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comparison output.json @ 4:254d284a5be9 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 19 May 2025 14:09:48 +0000
parents 044d36066cb3
children e1e985913204
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3:044d36066cb3 4:254d284a5be9
9 { 9 {
10 "data": { 10 "data": {
11 "inputs": { 11 "inputs": {
12 "adv|use_file_names_as_ids": true, 12 "adv|use_file_names_as_ids": true,
13 "assembly_csv": { 13 "assembly_csv": {
14 "id": "c02153e44a10e06a", 14 "id": "40769e0726e5d2f9",
15 "src": "hda" 15 "src": "hda"
16 }, 16 },
17 "assembly_plan_name": "Type2sRestrictionAssembly", 17 "assembly_plan_name": "Type2sRestrictionAssembly",
18 "genbank_files": { 18 "genbank_files": {
19 "id": "a7025157dd5d3039", 19 "id": "fd8809ceca5b90d8",
20 "src": "hdca" 20 "src": "hdca"
21 }, 21 },
22 "topology": "circular" 22 "topology": "circular"
23 }, 23 },
24 "job": { 24 "job": {
25 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/e/b/4/dataset_eb40ee5e-5155-4303-9230-94926c63daaf.dat,/tmp/tmph0r87skq/files/4/a/9/dataset_4a9a1335-c528-438d-b80a-62b9608dbade.dat,/tmp/tmph0r87skq/files/7/c/a/dataset_7caa4f6a-a734-461f-ac38-c95442632c5a.dat,/tmp/tmph0r87skq/files/9/3/1/dataset_93127db8-2409-4544-93e5-6243a6d253ef.dat,/tmp/tmph0r87skq/files/e/2/9/dataset_e292919e-0a9a-403a-aa6b-30aa552881bd.dat,/tmp/tmph0r87skq/files/4/a/7/dataset_4a7c1e6b-f470-414e-b533-7390f74a64fc.dat,/tmp/tmph0r87skq/files/7/f/3/dataset_7f3df904-0bc5-456a-8679-cc58d06e214e.dat,/tmp/tmph0r87skq/files/a/6/0/dataset_a605738c-9b6d-44c6-891e-01cb729ea4dc.dat,/tmp/tmph0r87skq/files/1/0/c/dataset_10c35405-af25-41d3-9dbd-a411b4b65b98.dat,/tmp/tmph0r87skq/files/1/8/4/dataset_184d9904-3705-424e-b3f7-e5b7b773880f.dat,/tmp/tmph0r87skq/files/4/a/1/dataset_4a10d392-6ebc-413c-bd71-db425aa1aa0a.dat,/tmp/tmph0r87skq/files/8/3/5/dataset_835878c6-84f1-465c-b34e-d177885e567d.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/a/5/2/dataset_a522972a-c994-4ec0-a130-e3e1e101d126.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/e/b/4/dataset_eb40ee5e-5155-4303-9230-94926c63daaf.dat:part_A.gb,/tmp/tmph0r87skq/files/4/a/9/dataset_4a9a1335-c528-438d-b80a-62b9608dbade.dat:part_B.gb,/tmp/tmph0r87skq/files/7/c/a/dataset_7caa4f6a-a734-461f-ac38-c95442632c5a.dat:part_C.gb,/tmp/tmph0r87skq/files/9/3/1/dataset_93127db8-2409-4544-93e5-6243a6d253ef.dat:part_D.gb,/tmp/tmph0r87skq/files/e/2/9/dataset_e292919e-0a9a-403a-aa6b-30aa552881bd.dat:part_E.gb,/tmp/tmph0r87skq/files/4/a/7/dataset_4a7c1e6b-f470-414e-b533-7390f74a64fc.dat:part_F.gb,/tmp/tmph0r87skq/files/7/f/3/dataset_7f3df904-0bc5-456a-8679-cc58d06e214e.dat:part_G.gb,/tmp/tmph0r87skq/files/a/6/0/dataset_a605738c-9b6d-44c6-891e-01cb729ea4dc.dat:part_H.gb,/tmp/tmph0r87skq/files/1/0/c/dataset_10c35405-af25-41d3-9dbd-a411b4b65b98.dat:part_I.gb,/tmp/tmph0r87skq/files/1/8/4/dataset_184d9904-3705-424e-b3f7-e5b7b773880f.dat:part_J.gb,/tmp/tmph0r87skq/files/4/a/1/dataset_4a10d392-6ebc-413c-bd71-db425aa1aa0a.dat:part_K.gb,/tmp/tmph0r87skq/files/8/3/5/dataset_835878c6-84f1-465c-b34e-d177885e567d.