Mercurial > repos > tduigou > cloning_simulation

comparison output.json @ 1:2655e08cd61a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
author tduigou
date Wed, 23 Jul 2025 09:46:59 +0000
parents
children
comparison
equal deleted inserted replaced
0:3a3b0f7cb5c2 1:2655e08cd61a
1 {
2 "summary": {
3 "num_errors": 0,
4 "num_failures": 0,
5 "num_skips": 0,
6 "num_tests": 7
7 },
8 "tests": [
9 {
10 "data": {
11 "inputs": {
12 "adv|use_file_names_as_ids": true,
13 "assembly_csv": {
14 "id": "5251f3a41a1cbe5c",
15 "src": "hda"
16 },
17 "assembly_plan_name": "Type2sRestrictionAssembly",
18 "genbank_files": {
19 "id": "b685bcc6830b171b",
20 "src": "hdca"
21 },
22 "topology": "circular"
23 },
24 "job": {
25 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/c/2/9/dataset_c29f7add-5948-4171-8ac2-f87d5bf0f6f6.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/e/6/3/dataset_e63928a2-379c-45c8-8839-98a0df69a5cb.dat,/tmp/tmp2jitj5ti/files/4/4/7/dataset_44790451-2c88-485c-b4d5-d0f4bf78a093.dat,/tmp/tmp2jitj5ti/files/7/3/5/dataset_7354b218-2236-4b40-bdcb-3a46917a6e0f.dat,/tmp/tmp2jitj5ti/files/a/8/e/dataset_a8e12f0e-8a7c-48dd-a8ef-6988c90a7e58.dat,/tmp/tmp2jitj5ti/files/a/2/9/dataset_a298e5dd-536e-4652-8690-5132027c738c.dat,/tmp/tmp2jitj5ti/files/d/c/d/dataset_dcd006e1-e03f-42ed-b029-00134dd29dd1.dat,/tmp/tmp2jitj5ti/files/2/a/f/dataset_2aff75ea-f829-4836-a3dc-7cb018e02383.dat,/tmp/tmp2jitj5ti/files/a/1/8/dataset_a180d7ab-0c41-48d4-8941-3d8d251808a6.dat,/tmp/tmp2jitj5ti/files/6/9/2/dataset_692e75b8-b311-48e4-9b81-92c7addf1f79.dat,/tmp/tmp2jitj5ti/files/9/b/3/dataset_9b37829a-f97b-4f67-8243-bf2bd14ae4b6.dat,/tmp/tmp2jitj5ti/files/c/1/2/dataset_c12c0090-a770-4e92-9398-1a66760dc274.dat,/tmp/tmp2jitj5ti/files/5/2/1/dataset_521c5340-7b41-4b46-aa04-9be9ab5e99fd.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/e/6/3/dataset_e63928a2-379c-45c8-8839-98a0df69a5cb.dat:part_A.gb,/tmp/tmp2jitj5ti/files/4/4/7/dataset_44790451-2c88-485c-b4d5-d0f4bf78a093.dat:part_B.gb,/tmp/tmp2jitj5ti/files/7/3/5/dataset_7354b218-2236-4b40-bdcb-3a46917a6e0f.dat:part_C.gb,/tmp/tmp2jitj5ti/files/a/8/e/dataset_a8e12f0e-8a7c-48dd-a8ef-6988c90a7e58.dat:part_D.gb,/tmp/tmp2jitj5ti/files/a/2/9/dataset_a298e5dd-536e-4652-8690-5132027c738c.dat:part_E.gb,/tmp/tmp2jitj5ti/files/d/c/d/dataset_dcd006e1-e03f-42ed-b029-00134dd29dd1.dat:part_F.gb,/tmp/tmp2jitj5ti/files/2/a/f/dataset_2aff75ea-f829-4836-a3dc-7cb018e02383.dat:part_G.gb,/tmp/tmp2jitj5ti/files/a/1/8/dataset_a180d7ab-0c41-48d4-8941-3d8d251808a6.dat:part_H.gb,/tmp/tmp2jitj5ti/files/6/9/2/dataset_692e75b8-b311-48e4-9b81-92c7addf1f79.dat:part_I.gb,/tmp/tmp2jitj5ti/files/9/b/3/dataset_9b37829a-f97b-4f67-8243-bf2bd14ae4b6.dat:part_J.gb,/tmp/tmp2jitj5ti/files/c/1/2/dataset_c12c0090-a770-4e92-9398-1a66760dc274.dat:part_K.gb,/tmp/tmp2jitj5ti/files/5/2/1/dataset_521c5340-7b41-4b46-aa04-9be9ab5e99fd.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp2jitj5ti/job_working_directory/000/14/outputs/dataset_d929e00d-64fe-466c-820f-898fef1ddd39.dat'",
26 "command_version": "",
27 "copied_from_job_id": null,
28 "create_time": "2025-06-06T10:05:03.918951",
29 "dependencies": [],
30 "exit_code": 0,
31 "external_id": "384868",
32 "galaxy_version": "24.2",
33 "handler": null,
34 "history_id": "b685bcc6830b171b",
35 "id": "382e0b9a3dd586fb",
36 "inputs": {
37 "assembly_csv": {
38 "id": "5251f3a41a1cbe5c",
39 "src": "hda",
40 "uuid": "c29f7add-5948-4171-8ac2-f87d5bf0f6f6"
41 },
42 "genbank_files1": {
43 "id": "b685bcc6830b171b",
44 "src": "hda",
45 "uuid": "e63928a2-379c-45c8-8839-98a0df69a5cb"
46 },
47 "genbank_files10": {
48 "id": "07723b52981231a1",
49 "src": "hda",
50 "uuid": "9b37829a-f97b-4f67-8243-bf2bd14ae4b6"
51 },
52 "genbank_files11": {
53 "id": "830f955cbdf9a561",
54 "src": "hda",
55 "uuid": "c12c0090-a770-4e92-9398-1a66760dc274"
56 },
57 "genbank_files12": {
58 "id": "71dab170b139725e",
59 "src": "hda",
60 "uuid": "521c5340-7b41-4b46-aa04-9be9ab5e99fd"
61 },
62 "genbank_files2": {
63 "id": "48e269c64ce4fce2",
64 "src": "hda",
65 "uuid": "44790451-2c88-485c-b4d5-d0f4bf78a093"
66 },
67 "genbank_files3": {
68 "id": "abbe1d9cd04428c7",
69 "src": "hda",
70 "uuid": "7354b218-2236-4b40-bdcb-3a46917a6e0f"
71 },
72 "genbank_files4": {
73 "id": "b93fb7c1f8bf7b46",
74 "src": "hda",
75 "uuid": "a8e12f0e-8a7c-48dd-a8ef-6988c90a7e58"
76 },
77 "genbank_files5": {
78 "id": "45bf0c3ad4473005",
79 "src": "hda",
80 "uuid": "a298e5dd-536e-4652-8690-5132027c738c"
81 },
82 "genbank_files6": {
83 "id": "4efa4181abcbfe3f",
84 "src": "hda",
85 "uuid": "dcd006e1-e03f-42ed-b029-00134dd29dd1"
86 },
87 "genbank_files7": {
88 "id": "beb5db8871971f36",
89 "src": "hda",
90 "uuid": "2aff75ea-f829-4836-a3dc-7cb018e02383"
91 },
92 "genbank_files8": {
93 "id": "bc095eef87c18a70",
94 "src": "hda",
95 "uuid": "a180d7ab-0c41-48d4-8941-3d8d251808a6"
96 },
97 "genbank_files9": {
98 "id": "9f6ba43f26fd6d3f",
99 "src": "hda",
100 "uuid": "692e75b8-b311-48e4-9b81-92c7addf1f79"
101 }
102 },
103 "job_messages": [],
104 "job_metrics": [],
105 "job_runner_name": null,
106 "job_stderr": "",
107 "job_stdout": "",
108 "model_class": "Job",
109 "output_collections": {
110 "construct_gb": {
111 "id": "48e269c64ce4fce2",
112 "src": "hdca"
113 }
114 },
115 "outputs": {
116 "__new_primary_file_construct_gb|construct_1__": {
117 "id": "56254918ce4e0956",
118 "src": "hda",
119 "uuid": "41a51dd8-721c-4361-8c96-d4e737f41eec"
120 },
121 "__new_primary_file_construct_gb|construct_2__": {
122 "id": "aad815be3bbd2bd5",
123 "src": "hda",
124 "uuid": "956b70c1-92eb-422d-ab4f-808a8b962d1f"
125 },
126 "__new_primary_file_construct_gb|construct_3__": {
127 "id": "720f24a804e8d612",
128 "src": "hda",
129 "uuid": "998417d6-f292-4477-a81c-962b56e7a0e0"
130 },
131 "__new_primary_file_construct_gb|construct_4__": {
132 "id": "d6de5bc932d51475",
133 "src": "hda",
134 "uuid": "e7c25803-f52c-4a42-8dc6-c9191701d749"
135 },
136 "output_zip": {
137 "id": "382e0b9a3dd586fb",
138 "src": "hda",
139 "uuid": "d929e00d-64fe-466c-820f-898fef1ddd39"
140 }
141 },
142 "params": {
143 "__input_ext": "\"input\"",
144 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
145 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
146 "chromInfo": "\"/tmp/tmp2jitj5ti/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
147 "dbkey": "\"?\"",
148 "domesticated_input": null,
149 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
150 "topology": "\"circular\""
151 },
152 "state": "ok",
153 "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.12it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.02it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.70it/s, now=None]\r \r",
154 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
155 "tool_id": "cloning_simulation",
156 "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.12it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.02it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.70it/s, now=None]\r \r",
157 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
158 "update_time": "2025-06-06T10:05:17.649698",
159 "user_email": "planemo@galaxyproject.org",
160 "user_id": "b685bcc6830b171b"
161 },
162 "status": "success",
163 "test_index": 0,
164 "time_seconds": 56.74104905128479,
165 "tool_id": "cloning_simulation",
166 "tool_version": "0.1.0+galaxy0"
167 },
168 "has_data": true,
169 "id": "cloning_simulation-0"
170 },
171 {
172 "data": {
173 "inputs": {
174 "adv|use_file_names_as_ids": true,
175 "assembly_csv": {
176 "id": "d765718fb46383bd",
177 "src": "hda"
178 },
179 "assembly_plan_name": "GibsonAssembly",
180 "genbank_files": {
181 "id": "abbe1d9cd04428c7",
182 "src": "hdca"
183 },
184 "topology": "circular"
185 },
186 "job": {
187 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/2/1/9/dataset_219d9b1e-e68c-4fb3-bcfe-e77aba638437.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/4/f/b/dataset_4fb22863-853c-4591-9c42-2bb9c71cf261.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/4/f/b/dataset_4fb22863-853c-4591-9c42-2bb9c71cf261.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp2jitj5ti/job_working_directory/000/17/outputs/dataset_a64ce795-3e43-4f34-aacf-aee1dd0b1f6e.dat'",
188 "command_version": "",
189 "copied_from_job_id": null,
190 "create_time": "2025-06-06T10:05:28.808016",
191 "dependencies": [
192 {
193 "cacheable": false,
194 "dependency_resolver": {
195 "auto_init": true,
196 "auto_install": true,
197 "can_uninstall_dependencies": true,
198 "ensure_channels": "conda-forge,bioconda",
199 "model_class": "CondaDependencyResolver",
200 "prefix": "/home/rkhaled/miniconda3",
201 "read_only": false,
202 "resolver_type": "conda",
203 "resolves_simple_dependencies": true,
204 "use_local": false,
205 "versionless": false
