | |
113 "seqindex": 19, | |
114 "name": "TREESPARROW_HENAN_2_2004", | |
115 "_id": "5446bc0d355080301f18a8db" | |
116 }, | |
117 { | |
118 "seqindex": 20, | |
119 "name": "HONGKONG_1_538_97", | |
120 "_id": "5446bc0d355080301f18a8dc" | |
121 } | |
122 ], | |
123 "partition_info": [ | |
124 { | |
125 "partition": 1, | |
126 "startcodon": 0, | |
127 "endcodon": 1697, | |
128 "span": 1698, | |
129 "_id": "5446bc0d355080301f18a8dd" | |
130 } | |
131 ] | |
132 } | |
133 ], | |
134 "analysis": { | |
135 "status": "In Queue", | |
136 "tagged_nwk_tree": "(((((((TREESPARROW_HENAN_1_2004{FG}:0.0111333782927653,TREESPARROW_HENAN_3_2004{FG}:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.00906278098731238):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97,(GOOSE_HONGKONG_W355_97,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)", | |
137 "_id": "5446bc0d355080301f18a8c6", | |
138 "__t": "Busted", | |
139 "mail": "sweaver@ucsd.edu", | |
140 "analysis_type": 1, | |
141 "__v": 0, | |
142 "msa": [ | |
143 { | |
144 "partition_info": [ | |
145 { | |
146 "_id": "5446bc0d355080301f18a8dd", | |
147 "span": 1698, | |
148 "endcodon": 1697, | |
149 "startcodon": 0, | |
150 "partition": 1 | |
151 } | |
152 ], | |
153 "sequence_info": [ | |
154 { | |
155 "_id": "5446bc0d355080301f18a8c8", | |
156 "name": "TREESPARROW_HENAN_1_2004", | |
157 "seqindex": 0 | |
158 }, | |
159 { | |
160 "_id": "5446bc0d355080301f18a8c9", | |
161 "name": "HUMAN_VIETNAM_CL105_2005", | |
162 "seqindex": 1 | |
163 }, | |
164 { | |
165 "_id": "5446bc0d355080301f18a8ca", | |
166 "name": "TREESPARROW_HENAN_4_2004", | |
167 "seqindex": 2 | |
168 }, | |
169 { | |
170 "_id": "5446bc0d355080301f18a8cb", | |
171 "name": "CHICKEN_HEBEI_326_2005", | |
172 "seqindex": 3 | |
173 }, | |
174 { | |
175 "_id": "5446bc0d355080301f18a8cc", | |
176 "name": "CHICKEN_HONGKONG_915_97", | |
177 "seqindex": 4 | |
178 }, | |
179 { | |
180 "_id": "5446bc0d355080301f18a8cd", | |
181 "name": "HUMAN_VIETNAM_3062_2004", | |
182 "seqindex": 5 | |
183 }, | |
184 { | |
185 "_id": "5446bc0d355080301f18a8ce", | |
186 "name": "GOOSE_HONGKONG_W355_97", | |
187 "seqindex": 6 | |
188 }, | |
189 { | |
190 "_id": "5446bc0d355080301f18a8cf", | |
191 "name": "DUCK_HONGKONG_Y283_97", | |
192 "seqindex": 7 | |
193 }, | |
194 { | |
195 "_id": "5446bc0d355080301f18a8d0", | |
196 "name": "DUCK_VIETNAM_376_2005", | |
197 "seqindex": 8 | |
198 }, | |
199 { | |
200 "_id": "5446bc0d355080301f18a8d1", | |
201 "name": "MALLARD_VIETNAM_16_2003", | |
202 "seqindex": 9 | |
203 }, | |
204 { | |
205 "_id": "5446bc0d355080301f18a8d2", | |
206 "name": "CHICKEN_CK_160_2005", | |
207 "seqindex": 10 | |
208 }, | |
209 { | |
210 "_id": "5446bc0d355080301f18a8d3", | |
211 "name": "DUCK_GUANGZHOU_20_2005", | |
212 "seqindex": 11 | |
213 }, | |
214 { | |
215 "_id": "5446bc0d355080301f18a8d4", | |
216 "name": "CK_HK_WF157_2003", | |
217 "seqindex": 12 | |
218 }, | |
219 { | |
220 "_id": "5446bc0d355080301f18a8d5", | |
221 "name": "SWINE_ANHUI_1_2004", | |
222 "seqindex": 13 | |
223 }, | |
224 { | |
225 "_id": "5446bc0d355080301f18a8d6", | |
226 "name": "DUCK_VIETNAM_272_2005", | |
227 "seqindex": 14 | |
228 }, | |
229 { | |
230 "_id": "5446bc0d355080301f18a8d7", | |
231 "name": "HONGKONG_1_97_98", | |
232 "seqindex": 15 | |
233 }, | |
234 { | |
235 "_id": "5446bc0d355080301f18a8d8", | |
236 "name": "GOOSE_SHANTOU_2216_2005", | |
237 "seqindex": 16 | |
238 }, | |
239 { | |
240 "_id": "5446bc0d355080301f18a8d9", | |
241 "name": "TREESPARROW_HENAN_3_2004", | |
242 "seqindex": 17 | |
243 }, | |
244 { | |
245 "_id": "5446bc0d355080301f18a8da", | |
246 "name": "PEREGRINEFALCON_HK_D0028_2004", | |
247 "seqindex": 18 | |
248 }, | |
249 { | |
250 "_id": "5446bc0d355080301f18a8db", | |
251 "name": "TREESPARROW_HENAN_2_2004", | |
252 "seqindex": 19 | |
253 }, | |
254 { | |
255 "_id": "5446bc0d355080301f18a8dc", | |
256 "name": "HONGKONG_1_538_97", | |
257 "seqindex": 20 | |
258 } | |
259 ], | |
260 "created": "2014-10-21T20:03:25.803Z", | |
261 "_id": "5446bc0d355080301f18a8c7", | |
262 "datatype": 0, | |
263 "gencodeid": 0, | |
264 "partitions": 1, | |
265 "sites": 566, | |
266 "sequences": 21, | |
267 "goodtree": 0, | |
268 "nj": "(((((((TREESPARROW_HENAN_1_2004:0.0111333782927653,TREESPARROW_HENAN_3_2004:0.006193745941169043):0.0009956664967877545,TREESPARROW_HENAN_4_2004:0.004351652686857959):0.002267763895256407,(CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516,TREESPARROW_HENAN_2_2004:0.009062780987312381):0.002095219592954275):0.003887237703073042):0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-0.001089936320307174,(GOOSE_HONGKONG_W355_97:-0.002798420018760263,DUCK_HONGKONG_Y283_97:0.002798420018760263):0.002899766890966483):0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716):0.000182535836694054,HONGKONG_1_538_97:-8.034074555865944e-05):0.02096173714686362):0.003130608143291779,(((DUCK_GUANGZHOU_20_2005:0.006299389645455026,GOOSE_SHANTOU_2216_2005:0.006207842095177651):0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232):0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001,DUCK_VIETNAM_376_2005:0.007877615936285868):0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184):0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849,DUCK_VIETNAM_272_2005:0.009465302724994452)", | |
269 "rawsites": 1698 | |
270 } | |
271 ], | |
272 "created": "2014-10-21T20:03:25.798Z" | |
273 }, | |
274 "status_stack": [ | |
275 "In Queue", | |
276 "Running", | |
277 "Completed" | |
278 ], | |
279 "type": "relax" | |
280 } |