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/tmph0r87skq/job_working_directory/000/14/outputs/dataset_109d2ac1-716e-4c47-a2b9-25e9d68cd9b7.dat'", 25 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/4/b/3/dataset_4b32c6a8-b39d-4f5f-9155-307e142d9193.dat,/tmp/tmpay0tme4v/files/8/e/f/dataset_8ef181dd-5c3a-40eb-9926-3738e1ae4be1.dat,/tmp/tmpay0tme4v/files/b/a/b/dataset_babba200-2afd-434f-8797-9b10cc736ba7.dat,/tmp/tmpay0tme4v/files/b/7/c/dataset_b7c5a88c-05ae-4efd-9887-47a899749178.dat,/tmp/tmpay0tme4v/files/7/f/e/dataset_7fea4ecf-be56-423d-8a11-d6491077e233.dat,/tmp/tmpay0tme4v/files/e/1/f/dataset_e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe.dat,/tmp/tmpay0tme4v/files/f/0/f/dataset_f0fe046c-6132-4bb9-b5dc-521edead32f2.dat,/tmp/tmpay0tme4v/files/e/e/c/dataset_eec197e7-d8fa-4c45-b5cb-89e51ee1db0e.dat,/tmp/tmpay0tme4v/files/3/2/1/dataset_32124f40-ed9b-4d25-b74f-a4ff44581962.dat,/tmp/tmpay0tme4v/files/e/1/2/dataset_e126fe05-d77c-4b33-9782-e5b1e7e6c7ad.dat,/tmp/tmpay0tme4v/files/2/3/4/dataset_234f9855-813e-4297-bbd4-d1327fb0cbad.dat,/tmp/tmpay0tme4v/files/6/b/2/dataset_6b23e127-e4a2-41b6-98f3-4f8f7214b209.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/1/4/6/dataset_14645e90-9105-48af-a071-6ea052fd4aad.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/4/b/3/dataset_4b32c6a8-b39d-4f5f-9155-307e142d9193.dat:part_A.gb,/tmp/tmpay0tme4v/files/8/e/f/dataset_8ef181dd-5c3a-40eb-9926-3738e1ae4be1.dat:part_B.gb,/tmp/tmpay0tme4v/files/b/a/b/dataset_babba200-2afd-434f-8797-9b10cc736ba7.dat:part_C.gb,/tmp/tmpay0tme4v/files/b/7/c/dataset_b7c5a88c-05ae-4efd-9887-47a899749178.dat:part_D.gb,/tmp/tmpay0tme4v/files/7/f/e/dataset_7fea4ecf-be56-423d-8a11-d6491077e233.dat:part_E.gb,/tmp/tmpay0tme4v/files/e/1/f/dataset_e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe.dat:part_F.gb,/tmp/tmpay0tme4v/files/f/0/f/dataset_f0fe046c-6132-4bb9-b5dc-521edead32f2.dat:part_G.gb,/tmp/tmpay0tme4v/files/e/e/c/dataset_eec197e7-d8fa-4c45-b5cb-89e51ee1db0e.dat:part_H.gb,/tmp/tmpay0tme4v/files/3/2/1/dataset_32124f40-ed9b-4d25-b74f-a4ff44581962.dat:part_I.gb,/tmp/tmpay0tme4v/files/e/1/2/dataset_e126fe05-d77c-4b33-9782-e5b1e7e6c7ad.dat:part_J.gb,/tmp/tmpay0tme4v/files/2/3/4/dataset_234f9855-813e-4297-bbd4-d1327fb0cbad.dat:part_K.gb,/tmp/tmpay0tme4v/files/6/b/2/dataset_6b23e127-e4a2-41b6-98f3-4f8f7214b209.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/tmpay0tme4v/job_working_directory/000/14/outputs/dataset_f30d906d-2ea4-4cde-b451-b7c6daf25a29.dat'",
26 "command_version": "", 26 "command_version": "",
27 "copied_from_job_id": null, 27 "copied_from_job_id": null,
28 "create_time": "2025-05-16T12:35:55.635805", 28 "create_time": "2025-05-19T13:45:01.696419",
29 "dependencies": [], 29 "dependencies": [],
30 "exit_code": 0, 30 "exit_code": 0,
31 "external_id": "205109", 31 "external_id": "245391",
32 "galaxy_version": "24.2", 32 "galaxy_version": "24.2",
33 "handler": null, 33 "handler": null,
34 "history_id": "a7025157dd5d3039", 34 "history_id": "fd8809ceca5b90d8",
35 "id": "d49d8be9932a8ee0", 35 "id": "d25964a649f0fc81",
36 "inputs": { 36 "inputs": {
37 "assembly_csv": { 37 "assembly_csv": {
38 "id": "c02153e44a10e06a", 38 "id": "40769e0726e5d2f9",
39 "src": "hda", 39 "src": "hda",
40 "uuid": "a522972a-c994-4ec0-a130-e3e1e101d126" 40 "uuid": "14645e90-9105-48af-a071-6ea052fd4aad"
41 }, 41 },
42 "genbank_files1": { 42 "genbank_files1": {
43 "id": "a7025157dd5d3039", 43 "id": "fd8809ceca5b90d8",