206 },
207 "dependency_type": "conda",
208 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
209 "exact": true,
210 "model_class": "MergedCondaDependency",
211 "name": "flametree",
212 "version": "0.1.11"
213 },
214 {
215 "cacheable": false,
216 "dependency_resolver": {
217 "auto_init": true,
218 "auto_install": true,
219 "can_uninstall_dependencies": true,
220 "ensure_channels": "conda-forge,bioconda",
221 "model_class": "CondaDependencyResolver",
222 "prefix": "/home/rkhaled/miniconda3",
223 "read_only": false,
224 "resolver_type": "conda",
225 "resolves_simple_dependencies": true,
226 "use_local": false,
227 "versionless": false
228 },
229 "dependency_type": "conda",
230 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
231 "exact": true,
232 "model_class": "MergedCondaDependency",
233 "name": "biopython",
234 "version": "1.85"
235 },
236 {
237 "cacheable": false,
238 "dependency_resolver": {
239 "auto_init": true,
240 "auto_install": true,
241 "can_uninstall_dependencies": true,
242 "ensure_channels": "conda-forge,bioconda",
243 "model_class": "CondaDependencyResolver",
244 "prefix": "/home/rkhaled/miniconda3",
245 "read_only": false,
246 "resolver_type": "conda",
247 "resolves_simple_dependencies": true,
248 "use_local": false,
249 "versionless": false
250 },
251 "dependency_type": "conda",
252 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
253 "exact": true,
254 "model_class": "MergedCondaDependency",
255 "name": "proglog",
256 "version": "0.1.10"
257 },
258 {
259 "cacheable": false,
260 "dependency_resolver": {
261 "auto_init": true,
262 "auto_install": true,
263 "can_uninstall_dependencies": true,
264 "ensure_channels": "conda-forge,bioconda",
265 "model_class": "CondaDependencyResolver",
266 "prefix": "/home/rkhaled/miniconda3",
267 "read_only": false,
268 "resolver_type": "conda",
269 "resolves_simple_dependencies": true,
270 "use_local": false,
271 "versionless": false
272 },
273 "dependency_type": "conda",
274 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
275 "exact": true,
276 "model_class": "MergedCondaDependency",
277 "name": "pandas",
278 "version": "2.2.3"
279 },
280 {
281 "cacheable": false,
282 "dependency_resolver": {
283 "auto_init": true,
284 "auto_install": true,
285 "can_uninstall_dependencies": true,
286 "ensure_channels": "conda-forge,bioconda",
287 "model_class": "CondaDependencyResolver",
288 "prefix": "/home/rkhaled/miniconda3",
289 "read_only": false,
290 "resolver_type": "conda",
291 "resolves_simple_dependencies": true,
292 "use_local": false,
293 "versionless": false
294 },
295 "dependency_type": "conda",
296 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
297 "exact": true,
298 "model_class": "MergedCondaDependency",
299 "name": "dnacauldron",
300 "version": "2.0.12"
301 },
302 {
303 "cacheable": false,
304 "dependency_resolver": {
305 "auto_init": true,
306 "auto_install": true,
307 "can_uninstall_dependencies": true,
308 "ensure_channels": "conda-forge,bioconda",
309 "model_class": "CondaDependencyResolver",
310 "prefix": "/home/rkhaled/miniconda3",
311 "read_only": false,
312 "resolver_type": "conda",
313 "resolves_simple_dependencies": true,
314 "use_local": false,
315 "versionless": false
316 },
317 "dependency_type": "conda",
318 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
319 "exact": true,
320 "model_class": "MergedCondaDependency",
321 "name": "pdf-reports",
322 "version": "0.3.9"
323 },
324 {
325 "cacheable": false,
326 "dependency_resolver": {
327 "auto_init": true,
328 "auto_install": true,
329 "can_uninstall_dependencies": true,
330 "ensure_channels": "conda-forge,bioconda",
331 "model_class": "CondaDependencyResolver",
332 "prefix": "/home/rkhaled/miniconda3",
333 "read_only": false,
334 "resolver_type": "conda",
335 "resolves_simple_dependencies": true,
336 "use_local": false,
337 "versionless": false
338 },
339 "dependency_type": "conda",
340 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
341 "exact": true,
342 "model_class": "MergedCondaDependency",
343 "name": "sequenticon",
344 "version": "0.1.8"
345 },
346 {
347 "cacheable": false,
348 "dependency_resolver": {
349 "auto_init": true,
350 "auto_install": true,
351 "can_uninstall_dependencies": true,
352 "ensure_channels": "conda-forge,bioconda",
353 "model_class": "CondaDependencyResolver",
354 "prefix": "/home/rkhaled/miniconda3",
355 "read_only": false,
356 "resolver_type": "conda",
357 "resolves_simple_dependencies": true,
358 "use_local": false,
359 "versionless": false
360 },
361 "dependency_type": "conda",
362 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
363 "exact": true,
364 "model_class": "MergedCondaDependency",
365 "name": "dna_features_viewer",
366 "version": "3.1.5"
367 }
368 ],
369 "exit_code": 0,
370 "external_id": "385227",
371 "galaxy_version": "24.2",
372 "handler": null,
373 "history_id": "48e269c64ce4fce2",
374 "id": "720f24a804e8d612",
375 "inputs": {
376 "assembly_csv": {
377 "id": "d765718fb46383bd",
378 "src": "hda",
379 "uuid": "219d9b1e-e68c-4fb3-bcfe-e77aba638437"
380 },
381 "genbank_files1": {
382 "id": "131ab6d9a01aeed2",
383 "src": "hda",
384 "uuid": "4fb22863-853c-4591-9c42-2bb9c71cf261"
385 }
386 },
387 "job_messages": [],
388 "job_metrics": [],
389 "job_runner_name": null,
390 "job_stderr": "",
391 "job_stdout": "",
392 "model_class": "Job",
393 "output_collections": {
394 "construct_gb": {
395 "id": "b93fb7c1f8bf7b46",
396 "src": "hdca"
397 }
398 },
399 "outputs": {
400 "__new_primary_file_construct_gb|construct_1__": {
401 "id": "140f14a546d19bc0",
402 "src": "hda",
403 "uuid": "00003b46-ce50-481a-9130-0ec3ae3b7897"
404 },
405 "__new_primary_file_construct_gb|construct_2__": {
406 "id": "2582d4726cd2a523",
407 "src": "hda",
408 "uuid": "1ac733ac-a271-491e-bd9e-24d18fff78bd"
409 },
410 "__new_primary_file_construct_gb|construct_3__": {
411 "id": "5e497037d2a37058",
412 "src": "hda",
413 "uuid": "70ddc686-3105-4962-93ca-511e60acfbcd"
414 },
415 "output_zip": {
416 "id": "26116ea06fd8375c",
417 "src": "hda",
418 "uuid": "a64ce795-3e43-4f34-aacf-aee1dd0b1f6e"
419 }
420 },
421 "params": {
422 "__input_ext": "\"input\"",
423 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
424 "assembly_plan_name": "\"GibsonAssembly\"",
425 "chromInfo": "\"/tmp/tmp2jitj5ti/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
426 "dbkey": "\"?\"",
427 "domesticated_input": null,
428 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
429 "topology": "\"circular\""
430 },
431 "state": "ok",
432 "stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.22it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.21it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.48it/s, now=None]\r \r",
433 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
434 "tool_id": "cloning_simulation",
435 "tool_stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]\rassembly: 40%|\u2588\u2588\u2588\u2588 | 2/5 [00:00<00:00, 4.22it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.21it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.48it/s, now=None]\r \r",
436 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
437 "update_time": "2025-06-06T10:05:41.041203",
438 "user_email": "planemo@galaxyproject.org",
439 "user_id": "b685bcc6830b171b"
440 },
441 "status": "success",
442 "test_index": 1,
443 "time_seconds": 23.27797245979309,
444 "tool_id": "cloning_simulation",
445 "tool_version": "0.1.0+galaxy0"
446 },
447 "has_data": true,
448 "id": "cloning_simulation-1"
449 },
450 {
451 "data": {
452 "inputs": {
453 "adv|use_file_names_as_ids": true,
454 "assembly_csv": {
455 "id": "68f713b93b311e6b",
456 "src": "hda"
457 },
458 "assembly_plan_name": "LigaseCyclingReactionAssembly",
459 "genbank_files": {
460 "id": "45bf0c3ad4473005",
461 "src": "hdca"
462 },
463 "topology": "circular"
464 },
465 "job": {
466 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/8/0/6/dataset_806117ae-d7a6-43e7-81c7-334a790a0d5e.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/c/c/e/dataset_cce9d6d4-372b-484c-9bf5-fe28e7899f4d.dat,/tmp/tmp2jitj5ti/files/c/8/e/dataset_c8e6cbdc-d108-4250-a1c5-1e88ee18d6d1.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/c/c/e/dataset_cce9d6d4-372b-484c-9bf5-fe28e7899f4d.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmp2jitj5ti/files/c/8/e/dataset_c8e6cbdc-d108-4250-a1c5-1e88ee18d6d1.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp2jitj5ti/job_working_directory/000/21/outputs/dataset_b7f1e2f4-2ca8-443b-8476-c078a5b5f15f.dat'",
467 "command_version": "",
468 "copied_from_job_id": null,
469 "create_time": "2025-06-06T10:05:53.421889",
470 "dependencies": [
471 {
472 "cacheable": false,
473 "dependency_resolver": {
474 "auto_init": true,
475 "auto_install": true,
476 "can_uninstall_dependencies": true,
477 "ensure_channels": "conda-forge,bioconda",
478 "model_class": "CondaDependencyResolver",
479 "prefix": "/home/rkhaled/miniconda3",
480 "read_only": false,
481 "resolver_type": "conda",
482 "resolves_simple_dependencies": true,
483 "use_local": false,
484 "versionless": false
485 },
486 "dependency_type": "conda",
487 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
488 "exact": true,
489 "model_class": "MergedCondaDependency",
490 "name": "flametree",
491 "version": "0.1.11"
492 },
493 {
494 "cacheable": false,
495 "dependency_resolver": {
496 "auto_init": true,
497 "auto_install": true,
498 "can_uninstall_dependencies": true,
499 "ensure_channels": "conda-forge,bioconda",
500 "model_class": "CondaDependencyResolver",
501 "prefix": "/home/rkhaled/miniconda3",
502 "read_only": false,
503 "resolver_type": "conda",
504 "resolves_simple_dependencies": true,
505 "use_local": false,
506 "versionless": false
507 },
508 "dependency_type": "conda",
509 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
510 "exact": true,
511 "model_class": "MergedCondaDependency",
512 "name": "biopython",
513 "version": "1.85"
514 },
515 {
516 "cacheable": false,
517 "dependency_resolver": {
518 "auto_init": true,
519 "auto_install": true,
520 "can_uninstall_dependencies": true,
521 "ensure_channels": "conda-forge,bioconda",
522 "model_class": "CondaDependencyResolver",
523 "prefix": "/home/rkhaled/miniconda3",
524 "read_only": false,
525 "resolver_type": "conda",
526 "resolves_simple_dependencies": true,
527 "use_local": false,
528 "versionless": false
529 },
530 "dependency_type": "conda",
531 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
532 "exact": true,
533 "model_class": "MergedCondaDependency",
534 "name": "proglog",
535 "version": "0.1.10"
536 },
537 {
538 "cacheable": false,
539 "dependency_resolver": {
540 "auto_init": true,
541 "auto_install": true,
542 "can_uninstall_dependencies": true,
543 "ensure_channels": "conda-forge,bioconda",
544 "model_class": "CondaDependencyResolver",
545 "prefix": "/home/rkhaled/miniconda3",
546 "read_only": false,
547 "resolver_type": "conda",
548 "resolves_simple_dependencies": true,
549 "use_local": false,
550 "versionless": false
551 },
552 "dependency_type": "conda",
553 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
554 "exact": true,
555 "model_class": "MergedCondaDependency",
556 "name": "pandas",
557 "version": "2.2.3"
558 },
559 {
560 "cacheable": false,
561 "dependency_resolver": {
562 "auto_init": true,
563 "auto_install": true,
564 "can_uninstall_dependencies": true,
565 "ensure_channels": "conda-forge,bioconda",
566 "model_class": "CondaDependencyResolver",
567 "prefix": "/home/rkhaled/miniconda3",
568 "read_only": false,
569 "resolver_type": "conda",
570 "resolves_simple_dependencies": true,
571 "use_local": false,
572 "versionless": false
573 },
574 "dependency_type": "conda",
575 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
576 "exact": true,
577 "model_class": "MergedCondaDependency",
578 "name": "dnacauldron",
579 "version": "2.0.12"
580 },
581 {
582 "cacheable": false,
583 "dependency_resolver": {
584 "auto_init": true,
585 "auto_install": true,
586 "can_uninstall_dependencies": true,
587 "ensure_channels": "conda-forge,bioconda",
588 "model_class": "CondaDependencyResolver",
589 "prefix": "/home/rkhaled/miniconda3",
590 "read_only": false,
591 "resolver_type": "conda",
592 "resolves_simple_dependencies": true,
593 "use_local": false,
594 "versionless": false
595 },
596 "dependency_type": "conda",
597 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
598 "exact": true,
599 "model_class": "MergedCondaDependency",
600 "name": "pdf-reports",
601 "version": "0.3.9"
602 },
603 {
604 "cacheable": false,
605 "dependency_resolver": {
606 "auto_init": true,
607 "auto_install": true,
608 "can_uninstall_dependencies": true,
609 "ensure_channels": "conda-forge,bioconda",
610 "model_class": "CondaDependencyResolver",
611 "prefix": "/home/rkhaled/miniconda3",
612 "read_only": false,
613 "resolver_type": "conda",
614 "resolves_simple_dependencies": true,
615 "use_local": false,
616 "versionless": false
617 },
618 "dependency_type": "conda",
619 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
620 "exact": true,
621 "model_class": "MergedCondaDependency",
622 "name": "sequenticon",
623 "version": "0.1.8"
624 },
625 {
626 "cacheable": false,
627 "dependency_resolver": {
628 "auto_init": true,
629 "auto_install": true,
630 "can_uninstall_dependencies": true,
631 "ensure_channels": "conda-forge,bioconda",
632 "model_class": "CondaDependencyResolver",
633 "prefix": "/home/rkhaled/miniconda3",
634 "read_only": false,
635 "resolver_type": "conda",
636 "resolves_simple_dependencies": true,
637 "use_local": false,
638 "versionless": false
639 },
640 "dependency_type": "conda",
641 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
642 "exact": true,
643 "model_class": "MergedCondaDependency",
644 "name": "dna_features_viewer",
645 "version": "3.1.5"
646 }
647 ],
648 "exit_code": 0,
649 "external_id": "385648",
650 "galaxy_version": "24.2",
651 "handler": null,
652 "history_id": "abbe1d9cd04428c7",
653 "id": "26116ea06fd8375c",
654 "inputs": {
655 "assembly_csv": {
656 "id": "68f713b93b311e6b",
657 "src": "hda",
658 "uuid": "806117ae-d7a6-43e7-81c7-334a790a0d5e"
659 },
660 "genbank_files1": {
661 "id": "9573dab05c8aede5",
662 "src": "hda",
663 "uuid": "cce9d6d4-372b-484c-9bf5-fe28e7899f4d"
664 },
665 "genbank_files2": {
666 "id": "9797c20d21b6409b",
667 "src": "hda",
668 "uuid": "c8e6cbdc-d108-4250-a1c5-1e88ee18d6d1"
669 }
670 },
671 "job_messages": [],
672 "job_metrics": [],
673 "job_runner_name": null,
674 "job_stderr": "",
675 "job_stdout": "",
676 "model_class": "Job",
677 "output_collections": {
678 "construct_gb": {
679 "id": "4efa4181abcbfe3f",
680 "src": "hdca"
681 }
682 },
683 "outputs": {
684 "output_zip": {
685 "id": "37fc10922a844411",
686 "src": "hda",
687 "uuid": "b7f1e2f4-2ca8-443b-8476-c078a5b5f15f"
688 }
689 },
690 "params": {
691 "__input_ext": "\"input\"",
692 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
693 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"",
694 "chromInfo": "\"/tmp/tmp2jitj5ti/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
695 "dbkey": "\"?\"",
696 "domesticated_input": null,
697 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}",
698 "topology": "\"circular\""
699 },
700 "state": "ok",
701 "stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.30it/s, now=None]\r \r",
702 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
703 "tool_id": "cloning_simulation",
704 "tool_stderr": "\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/2 [00:00<?, ?it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 2/2 [00:00<00:00, 2.30it/s, now=None]\r \r",
705 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
706 "update_time": "2025-06-06T10:06:05.965130",
707 "user_email": "planemo@galaxyproject.org",
708 "user_id": "b685bcc6830b171b"
709 },
710 "status": "success",
711 "test_index": 2,
712 "time_seconds": 24.72797989845276,
713 "tool_id": "cloning_simulation",
714 "tool_version": "0.1.0+galaxy0"
715 },
716 "has_data": true,
717 "id": "cloning_simulation-2"
718 },
719 {
720 "data": {
721 "inputs": {
722 "adv|use_file_names_as_ids": true,
723 "assembly_csv": {
724 "id": "a8e6431fd79f2b52",
725 "src": "hda"
726 },
727 "assembly_plan_name": "BASICAssembly",
728 "genbank_files": {
729 "id": "beb5db8871971f36",
730 "src": "hdca"
731 },
732 "topology": "circular"
733 },
734 "job": {
735 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/a/8/a/dataset_a8ac250f-f914-442e-b1ba-8cad2b7be6c4.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/7/9/d/dataset_79d3620b-c739-4658-a206-77de935d7c60.dat,/tmp/tmp2jitj5ti/files/4/0/3/dataset_403e3d7a-5c6a-475b-9a3d-3c4472aa6a64.dat,/tmp/tmp2jitj5ti/files/5/2/c/dataset_52c35275-6fd5-4c5a-bf8a-a934f837b172.dat,/tmp/tmp2jitj5ti/files/0/4/d/dataset_04dbf80b-1125-481f-bf1c-ffec452c3c03.dat,/tmp/tmp2jitj5ti/files/2/2/2/dataset_222d6a4a-1e02-463b-8f83-1acac5decea9.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/7/9/d/dataset_79d3620b-c739-4658-a206-77de935d7c60.dat:GFP.gb,/tmp/tmp2jitj5ti/files/4/0/3/dataset_403e3d7a-5c6a-475b-9a3d-3c4472aa6a64.dat:p15A_kan.gb,/tmp/tmp2jitj5ti/files/5/2/c/dataset_52c35275-6fd5-4c5a-bf8a-a934f837b172.dat:promoter.gb,/tmp/tmp2jitj5ti/files/0/4/d/dataset_04dbf80b-1125-481f-bf1c-ffec452c3c03.dat:RFP.gb,/tmp/tmp2jitj5ti/files/2/2/2/dataset_222d6a4a-1e02-463b-8f83-1acac5decea9.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp2jitj5ti/job_working_directory/000/28/outputs/dataset_bd5f0d5e-6a92-4182-b21d-0835394ab658.dat'",