44 "src": "hda", 44 "src": "hda",
45 "uuid": "eb40ee5e-5155-4303-9230-94926c63daaf" 45 "uuid": "4b32c6a8-b39d-4f5f-9155-307e142d9193"
46 }, 46 },
47 "genbank_files10": { 47 "genbank_files10": {
48 "id": "26800a0030991202", 48 "id": "171b3bd3b2ffa75e",
49 "src": "hda", 49 "src": "hda",
50 "uuid": "184d9904-3705-424e-b3f7-e5b7b773880f" 50 "uuid": "e126fe05-d77c-4b33-9782-e5b1e7e6c7ad"
51 }, 51 },
52 "genbank_files11": { 52 "genbank_files11": {
53 "id": "9e9c740782c078df", 53 "id": "ec7f951857c74506",
54 "src": "hda", 54 "src": "hda",
55 "uuid": "4a10d392-6ebc-413c-bd71-db425aa1aa0a" 55 "uuid": "234f9855-813e-4297-bbd4-d1327fb0cbad"
56 }, 56 },
57 "genbank_files12": { 57 "genbank_files12": {
58 "id": "d70a40a14f24deac", 58 "id": "8c74660869d2dd19",
59 "src": "hda", 59 "src": "hda",
60 "uuid": "835878c6-84f1-465c-b34e-d177885e567d" 60 "uuid": "6b23e127-e4a2-41b6-98f3-4f8f7214b209"
61 }, 61 },
62 "genbank_files2": { 62 "genbank_files2": {
63 "id": "ce87194f2a532da8", 63 "id": "132b871e5e3014ee",
64 "src": "hda", 64 "src": "hda",
65 "uuid": "4a9a1335-c528-438d-b80a-62b9608dbade" 65 "uuid": "8ef181dd-5c3a-40eb-9926-3738e1ae4be1"
66 }, 66 },
67 "genbank_files3": { 67 "genbank_files3": {
68 "id": "e52e8d0a017d5bd2", 68 "id": "65f48584dd2a1828",
69 "src": "hda", 69 "src": "hda",
70 "uuid": "7caa4f6a-a734-461f-ac38-c95442632c5a" 70 "uuid": "babba200-2afd-434f-8797-9b10cc736ba7"
71 }, 71 },
72 "genbank_files4": { 72 "genbank_files4": {
73 "id": "4dd0eedec5562f6e", 73 "id": "543bb64c618cca80",
74 "src": "hda", 74 "src": "hda",
75 "uuid": "93127db8-2409-4544-93e5-6243a6d253ef" 75 "uuid": "b7c5a88c-05ae-4efd-9887-47a899749178"
76 }, 76 },
77 "genbank_files5": { 77 "genbank_files5": {
78 "id": "d1cbd0905c1fc860", 78 "id": "e550d863bf084702",
79 "src": "hda", 79 "src": "hda",
80 "uuid": "e292919e-0a9a-403a-aa6b-30aa552881bd" 80 "uuid": "7fea4ecf-be56-423d-8a11-d6491077e233"
81 }, 81 },
82 "genbank_files6": { 82 "genbank_files6": {
83 "id": "0494b81690cb2f5c", 83 "id": "6a73e15df176b356",
84 "src": "hda", 84 "src": "hda",
85 "uuid": "4a7c1e6b-f470-414e-b533-7390f74a64fc" 85 "uuid": "e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe"
86 }, 86 },
87 "genbank_files7": { 87 "genbank_files7": {
88 "id": "edce0bc0654ca8cc", 88 "id": "7faba24a30f85c9d",
89 "src": "hda", 89 "src": "hda",
90 "uuid": "7f3df904-0bc5-456a-8679-cc58d06e214e" 90 "uuid": "f0fe046c-6132-4bb9-b5dc-521edead32f2"
91 }, 91 },
92 "genbank_files8": { 92 "genbank_files8": {
93 "id": "052d0d471d180256", 93 "id": "f121a1ae40e58e96",
94 "src": "hda", 94 "src": "hda",
95 "uuid": "a605738c-9b6d-44c6-891e-01cb729ea4dc" 95 "uuid": "eec197e7-d8fa-4c45-b5cb-89e51ee1db0e"
96 }, 96 },
97 "genbank_files9": { 97 "genbank_files9": {
98 "id": "5827a0347340e98b", 98 "id": "fc2d53421d7989de",
99 "src": "hda", 99 "src": "hda",
100 "uuid": "10c35405-af25-41d3-9dbd-a411b4b65b98" 100 "uuid": "32124f40-ed9b-4d25-b74f-a4ff44581962"
101 } 101 }
102 }, 102 },
103 "job_messages": [], 103 "job_messages": [],
104 "job_metrics": [], 104 "job_metrics": [],
105 "job_runner_name": null, 105 "job_runner_name": null,
106 "job_stderr": "", 106 "job_stderr": "",
107 "job_stdout": "", 107 "job_stdout": "",
108 "model_class": "Job", 108 "model_class": "Job",
109 "output_collections": { 109 "output_collections": {