736 "command_version": "",
737 "copied_from_job_id": null,
738 "create_time": "2025-06-06T10:06:28.456243",
739 "dependencies": [
740 {
741 "cacheable": false,
742 "dependency_resolver": {
743 "auto_init": true,
744 "auto_install": true,
745 "can_uninstall_dependencies": true,
746 "ensure_channels": "conda-forge,bioconda",
747 "model_class": "CondaDependencyResolver",
748 "prefix": "/home/rkhaled/miniconda3",
749 "read_only": false,
750 "resolver_type": "conda",
751 "resolves_simple_dependencies": true,
752 "use_local": false,
753 "versionless": false
754 },
755 "dependency_type": "conda",
756 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
757 "exact": true,
758 "model_class": "MergedCondaDependency",
759 "name": "flametree",
760 "version": "0.1.11"
761 },
762 {
763 "cacheable": false,
764 "dependency_resolver": {
765 "auto_init": true,
766 "auto_install": true,
767 "can_uninstall_dependencies": true,
768 "ensure_channels": "conda-forge,bioconda",
769 "model_class": "CondaDependencyResolver",
770 "prefix": "/home/rkhaled/miniconda3",
771 "read_only": false,
772 "resolver_type": "conda",
773 "resolves_simple_dependencies": true,
774 "use_local": false,
775 "versionless": false
776 },
777 "dependency_type": "conda",
778 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
779 "exact": true,
780 "model_class": "MergedCondaDependency",
781 "name": "biopython",
782 "version": "1.85"
783 },
784 {
785 "cacheable": false,
786 "dependency_resolver": {
787 "auto_init": true,
788 "auto_install": true,
789 "can_uninstall_dependencies": true,
790 "ensure_channels": "conda-forge,bioconda",
791 "model_class": "CondaDependencyResolver",
792 "prefix": "/home/rkhaled/miniconda3",
793 "read_only": false,
794 "resolver_type": "conda",
795 "resolves_simple_dependencies": true,
796 "use_local": false,
797 "versionless": false
798 },
799 "dependency_type": "conda",
800 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
801 "exact": true,
802 "model_class": "MergedCondaDependency",
803 "name": "proglog",
804 "version": "0.1.10"
805 },
806 {
807 "cacheable": false,
808 "dependency_resolver": {
809 "auto_init": true,
810 "auto_install": true,
811 "can_uninstall_dependencies": true,
812 "ensure_channels": "conda-forge,bioconda",
813 "model_class": "CondaDependencyResolver",
814 "prefix": "/home/rkhaled/miniconda3",
815 "read_only": false,
816 "resolver_type": "conda",
817 "resolves_simple_dependencies": true,
818 "use_local": false,
819 "versionless": false
820 },
821 "dependency_type": "conda",
822 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
823 "exact": true,
824 "model_class": "MergedCondaDependency",
825 "name": "pandas",
826 "version": "2.2.3"
827 },
828 {
829 "cacheable": false,
830 "dependency_resolver": {
831 "auto_init": true,
832 "auto_install": true,
833 "can_uninstall_dependencies": true,
834 "ensure_channels": "conda-forge,bioconda",
835 "model_class": "CondaDependencyResolver",
836 "prefix": "/home/rkhaled/miniconda3",
837 "read_only": false,
838 "resolver_type": "conda",
839 "resolves_simple_dependencies": true,
840 "use_local": false,
841 "versionless": false
842 },
843 "dependency_type": "conda",
844 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
845 "exact": true,
846 "model_class": "MergedCondaDependency",
847 "name": "dnacauldron",
848 "version": "2.0.12"
849 },
850 {
851 "cacheable": false,
852 "dependency_resolver": {
853 "auto_init": true,
854 "auto_install": true,
855 "can_uninstall_dependencies": true,
856 "ensure_channels": "conda-forge,bioconda",
857 "model_class": "CondaDependencyResolver",
858 "prefix": "/home/rkhaled/miniconda3",
859 "read_only": false,
860 "resolver_type": "conda",
861 "resolves_simple_dependencies": true,
862 "use_local": false,
863 "versionless": false
864 },
865 "dependency_type": "conda",
866 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
867 "exact": true,
868 "model_class": "MergedCondaDependency",
869 "name": "pdf-reports",
870 "version": "0.3.9"
871 },
872 {
873 "cacheable": false,
874 "dependency_resolver": {
875 "auto_init": true,
876 "auto_install": true,
877 "can_uninstall_dependencies": true,
878 "ensure_channels": "conda-forge,bioconda",
879 "model_class": "CondaDependencyResolver",
880 "prefix": "/home/rkhaled/miniconda3",
881 "read_only": false,
882 "resolver_type": "conda",
883 "resolves_simple_dependencies": true,
884 "use_local": false,
885 "versionless": false
886 },
887 "dependency_type": "conda",
888 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
889 "exact": true,
890 "model_class": "MergedCondaDependency",
891 "name": "sequenticon",
892 "version": "0.1.8"
893 },
894 {
895 "cacheable": false,
896 "dependency_resolver": {
897 "auto_init": true,
898 "auto_install": true,
899 "can_uninstall_dependencies": true,
900 "ensure_channels": "conda-forge,bioconda",
901 "model_class": "CondaDependencyResolver",
902 "prefix": "/home/rkhaled/miniconda3",
903 "read_only": false,
904 "resolver_type": "conda",
905 "resolves_simple_dependencies": true,
906 "use_local": false,
907 "versionless": false
908 },
909 "dependency_type": "conda",
910 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
911 "exact": true,
912 "model_class": "MergedCondaDependency",
913 "name": "dna_features_viewer",
914 "version": "3.1.5"
915 }
916 ],
917 "exit_code": 0,
918 "external_id": "386275",
919 "galaxy_version": "24.2",
920 "handler": null,
921 "history_id": "b93fb7c1f8bf7b46",
922 "id": "37fc10922a844411",
923 "inputs": {
924 "assembly_csv": {
925 "id": "a8e6431fd79f2b52",
926 "src": "hda",
927 "uuid": "a8ac250f-f914-442e-b1ba-8cad2b7be6c4"
928 },
929 "genbank_files1": {
930 "id": "a018d9b816e95d65",
931 "src": "hda",
932 "uuid": "79d3620b-c739-4658-a206-77de935d7c60"
933 },
934 "genbank_files2": {
935 "id": "e681bc44c9405e4c",
936 "src": "hda",
937 "uuid": "403e3d7a-5c6a-475b-9a3d-3c4472aa6a64"
938 },
939 "genbank_files3": {
940 "id": "b64509f9b279aeab",
941 "src": "hda",
942 "uuid": "52c35275-6fd5-4c5a-bf8a-a934f837b172"
943 },
944 "genbank_files4": {
945 "id": "0cded9ae6d76e247",
946 "src": "hda",
947 "uuid": "04dbf80b-1125-481f-bf1c-ffec452c3c03"
948 },
949 "genbank_files5": {
950 "id": "e7ab3f008685294c",
951 "src": "hda",
952 "uuid": "222d6a4a-1e02-463b-8f83-1acac5decea9"
953 }
954 },
955 "job_messages": [],
956 "job_metrics": [],
957 "job_runner_name": null,
958 "job_stderr": "",
959 "job_stdout": "",
960 "model_class": "Job",
961 "output_collections": {
962 "construct_gb": {
963 "id": "bc095eef87c18a70",
964 "src": "hdca"
965 }
966 },
967 "outputs": {
968 "output_zip": {
969 "id": "d2ea46ccc79974d1",
970 "src": "hda",
971 "uuid": "bd5f0d5e-6a92-4182-b21d-0835394ab658"
972 }
973 },
974 "params": {
975 "__input_ext": "\"input\"",
976 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
977 "assembly_plan_name": "\"BASICAssembly\"",
978 "chromInfo": "\"/tmp/tmp2jitj5ti/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
979 "dbkey": "\"?\"",
980 "domesticated_input": null,
981 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}",
982 "topology": "\"circular\""
983 },
984 "state": "ok",
985 "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 47.57it/s, now=None]\r \r",
986 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
987 "tool_id": "cloning_simulation",
988 "tool_stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 47.57it/s, now=None]\r \r",
989 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
990 "update_time": "2025-06-06T10:06:39.681856",
991 "user_email": "planemo@galaxyproject.org",
992 "user_id": "b685bcc6830b171b"
993 },
994 "status": "success",
995 "test_index": 3,
996 "time_seconds": 33.660860538482666,
997 "tool_id": "cloning_simulation",
998 "tool_version": "0.1.0+galaxy0"
999 },
1000 "has_data": true,
1001 "id": "cloning_simulation-3"
1002 },
1003 {
1004 "data": {
1005 "inputs": {
1006 "adv|use_file_names_as_ids": true,
1007 "assembly_csv": {
1008 "id": "870b7dd1dbdb30fc",
1009 "src": "hda"
1010 },
1011 "assembly_plan_name": "BioBrickStandardAssembly",
1012 "genbank_files": {
1013 "id": "9f6ba43f26fd6d3f",
1014 "src": "hdca"
1015 },
1016 "topology": "circular"
1017 },
1018 "job": {
1019 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/2/d/8/dataset_2d854388-fb71-4200-9b83-2ce86dc98358.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/5/7/3/dataset_57391f80-f9db-4df5-b819-da6d762aece4.dat,/tmp/tmp2jitj5ti/files/3/d/f/dataset_3df8cee0-18b2-40ae-9075-7f585f82e90e.dat,/tmp/tmp2jitj5ti/files/4/3/2/dataset_4322df44-7abe-4c76-9d5f-2c19d97a9117.dat,/tmp/tmp2jitj5ti/files/6/7/1/dataset_67150b86-6b40-4e07-9809-31e5e59ab2f5.dat,/tmp/tmp2jitj5ti/files/4/2/1/dataset_421ffb55-adfd-4e9b-a5cc-8144862c99e4.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/5/7/3/dataset_57391f80-f9db-4df5-b819-da6d762aece4.dat:BBa_E0040_GFP.gb,/tmp/tmp2jitj5ti/files/3/d/f/dataset_3df8cee0-18b2-40ae-9075-7f585f82e90e.dat:BBa_J23119_prom.gb,/tmp/tmp2jitj5ti/files/4/3/2/dataset_4322df44-7abe-4c76-9d5f-2c19d97a9117.dat:BBa_J23119_prom_flawed.gb,/tmp/tmp2jitj5ti/files/6/7/1/dataset_67150b86-6b40-4e07-9809-31e5e59ab2f5.dat:BBa_J61048_term.gb,/tmp/tmp2jitj5ti/files/4/2/1/dataset_421ffb55-adfd-4e9b-a5cc-8144862c99e4.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp2jitj5ti/job_working_directory/000/35/outputs/dataset_7b0034ef-60d7-4a10-b78c-75301b71c879.dat'",
1020 "command_version": "",
1021 "copied_from_job_id": null,
1022 "create_time": "2025-06-06T10:07:01.286437",
1023 "dependencies": [
1024 {
1025 "cacheable": false,
1026 "dependency_resolver": {
1027 "auto_init": true,
1028 "auto_install": true,
1029 "can_uninstall_dependencies": true,
1030 "ensure_channels": "conda-forge,bioconda",
1031 "model_class": "CondaDependencyResolver",
1032 "prefix": "/home/rkhaled/miniconda3",
1033 "read_only": false,
1034 "resolver_type": "conda",
1035 "resolves_simple_dependencies": true,
1036 "use_local": false,
1037 "versionless": false
1038 },
1039 "dependency_type": "conda",
1040 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1041 "exact": true,
1042 "model_class": "MergedCondaDependency",
1043 "name": "flametree",
1044 "version": "0.1.11"
1045 },
1046 {
1047 "cacheable": false,
1048 "dependency_resolver": {
1049 "auto_init": true,
1050 "auto_install": true,
1051 "can_uninstall_dependencies": true,
1052 "ensure_channels": "conda-forge,bioconda",
1053 "model_class": "CondaDependencyResolver",
1054 "prefix": "/home/rkhaled/miniconda3",
1055 "read_only": false,
1056 "resolver_type": "conda",
1057 "resolves_simple_dependencies": true,
1058 "use_local": false,
1059 "versionless": false
1060 },
1061 "dependency_type": "conda",
1062 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1063 "exact": true,
1064 "model_class": "MergedCondaDependency",
1065 "name": "biopython",
1066 "version": "1.85"
1067 },
1068 {
1069 "cacheable": false,
1070 "dependency_resolver": {
1071 "auto_init": true,
1072 "auto_install": true,
1073 "can_uninstall_dependencies": true,
1074 "ensure_channels": "conda-forge,bioconda",
1075 "model_class": "CondaDependencyResolver",
1076 "prefix": "/home/rkhaled/miniconda3",
1077 "read_only": false,
1078 "resolver_type": "conda",
1079 "resolves_simple_dependencies": true,
1080 "use_local": false,
1081 "versionless": false
1082 },
1083 "dependency_type": "conda",
1084 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1085 "exact": true,
1086 "model_class": "MergedCondaDependency",
1087 "name": "proglog",
1088 "version": "0.1.10"
1089 },
1090 {
1091 "cacheable": false,
1092 "dependency_resolver": {
1093 "auto_init": true,
1094 "auto_install": true,
1095 "can_uninstall_dependencies": true,
1096 "ensure_channels": "conda-forge,bioconda",
1097 "model_class": "CondaDependencyResolver",
1098 "prefix": "/home/rkhaled/miniconda3",
1099 "read_only": false,
1100 "resolver_type": "conda",
1101 "resolves_simple_dependencies": true,
1102 "use_local": false,
1103 "versionless": false
1104 },
1105 "dependency_type": "conda",
1106 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1107 "exact": true,
1108 "model_class": "MergedCondaDependency",
1109 "name": "pandas",
1110 "version": "2.2.3"
1111 },
1112 {
1113 "cacheable": false,
1114 "dependency_resolver": {
1115 "auto_init": true,
1116 "auto_install": true,
1117 "can_uninstall_dependencies": true,
1118 "ensure_channels": "conda-forge,bioconda",
1119 "model_class": "CondaDependencyResolver",
1120 "prefix": "/home/rkhaled/miniconda3",
1121 "read_only": false,
1122 "resolver_type": "conda",
1123 "resolves_simple_dependencies": true,
1124 "use_local": false,
1125 "versionless": false
1126 },
1127 "dependency_type": "conda",
1128 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1129 "exact": true,
1130 "model_class": "MergedCondaDependency",
1131 "name": "dnacauldron",
1132 "version": "2.0.12"
1133 },
1134 {
1135 "cacheable": false,
1136 "dependency_resolver": {
1137 "auto_init": true,
1138 "auto_install": true,
1139 "can_uninstall_dependencies": true,
1140 "ensure_channels": "conda-forge,bioconda",
1141 "model_class": "CondaDependencyResolver",
1142 "prefix": "/home/rkhaled/miniconda3",
1143 "read_only": false,
1144 "resolver_type": "conda",
1145 "resolves_simple_dependencies": true,
1146 "use_local": false,
1147 "versionless": false
1148 },
1149 "dependency_type": "conda",
1150 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1151 "exact": true,
1152 "model_class": "MergedCondaDependency",
1153 "name": "pdf-reports",
1154 "version": "0.3.9"
1155 },
1156 {
1157 "cacheable": false,
1158 "dependency_resolver": {
1159 "auto_init": true,
1160 "auto_install": true,
1161 "can_uninstall_dependencies": true,
1162 "ensure_channels": "conda-forge,bioconda",
1163 "model_class": "CondaDependencyResolver",
1164 "prefix": "/home/rkhaled/miniconda3",
1165 "read_only": false,
1166 "resolver_type": "conda",
1167 "resolves_simple_dependencies": true,
1168 "use_local": false,
1169 "versionless": false
1170 },
1171 "dependency_type": "conda",
1172 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1173 "exact": true,
1174 "model_class": "MergedCondaDependency",
1175 "name": "sequenticon",
1176 "version": "0.1.8"
1177 },
1178 {
1179 "cacheable": false,
1180 "dependency_resolver": {
1181 "auto_init": true,
1182 "auto_install": true,
1183 "can_uninstall_dependencies": true,
1184 "ensure_channels": "conda-forge,bioconda",
1185 "model_class": "CondaDependencyResolver",
1186 "prefix": "/home/rkhaled/miniconda3",
1187 "read_only": false,
1188 "resolver_type": "conda",
1189 "resolves_simple_dependencies": true,
1190 "use_local": false,
1191 "versionless": false
1192 },
1193 "dependency_type": "conda",
1194 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1195 "exact": true,
1196 "model_class": "MergedCondaDependency",
1197 "name": "dna_features_viewer",
1198 "version": "3.1.5"
1199 }
1200 ],
1201 "exit_code": 0,
1202 "external_id": "386883",
1203 "galaxy_version": "24.2",
1204 "handler": null,
1205 "history_id": "45bf0c3ad4473005",
1206 "id": "d2ea46ccc79974d1",
1207 "inputs": {
1208 "assembly_csv": {
1209 "id": "870b7dd1dbdb30fc",
1210 "src": "hda",
1211 "uuid": "2d854388-fb71-4200-9b83-2ce86dc98358"
1212 },
1213 "genbank_files1": {
1214 "id": "5d242fab331df92f",
1215 "src": "hda",
1216 "uuid": "57391f80-f9db-4df5-b819-da6d762aece4"
1217 },
1218 "genbank_files2": {
1219 "id": "bdeadb8314ea6602",
1220 "src": "hda",
1221 "uuid": "3df8cee0-18b2-40ae-9075-7f585f82e90e"
1222 },
1223 "genbank_files3": {
1224 "id": "4b1f0f6cb8a7a593",
1225 "src": "hda",
1226 "uuid": "4322df44-7abe-4c76-9d5f-2c19d97a9117"
1227 },
1228 "genbank_files4": {
1229 "id": "1cbd0a844497b2d5",
1230 "src": "hda",
1231 "uuid": "67150b86-6b40-4e07-9809-31e5e59ab2f5"
1232 },
1233 "genbank_files5": {
1234 "id": "cd6794c2fc579376",
1235 "src": "hda",
1236 "uuid": "421ffb55-adfd-4e9b-a5cc-8144862c99e4"
1237 }
1238 },
1239 "job_messages": [],
1240 "job_metrics": [],
1241 "job_runner_name": null,
1242 "job_stderr": "",
1243 "job_stdout": "",
1244 "model_class": "Job",
1245 "output_collections": {
1246 "construct_gb": {
1247 "id": "07723b52981231a1",
1248 "src": "hdca"
1249 }
1250 },
1251 "outputs": {
1252 "__new_primary_file_construct_gb|C1_prom_barcode__": {
1253 "id": "a3d311637d661498",
1254 "src": "hda",
1255 "uuid": "32cddc11-8c27-4a46-86da-29c2a2b43b49"
1256 },
1257 "__new_primary_file_construct_gb|C2_gfp_term__": {
1258 "id": "c9508541650f65fa",
1259 "src": "hda",
1260 "uuid": "b8457751-97a9-4b80-8ce4-987e02aadef4"
1261 },
1262 "__new_primary_file_construct_gb|C3_final__": {
1263 "id": "2dd6c8d9ce5577ac",
1264 "src": "hda",
1265 "uuid": "467a54f1-7fa8-48d3-b4f9-253d52e75241"
1266 },
1267 "output_zip": {
1268 "id": "59f530fda97252d9",
1269 "src": "hda",
1270 "uuid": "7b0034ef-60d7-4a10-b78c-75301b71c879"
1271 }
1272 },
1273 "params": {
1274 "__input_ext": "\"input\"",
1275 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1276 "assembly_plan_name": "\"BioBrickStandardAssembly\"",
1277 "chromInfo": "\"/tmp/tmp2jitj5ti/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1278 "dbkey": "\"?\"",
1279 "domesticated_input": null,
1280 "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}",
1281 "topology": "\"circular\""
1282 },
1283 "state": "ok",
1284 "stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.86it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.53it/s, now=None]\r \r",
1285 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