110 "construct_gb": { 110 "construct_gb": {
111 "id": "ce87194f2a532da8", 111 "id": "132b871e5e3014ee",
112 "src": "hdca" 112 "src": "hdca"
113 } 113 }
114 }, 114 },
115 "outputs": { 115 "outputs": {
116 "__new_primary_file_construct_gb|construct_1__": { 116 "__new_primary_file_construct_gb|construct_1__": {
117 "id": "68bcb17f47b988de", 117 "id": "6d4f2c14c91fd6e1",
118 "src": "hda", 118 "src": "hda",
119 "uuid": "2c9a5458-38f0-4591-bb2d-452aac86ce0b" 119 "uuid": "32687278-a139-4ee2-bfc0-86735e813b3e"
120 }, 120 },
121 "__new_primary_file_construct_gb|construct_2__": { 121 "__new_primary_file_construct_gb|construct_2__": {
122 "id": "7cb8b41737d3d7aa", 122 "id": "ce0686b9d731295a",
123 "src": "hda", 123 "src": "hda",
124 "uuid": "026f0937-350b-4ae7-96da-1e685237a8c8" 124 "uuid": "a78e87bc-7aa1-4e9e-8625-78450d68b18d"
125 }, 125 },
126 "__new_primary_file_construct_gb|construct_3__": { 126 "__new_primary_file_construct_gb|construct_3__": {
127 "id": "e558db6e0f20f34c", 127 "id": "9fb491af1d40ed73",
128 "src": "hda", 128 "src": "hda",
129 "uuid": "df750e5d-b2f4-43f1-bf95-aa0d980bb98a" 129 "uuid": "6ce970af-f5f4-4193-9d0a-d1fc701d17d5"
130 }, 130 },
131 "__new_primary_file_construct_gb|construct_4__": { 131 "__new_primary_file_construct_gb|construct_4__": {
132 "id": "87544afc708050c8", 132 "id": "0a54ce1a82948d59",
133 "src": "hda", 133 "src": "hda",
134 "uuid": "0ba9a694-1b4e-4ff4-b6f2-87503d04cd66" 134 "uuid": "b76d3345-d556-4f55-9285-6a7ce76d9150"
135 }, 135 },
136 "output_zip": { 136 "output_zip": {
137 "id": "d49d8be9932a8ee0", 137 "id": "d25964a649f0fc81",
138 "src": "hda", 138 "src": "hda",
139 "uuid": "109d2ac1-716e-4c47-a2b9-25e9d68cd9b7" 139 "uuid": "f30d906d-2ea4-4cde-b451-b7c6daf25a29"
140 } 140 }
141 }, 141 },
142 "params": { 142 "params": {
143 "__input_ext": "\"input\"", 143 "__input_ext": "\"input\"",
144 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 144 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
145 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", 145 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
146 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 146 "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
147 "dbkey": "\"?\"", 147 "dbkey": "\"?\"",
148 "domesticated_input": null, 148 "domesticated_input": null,
149 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", 149 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
150 "topology": "\"circular\"" 150 "topology": "\"circular\""
151 }, 151 },
152 "state": "ok", 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, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/s, now=None]\r \r", 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, 2.14it/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, 1.77it/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", 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", 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, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.82it/s, now=None]\r \r", 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, 2.14it/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, 1.77it/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", 157 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