1286 "tool_id": "cloning_simulation",
1287 "tool_stderr": "\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/3 [00:00<?, ?it/s, now=None]\rassembly: 67%|\u2588\u2588\u2588\u2588\u2588\u2588\u258b | 2/3 [00:01<00:00, 1.86it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.53it/s, now=None]\r \r",
1288 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
1289 "update_time": "2025-06-06T10:07:15.132596",
1290 "user_email": "planemo@galaxyproject.org",
1291 "user_id": "b685bcc6830b171b"
1292 },
1293 "status": "success",
1294 "test_index": 4,
1295 "time_seconds": 35.4639618396759,
1296 "tool_id": "cloning_simulation",
1297 "tool_version": "0.1.0+galaxy0"
1298 },
1299 "has_data": true,
1300 "id": "cloning_simulation-4"
1301 },
1302 {
1303 "data": {
1304 "inputs": {
1305 "adv|use_file_names_as_ids": true,
1306 "assembly_csv": {
1307 "id": "b6eaafbbca788aef",
1308 "src": "hda"
1309 },
1310 "assembly_plan_name": "Type2sRestrictionAssembly",
1311 "domesticated_input": {
1312 "id": "830f955cbdf9a561",
1313 "src": "hdca"
1314 },
1315 "genbank_files": {
1316 "id": "71dab170b139725e",
1317 "src": "hdca"
1318 },
1319 "topology": "circular"
1320 },
1321 "job": {
1322 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/9/d/9/dataset_9d9d9de0-0ef0-45b2-a122-cf3a6b4ad650.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/8/3/7/dataset_837c1c85-f287-41c8-9851-10dfb88a9fce.dat,/tmp/tmp2jitj5ti/files/0/9/8/dataset_098eeccf-1536-4ae9-b4ab-e0dfb2b8d0ea.dat,/tmp/tmp2jitj5ti/files/9/6/0/dataset_9607dfc5-cbbf-4445-b2f0-ad0e6b29415c.dat,/tmp/tmp2jitj5ti/files/d/3/3/dataset_d337288e-d007-49d9-a3f0-5ddc75b8c1a7.dat,/tmp/tmp2jitj5ti/files/3/f/0/dataset_3f0b935c-0a99-4d65-9f9e-67077025d92d.dat,/tmp/tmp2jitj5ti/files/5/5/e/dataset_55e788cd-b786-481d-81b3-366b2ca66346.dat,/tmp/tmp2jitj5ti/files/b/2/7/dataset_b275d8fc-8961-49f8-9829-8afe0fb272f6.dat' --domesticated_seq '/tmp/tmp2jitj5ti/files/5/3/a/dataset_53aaa086-f9d0-4702-9104-e1129b9478f5.dat,/tmp/tmp2jitj5ti/files/9/8/3/dataset_98347337-70cf-49bc-a520-7ce28dba7552.dat,/tmp/tmp2jitj5ti/files/4/5/f/dataset_45f979d2-11d9-4eed-81cd-775c9592d31a.dat,/tmp/tmp2jitj5ti/files/3/b/0/dataset_3b0d27f7-3a16-4662-b26b-8fbef1641a3b.dat,/tmp/tmp2jitj5ti/files/0/f/3/dataset_0f35d30e-174f-4177-8881-a8d0e2e56e97.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/8/3/7/dataset_837c1c85-f287-41c8-9851-10dfb88a9fce.dat:part_A.gb,/tmp/tmp2jitj5ti/files/0/9/8/dataset_098eeccf-1536-4ae9-b4ab-e0dfb2b8d0ea.dat:part_B.gb,/tmp/tmp2jitj5ti/files/9/6/0/dataset_9607dfc5-cbbf-4445-b2f0-ad0e6b29415c.dat:part_C.gb,/tmp/tmp2jitj5ti/files/d/3/3/dataset_d337288e-d007-49d9-a3f0-5ddc75b8c1a7.dat:part_D.gb,/tmp/tmp2jitj5ti/files/3/f/0/dataset_3f0b935c-0a99-4d65-9f9e-67077025d92d.dat:part_E.gb,/tmp/tmp2jitj5ti/files/5/5/e/dataset_55e788cd-b786-481d-81b3-366b2ca66346.dat:part_F.gb,/tmp/tmp2jitj5ti/files/b/2/7/dataset_b275d8fc-8961-49f8-9829-8afe0fb272f6.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmp2jitj5ti/files/5/3/a/dataset_53aaa086-f9d0-4702-9104-e1129b9478f5.dat:part_H.gb,/tmp/tmp2jitj5ti/files/9/8/3/dataset_98347337-70cf-49bc-a520-7ce28dba7552.dat:part_I.gb,/tmp/tmp2jitj5ti/files/4/5/f/dataset_45f979d2-11d9-4eed-81cd-775c9592d31a.dat:part_J.gb,/tmp/tmp2jitj5ti/files/3/b/0/dataset_3b0d27f7-3a16-4662-b26b-8fbef1641a3b.dat:part_K.gb,/tmp/tmp2jitj5ti/files/0/f/3/dataset_0f35d30e-174f-4177-8881-a8d0e2e56e97.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp2jitj5ti/job_working_directory/000/49/outputs/dataset_d76108d3-5679-4105-8d35-0311a40cc2bb.dat'",
1323 "command_version": "",
1324 "copied_from_job_id": null,
1325 "create_time": "2025-06-06T10:07:58.337850",
1326 "dependencies": [
1327 {
1328 "cacheable": false,
1329 "dependency_resolver": {
1330 "auto_init": true,
1331 "auto_install": true,
1332 "can_uninstall_dependencies": true,
1333 "ensure_channels": "conda-forge,bioconda",
1334 "model_class": "CondaDependencyResolver",
1335 "prefix": "/home/rkhaled/miniconda3",
1336 "read_only": false,
1337 "resolver_type": "conda",
1338 "resolves_simple_dependencies": true,
1339 "use_local": false,
1340 "versionless": false
1341 },
1342 "dependency_type": "conda",
1343 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1344 "exact": true,
1345 "model_class": "MergedCondaDependency",
1346 "name": "flametree",
1347 "version": "0.1.11"
1348 },
1349 {
1350 "cacheable": false,
1351 "dependency_resolver": {
1352 "auto_init": true,
1353 "auto_install": true,
1354 "can_uninstall_dependencies": true,
1355 "ensure_channels": "conda-forge,bioconda",
1356 "model_class": "CondaDependencyResolver",
1357 "prefix": "/home/rkhaled/miniconda3",
1358 "read_only": false,
1359 "resolver_type": "conda",
1360 "resolves_simple_dependencies": true,
1361 "use_local": false,
1362 "versionless": false
1363 },
1364 "dependency_type": "conda",
1365 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1366 "exact": true,
1367 "model_class": "MergedCondaDependency",
1368 "name": "biopython",
1369 "version": "1.85"
1370 },
1371 {
1372 "cacheable": false,
1373 "dependency_resolver": {
1374 "auto_init": true,
1375 "auto_install": true,
1376 "can_uninstall_dependencies": true,
1377 "ensure_channels": "conda-forge,bioconda",
1378 "model_class": "CondaDependencyResolver",
1379 "prefix": "/home/rkhaled/miniconda3",
1380 "read_only": false,
1381 "resolver_type": "conda",
1382 "resolves_simple_dependencies": true,
1383 "use_local": false,
1384 "versionless": false
1385 },
1386 "dependency_type": "conda",
1387 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1388 "exact": true,
1389 "model_class": "MergedCondaDependency",
1390 "name": "proglog",
1391 "version": "0.1.10"
1392 },
1393 {
1394 "cacheable": false,
1395 "dependency_resolver": {
1396 "auto_init": true,
1397 "auto_install": true,
1398 "can_uninstall_dependencies": true,
1399 "ensure_channels": "conda-forge,bioconda",
1400 "model_class": "CondaDependencyResolver",
1401 "prefix": "/home/rkhaled/miniconda3",
1402 "read_only": false,
1403 "resolver_type": "conda",
1404 "resolves_simple_dependencies": true,
1405 "use_local": false,
1406 "versionless": false
1407 },
1408 "dependency_type": "conda",
1409 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1410 "exact": true,
1411 "model_class": "MergedCondaDependency",
1412 "name": "pandas",
1413 "version": "2.2.3"
1414 },
1415 {
1416 "cacheable": false,
1417 "dependency_resolver": {
1418 "auto_init": true,
1419 "auto_install": true,
1420 "can_uninstall_dependencies": true,
1421 "ensure_channels": "conda-forge,bioconda",
1422 "model_class": "CondaDependencyResolver",
1423 "prefix": "/home/rkhaled/miniconda3",
1424 "read_only": false,
1425 "resolver_type": "conda",
1426 "resolves_simple_dependencies": true,
1427 "use_local": false,
1428 "versionless": false
1429 },
1430 "dependency_type": "conda",
1431 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1432 "exact": true,
1433 "model_class": "MergedCondaDependency",
1434 "name": "dnacauldron",
1435 "version": "2.0.12"
1436 },
1437 {
1438 "cacheable": false,
1439 "dependency_resolver": {
1440 "auto_init": true,
1441 "auto_install": true,
1442 "can_uninstall_dependencies": true,
1443 "ensure_channels": "conda-forge,bioconda",
1444 "model_class": "CondaDependencyResolver",
1445 "prefix": "/home/rkhaled/miniconda3",
1446 "read_only": false,
1447 "resolver_type": "conda",
1448 "resolves_simple_dependencies": true,
1449 "use_local": false,
1450 "versionless": false
1451 },
1452 "dependency_type": "conda",
1453 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1454 "exact": true,
1455 "model_class": "MergedCondaDependency",
1456 "name": "pdf-reports",
1457 "version": "0.3.9"
1458 },
1459 {
1460 "cacheable": false,
1461 "dependency_resolver": {
1462 "auto_init": true,
1463 "auto_install": true,
1464 "can_uninstall_dependencies": true,
1465 "ensure_channels": "conda-forge,bioconda",
1466 "model_class": "CondaDependencyResolver",
1467 "prefix": "/home/rkhaled/miniconda3",
1468 "read_only": false,
1469 "resolver_type": "conda",
1470 "resolves_simple_dependencies": true,
1471 "use_local": false,
1472 "versionless": false
1473 },
1474 "dependency_type": "conda",
1475 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1476 "exact": true,
1477 "model_class": "MergedCondaDependency",
1478 "name": "sequenticon",
1479 "version": "0.1.8"
1480 },
1481 {
1482 "cacheable": false,
1483 "dependency_resolver": {
1484 "auto_init": true,
1485 "auto_install": true,
1486 "can_uninstall_dependencies": true,
1487 "ensure_channels": "conda-forge,bioconda",
1488 "model_class": "CondaDependencyResolver",
1489 "prefix": "/home/rkhaled/miniconda3",
1490 "read_only": false,
1491 "resolver_type": "conda",
1492 "resolves_simple_dependencies": true,
1493 "use_local": false,
1494 "versionless": false
1495 },
1496 "dependency_type": "conda",
1497 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1498 "exact": true,
1499 "model_class": "MergedCondaDependency",
1500 "name": "dna_features_viewer",
1501 "version": "3.1.5"
1502 }
1503 ],
1504 "exit_code": 0,
1505 "external_id": "388721",
1506 "galaxy_version": "24.2",
1507 "handler": null,
1508 "history_id": "4efa4181abcbfe3f",
1509 "id": "247764bf93430d44",
1510 "inputs": {
1511 "assembly_csv": {
1512 "id": "b6eaafbbca788aef",
1513 "src": "hda",
1514 "uuid": "9d9d9de0-0ef0-45b2-a122-cf3a6b4ad650"
1515 },
1516 "domesticated_input1": {
1517 "id": "a1189164982cb43d",
1518 "src": "hda",
1519 "uuid": "53aaa086-f9d0-4702-9104-e1129b9478f5"
1520 },
1521 "domesticated_input2": {
1522 "id": "44989d335db736e0",
1523 "src": "hda",
1524 "uuid": "98347337-70cf-49bc-a520-7ce28dba7552"
1525 },
1526 "domesticated_input3": {
1527 "id": "03cca6cadcbcac8e",
1528 "src": "hda",
1529 "uuid": "45f979d2-11d9-4eed-81cd-775c9592d31a"
1530 },
1531 "domesticated_input4": {
1532 "id": "d642fe61dbbb1956",
1533 "src": "hda",
1534 "uuid": "3b0d27f7-3a16-4662-b26b-8fbef1641a3b"
1535 },
1536 "domesticated_input5": {
1537 "id": "0db781d633f10d33",
1538 "src": "hda",
1539 "uuid": "0f35d30e-174f-4177-8881-a8d0e2e56e97"
1540 },
1541 "genbank_files1": {
1542 "id": "cf3cf117b1fd29b8",
1543 "src": "hda",
1544 "uuid": "837c1c85-f287-41c8-9851-10dfb88a9fce"
1545 },
1546 "genbank_files2": {
1547 "id": "d4b38da3c0d76cb5",
1548 "src": "hda",
1549 "uuid": "098eeccf-1536-4ae9-b4ab-e0dfb2b8d0ea"
1550 },
1551 "genbank_files3": {
1552 "id": "2ca78c9590a534f7",
1553 "src": "hda",
1554 "uuid": "9607dfc5-cbbf-4445-b2f0-ad0e6b29415c"
1555 },
1556 "genbank_files4": {
1557 "id": "247764bf93430d44",
1558 "src": "hda",
1559 "uuid": "d337288e-d007-49d9-a3f0-5ddc75b8c1a7"
1560 },
1561 "genbank_files5": {
1562 "id": "463014d955d5fd42",
1563 "src": "hda",
1564 "uuid": "3f0b935c-0a99-4d65-9f9e-67077025d92d"
1565 },
1566 "genbank_files6": {
1567 "id": "a4df66e73e6d9e95",
1568 "src": "hda",
1569 "uuid": "55e788cd-b786-481d-81b3-366b2ca66346"
1570 },
1571 "genbank_files7": {
1572 "id": "913dff628ac44951",
1573 "src": "hda",
1574 "uuid": "b275d8fc-8961-49f8-9829-8afe0fb272f6"
1575 }
1576 },
1577 "job_messages": [],
1578 "job_metrics": [],
1579 "job_runner_name": null,
1580 "job_stderr": "",
1581 "job_stdout": "",
1582 "model_class": "Job",
1583 "output_collections": {
1584 "construct_gb": {
1585 "id": "5251f3a41a1cbe5c",
1586 "src": "hdca"
1587 }
1588 },
1589 "outputs": {
1590 "__new_primary_file_construct_gb|construct_1__": {
1591 "id": "a392596aa79c7e90",
1592 "src": "hda",
1593 "uuid": "5b1744ae-2358-4704-963c-ae095d2865b9"
1594 },
1595 "__new_primary_file_construct_gb|construct_2__": {
1596 "id": "f3fa25c91edfe6df",
1597 "src": "hda",
1598 "uuid": "b1f5b359-a374-4545-bb66-c00344cfca68"
1599 },
1600 "__new_primary_file_construct_gb|construct_3__": {
1601 "id": "706ccd94442462f8",
1602 "src": "hda",
1603 "uuid": "691b1282-afae-46f8-8741-4314f28c3613"
1604 },
1605 "__new_primary_file_construct_gb|construct_4__": {
1606 "id": "ebae0af133eaa0bc",
1607 "src": "hda",
1608 "uuid": "48ad1713-0702-4178-81bd-20cb2d09349e"
1609 },
1610 "output_zip": {
1611 "id": "d0372853ed459b21",
1612 "src": "hda",
1613 "uuid": "d76108d3-5679-4105-8d35-0311a40cc2bb"
1614 }
1615 },
1616 "params": {
1617 "__input_ext": "\"input\"",
1618 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1619 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
1620 "chromInfo": "\"/tmp/tmp2jitj5ti/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1621 "dbkey": "\"?\"",
1622 "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}",
1623 "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}",
1624 "topology": "\"circular\""
1625 },
1626 "state": "ok",
1627 "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.75it/s, now=None]\r \r",
1628 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
1629 "tool_id": "cloning_simulation",
1630 "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.75it/s, now=None]\r \r",
1631 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
1632 "update_time": "2025-06-06T10:08:11.535478",
1633 "user_email": "planemo@galaxyproject.org",
1634 "user_id": "b685bcc6830b171b"
1635 },
1636 "status": "success",
1637 "test_index": 5,
1638 "time_seconds": 56.084434032440186,
1639 "tool_id": "cloning_simulation",
1640 "tool_version": "0.1.0+galaxy0"
1641 },
1642 "has_data": true,
1643 "id": "cloning_simulation-5"
1644 },
1645 {
1646 "data": {
1647 "inputs": {
1648 "adv|use_file_names_as_ids": true,
1649 "assembly_csv": {
1650 "id": "85e42f4d247fa0dd",
1651 "src": "hda"
1652 },
1653 "assembly_plan_name": "Type2sRestrictionAssembly",
1654 "domesticated_input": {
1655 "id": "382e0b9a3dd586fb",
1656 "src": "hdca"
1657 },
1658 "topology": "circular"
1659 },
1660 "job": {
1661 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp2jitj5ti/files/4/f/5/dataset_4f53254a-8cbc-44ed-b07f-51c7b0ba70bf.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp2jitj5ti/files/0/3/4/dataset_03437b47-00b6-420f-a71d-dc13cfa4420f.dat,/tmp/tmp2jitj5ti/files/7/3/0/dataset_7302922c-3802-4ec1-8fa6-2aeda8c3f773.dat,/tmp/tmp2jitj5ti/files/4/3/f/dataset_43f8a937-90f1-4ca8-9e1e-ffd4d438b8e3.dat,/tmp/tmp2jitj5ti/files/2/d/a/dataset_2da8d496-7007-408f-8f0d-9bb1bfc6cc89.dat,/tmp/tmp2jitj5ti/files/7/7/e/dataset_77e28f02-e173-4f1b-aa95-ab810151814c.dat,/tmp/tmp2jitj5ti/files/1/d/b/dataset_1db54aac-485c-43e5-b88e-78727df8f24d.dat,/tmp/tmp2jitj5ti/files/e/6/c/dataset_e6c10e1b-4881-49ef-b382-70333c02a312.dat,/tmp/tmp2jitj5ti/files/2/a/7/dataset_2a714c72-017a-4719-b5f6-7258096c4db6.dat,/tmp/tmp2jitj5ti/files/f/5/6/dataset_f56927c8-9d8a-44fc-a5b3-7929dfc14349.dat,/tmp/tmp2jitj5ti/files/7/9/0/dataset_7902eea5-11c6-4d21-950e-e4f1217a3efb.dat,/tmp/tmp2jitj5ti/files/4/9/3/dataset_493c970b-5c95-4af6-afb2-091bbfcad2fb.dat,/tmp/tmp2jitj5ti/files/3/2/a/dataset_32ae37e3-7d24-411c-8633-c253860693e3.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp2jitj5ti/files/0/3/4/dataset_03437b47-00b6-420f-a71d-dc13cfa4420f.dat:part_A.gb,/tmp/tmp2jitj5ti/files/7/3/0/dataset_7302922c-3802-4ec1-8fa6-2aeda8c3f773.dat:part_B.gb,/tmp/tmp2jitj5ti/files/4/3/f/dataset_43f8a937-90f1-4ca8-9e1e-ffd4d438b8e3.dat:part_C.gb,/tmp/tmp2jitj5ti/files/2/d/a/dataset_2da8d496-7007-408f-8f0d-9bb1bfc6cc89.dat:part_D.gb,/tmp/tmp2jitj5ti/files/7/7/e/dataset_77e28f02-e173-4f1b-aa95-ab810151814c.dat:part_E.gb,/tmp/tmp2jitj5ti/files/1/d/b/dataset_1db54aac-485c-43e5-b88e-78727df8f24d.dat:part_F.gb,/tmp/tmp2jitj5ti/files/e/6/c/dataset_e6c10e1b-4881-49ef-b382-70333c02a312.dat:part_G.gb,/tmp/tmp2jitj5ti/files/2/a/7/dataset_2a714c72-017a-4719-b5f6-7258096c4db6.dat:part_H.gb,/tmp/tmp2jitj5ti/files/f/5/6/dataset_f56927c8-9d8a-44fc-a5b3-7929dfc14349.dat:part_I.gb,/tmp/tmp2jitj5ti/files/7/9/0/dataset_7902eea5-11c6-4d21-950e-e4f1217a3efb.dat:part_J.gb,/tmp/tmp2jitj5ti/files/4/9/3/dataset_493c970b-5c95-4af6-afb2-091bbfcad2fb.dat:part_K.gb,/tmp/tmp2jitj5ti/files/3/2/a/dataset_32ae37e3-7d24-411c-8633-c253860693e3.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular' && cp 'output_zip.zip' '/tmp/tmp2jitj5ti/job_working_directory/000/63/outputs/dataset_0d841edc-5cb0-451d-807c-1e38179edf75.dat'",
1662 "command_version": "",
1663 "copied_from_job_id": null,
1664 "create_time": "2025-06-06T10:08:55.121816",
1665 "dependencies": [
1666 {
1667 "cacheable": false,
1668 "dependency_resolver": {
1669 "auto_init": true,
1670 "auto_install": true,
1671 "can_uninstall_dependencies": true,
1672 "ensure_channels": "conda-forge,bioconda",
1673 "model_class": "CondaDependencyResolver",
1674 "prefix": "/home/rkhaled/miniconda3",
1675 "read_only": false,
1676 "resolver_type": "conda",
1677 "resolves_simple_dependencies": true,
1678 "use_local": false,
1679 "versionless": false
1680 },
1681 "dependency_type": "conda",
1682 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1683 "exact": true,
1684 "model_class": "MergedCondaDependency",
1685 "name": "flametree",
1686 "version": "0.1.11"
1687 },
1688 {
1689 "cacheable": false,
1690 "dependency_resolver": {
1691 "auto_init": true,
1692 "auto_install": true,
1693 "can_uninstall_dependencies": true,
1694 "ensure_channels": "conda-forge,bioconda",
1695 "model_class": "CondaDependencyResolver",
1696 "prefix": "/home/rkhaled/miniconda3",
1697 "read_only": false,
1698 "resolver_type": "conda",
1699 "resolves_simple_dependencies": true,
1700 "use_local": false,
1701 "versionless": false
1702 },
1703 "dependency_type": "conda",
1704 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1705 "exact": true,
1706 "model_class": "MergedCondaDependency",
1707 "name": "biopython",
1708 "version": "1.85"
1709 },
1710 {
1711 "cacheable": false,
1712 "dependency_resolver": {
1713 "auto_init": true,
1714 "auto_install": true,
1715 "can_uninstall_dependencies": true,
1716 "ensure_channels": "conda-forge,bioconda",
1717 "model_class": "CondaDependencyResolver",
1718 "prefix": "/home/rkhaled/miniconda3",
1719 "read_only": false,
1720 "resolver_type": "conda",
1721 "resolves_simple_dependencies": true,
1722 "use_local": false,
1723 "versionless": false
1724 },
1725 "dependency_type": "conda",
1726 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1727 "exact": true,
1728 "model_class": "MergedCondaDependency",
1729 "name": "proglog",
1730 "version": "0.1.10"
1731 },
1732 {
1733 "cacheable": false,
1734 "dependency_resolver": {
1735 "auto_init": true,
1736 "auto_install": true,
1737 "can_uninstall_dependencies": true,
1738 "ensure_channels": "conda-forge,bioconda",
1739 "model_class": "CondaDependencyResolver",
1740 "prefix": "/home/rkhaled/miniconda3",
1741 "read_only": false,
1742 "resolver_type": "conda",
1743 "resolves_simple_dependencies": true,
1744 "use_local": false,
1745 "versionless": false
1746 },
1747 "dependency_type": "conda",
1748 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1749 "exact": true,
1750 "model_class": "MergedCondaDependency",
1751 "name": "pandas",
1752 "version": "2.2.3"
1753 },
1754 {
1755 "cacheable": false,
1756 "dependency_resolver": {
1757 "auto_init": true,
1758 "auto_install": true,
1759 "can_uninstall_dependencies": true,
1760 "ensure_channels": "conda-forge,bioconda",
1761 "model_class": "CondaDependencyResolver",
1762 "prefix": "/home/rkhaled/miniconda3",
1763 "read_only": false,
1764 "resolver_type": "conda",
1765 "resolves_simple_dependencies": true,
1766 "use_local": false,
1767 "versionless": false
1768 },
1769 "dependency_type": "conda",
1770 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1771 "exact": true,
1772 "model_class": "MergedCondaDependency",
1773 "name": "dnacauldron",
1774 "version": "2.0.12"
1775 },
1776 {
1777 "cacheable": false,
1778 "dependency_resolver": {
1779 "auto_init": true,
1780 "auto_install": true,
1781 "can_uninstall_dependencies": true,
1782 "ensure_channels": "conda-forge,bioconda",
1783 "model_class": "CondaDependencyResolver",
1784 "prefix": "/home/rkhaled/miniconda3",
1785 "read_only": false,
1786 "resolver_type": "conda",
1787 "resolves_simple_dependencies": true,
1788 "use_local": false,
1789 "versionless": false
1790 },
1791 "dependency_type": "conda",
1792 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1793 "exact": true,
1794 "model_class": "MergedCondaDependency",
1795 "name": "pdf-reports",
1796 "version": "0.3.9"
1797 },
1798 {
1799 "cacheable": false,
1800 "dependency_resolver": {
1801 "auto_init": true,
1802 "auto_install": true,
1803 "can_uninstall_dependencies": true,
1804 "ensure_channels": "conda-forge,bioconda",
1805 "model_class": "CondaDependencyResolver",
1806 "prefix": "/home/rkhaled/miniconda3",
1807 "read_only": false,
1808 "resolver_type": "conda",
1809 "resolves_simple_dependencies": true,
1810 "use_local": false,
1811 "versionless": false
1812 },
1813 "dependency_type": "conda",
1814 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1815 "exact": true,
1816 "model_class": "MergedCondaDependency",
1817 "name": "sequenticon",
1818 "version": "0.1.8"
1819 },
1820 {
1821 "cacheable": false,
1822 "dependency_resolver": {
1823 "auto_init": true,
1824 "auto_install": true,
1825 "can_uninstall_dependencies": true,
1826 "ensure_channels": "conda-forge,bioconda",
1827 "model_class": "CondaDependencyResolver",
1828 "prefix": "/home/rkhaled/miniconda3",
1829 "read_only": false,
1830 "resolver_type": "conda",
1831 "resolves_simple_dependencies": true,
1832 "use_local": false,
1833 "versionless": false
1834 },
1835 "dependency_type": "conda",
1836 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1837 "exact": true,
1838 "model_class": "MergedCondaDependency",
1839 "name": "dna_features_viewer",
1840 "version": "3.1.5"
1841 }
1842 ],
1843 "exit_code": 0,
1844 "external_id": "390797",
1845 "galaxy_version": "24.2",
1846 "handler": null,
1847 "history_id": "beb5db8871971f36",
1848 "id": "ebae0af133eaa0bc",
1849 "inputs": {
1850 "assembly_csv": {
1851 "id": "85e42f4d247fa0dd",
1852 "src": "hda",
1853 "uuid": "4f53254a-8cbc-44ed-b07f-51c7b0ba70bf"
1854 },
1855 "domesticated_input1": {
1856 "id": "432a266b74c649c8",
1857 "src": "hda",
1858 "uuid": "03437b47-00b6-420f-a71d-dc13cfa4420f"
1859 },
1860 "domesticated_input10": {
1861 "id": "e3d9dfc153bf32e3",
1862 "src": "hda",
1863 "uuid": "7902eea5-11c6-4d21-950e-e4f1217a3efb"
1864 },
1865 "domesticated_input11": {
1866 "id": "c1ea56104c142f07",
1867 "src": "hda",
1868 "uuid": "493c970b-5c95-4af6-afb2-091bbfcad2fb"
1869 },
1870 "domesticated_input12": {
1871 "id": "4ae136bac02871c3",
1872 "src": "hda",
1873 "uuid": "32ae37e3-7d24-411c-8633-c253860693e3"
1874 },
1875 "domesticated_input2": {
1876 "id": "8ae4a94215cab68a",
1877 "src": "hda",
1878 "uuid": "7302922c-3802-4ec1-8fa6-2aeda8c3f773"
1879 },
1880 "domesticated_input3": {
1881 "id": "9d696692b4564172",
1882 "src": "hda",
1883 "uuid": "43f8a937-90f1-4ca8-9e1e-ffd4d438b8e3"
1884 },
1885 "domesticated_input4": {
1886 "id": "a274b866ba6c733f",
1887 "src": "hda",
1888 "uuid": "2da8d496-7007-408f-8f0d-9bb1bfc6cc89"
1889 },
1890 "domesticated_input5": {
1891 "id": "0e826cbc94bac0c7",
1892 "src": "hda",
1893 "uuid": "77e28f02-e173-4f1b-aa95-ab810151814c"
1894 },
1895 "domesticated_input6": {
1896 "id": "003f9c5a1beb71dd",
1897 "src": "hda",
1898 "uuid": "1db54aac-485c-43e5-b88e-78727df8f24d"
1899 },
1900 "domesticated_input7": {
1901 "id": "bcc266a3685d35dc",
1902 "src": "hda",
1903 "uuid": "e6c10e1b-4881-49ef-b382-70333c02a312"
1904 },
1905 "domesticated_input8": {
1906 "id": "eeca8961662723d3",
1907 "src": "hda",
1908 "uuid": "2a714c72-017a-4719-b5f6-7258096c4db6"
1909 },
1910 "domesticated_input9": {
1911 "id": "f46e9c37002996c5",
1912 "src": "hda",
1913 "uuid": "f56927c8-9d8a-44fc-a5b3-7929dfc14349"
1914 }
1915 },
1916 "job_messages": [],
1917 "job_metrics": [],
1918 "job_runner_name": null,
1919 "job_stderr": "",
1920 "job_stdout": "",
1921 "model_class": "Job",
1922 "output_collections": {
1923 "construct_gb": {
1924 "id": "56254918ce4e0956",
1925 "src": "hdca"
1926 }
1927 },
1928 "outputs": {
1929 "__new_primary_file_construct_gb|construct_1__": {
1930 "id": "c968bb70b6d3ea01",
1931 "src": "hda",
1932 "uuid": "15b8c210-4e71-4693-a986-851b2c3daa1a"
1933 },
1934 "__new_primary_file_construct_gb|construct_2__": {
1935 "id": "98571b3ff7e0e92a",
1936 "src": "hda",
1937 "uuid": "6acdb8a5-ae71-4344-acd6-ed81d59e13d6"
1938 },
1939 "__new_primary_file_construct_gb|construct_3__": {
1940 "id": "20333728d67b5515",
1941 "src": "hda",
1942 "uuid": "27cc732f-f580-4157-bfbe-cfa94a048bc1"
1943 },
1944 "__new_primary_file_construct_gb|construct_4__": {
1945 "id": "2da4f10a39324fce",
1946 "src": "hda",
1947 "uuid": "0b7e65dc-44ca-48ec-a159-a72ae98c24dd"
1948 },
1949 "output_zip": {
1950 "id": "46d30791dc86792c",
1951 "src": "hda",
1952 "uuid": "0d841edc-5cb0-451d-807c-1e38179edf75"
1953 }
1954 },
1955 "params": {
1956 "__input_ext": "\"input\"",
1957 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1958 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
1959 "chromInfo": "\"/tmp/tmp2jitj5ti/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1960 "dbkey": "\"?\"",
1961 "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}",
1962 "genbank_files": null,
1963 "topology": "\"circular\""
1964 },
1965 "state": "ok",
1966 "stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.35it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.16it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.76it/s, now=None]\r \r",
1967 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
1968 "tool_id": "cloning_simulation",
1969 "tool_stderr": "\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/4 [00:00<?, ?it/s, now=None]\rassembly: 50%|\u2588\u2588\u2588\u2588\u2588 | 2/4 [00:00<00:00, 2.35it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.16it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.76it/s, now=None]\r \r",
1970 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
1971 "update_time": "2025-06-06T10:09:07.953690",
1972 "user_email": "planemo@galaxyproject.org",
1973 "user_id": "b685bcc6830b171b"
1974 },
1975 "status": "success",
1976 "test_index": 6,
1977 "time_seconds": 56.49321532249451,
1978 "tool_id": "cloning_simulation",
1979 "tool_version": "0.1.0+galaxy0"
1980 },
1981 "has_data": true,
1982 "id": "cloning_simulation-6"
1983 }
1984 ],
1985 "version": "0.1"
1986 }