158 "update_time": "2025-05-16T12:36:09.065234", 158 "update_time": "2025-05-19T13:45:15.319665",
159 "user_email": "planemo@galaxyproject.org", 159 "user_email": "planemo@galaxyproject.org",
160 "user_id": "a7025157dd5d3039" 160 "user_id": "fd8809ceca5b90d8"
161 }, 161 },
162 "status": "success", 162 "status": "success",
163 "test_index": 0, 163 "test_index": 0,
164 "time_seconds": 54.82133865356445, 164 "time_seconds": 54.20177435874939,
165 "tool_id": "cloning_simulation", 165 "tool_id": "cloning_simulation",
166 "tool_version": "0.1.0+galaxy0" 166 "tool_version": "0.1.0+galaxy0"
167 }, 167 },
168 "has_data": true, 168 "has_data": true,
169 "id": "cloning_simulation-0" 169 "id": "cloning_simulation-0"
171 { 171 {
172 "data": { 172 "data": {
173 "inputs": { 173 "inputs": {
174 "adv|use_file_names_as_ids": true, 174 "adv|use_file_names_as_ids": true,
175 "assembly_csv": { 175 "assembly_csv": {
176 "id": "13b114ac662002c6", 176 "id": "e820aa9b959ea863",
177 "src": "hda" 177 "src": "hda"
178 }, 178 },
179 "assembly_plan_name": "GibsonAssembly", 179 "assembly_plan_name": "GibsonAssembly",
180 "genbank_files": { 180 "genbank_files": {
181 "id": "e52e8d0a017d5bd2", 181 "id": "65f48584dd2a1828",
182 "src": "hdca" 182 "src": "hdca"
183 }, 183 },
184 "topology": "circular" 184 "topology": "circular"
185 }, 185 },
186 "job": { 186 "job": {
187 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/f/2/e/dataset_f2e8406c-fdb7-4b30-aa74-202b93292a26.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/5/7/9/dataset_579b13e6-f14d-401c-88ee-b25ed3bf42dc.dat' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/f/2/e/dataset_f2e8406c-fdb7-4b30-aa74-202b93292a26.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/tmph0r87skq/job_working_directory/000/17/outputs/dataset_36e0457f-1da8-456a-86c9-20ea242688bc.dat'", 187 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/0/6/9/dataset_069f9137-705b-4e17-b931-1ebd547a7fe4.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/3/d/1/dataset_3d1a91ee-d9ba-41fc-bd79-f012ae654250.dat' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/0/6/9/dataset_069f9137-705b-4e17-b931-1ebd547a7fe4.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/tmpay0tme4v/job_working_directory/000/17/outputs/dataset_3327e282-d219-43e3-94d7-88fd08aa6867.dat'",
188 "command_version": "", 188 "command_version": "",
189 "copied_from_job_id": null, 189 "copied_from_job_id": null,
190 "create_time": "2025-05-16T12:36:19.661290", 190 "create_time": "2025-05-19T13:45:26.929597",
191 "dependencies": [ 191 "dependencies": [
192 { 192 {
193 "cacheable": false, 193 "cacheable": false,
194 "dependency_resolver": { 194 "dependency_resolver": {
195 "auto_init": true, 195 "auto_init": true,
365 "name": "dna_features_viewer", 365 "name": "dna_features_viewer",
366 "version": "3.1.5" 366 "version": "3.1.5"
367 } 367 }
368 ], 368 ],
369 "exit_code": 0, 369 "exit_code": 0,
370 "external_id": "205459", 370 "external_id": "245766",
371 "galaxy_version": "24.2", 371 "galaxy_version": "24.2",
372 "handler": null, 372 "handler": null,
373 "history_id": "ce87194f2a532da8", 373 "history_id": "132b871e5e3014ee",
374 "id": "e558db6e0f20f34c", 374 "id": "9fb491af1d40ed73",
375 "inputs": { 375 "inputs": {
376 "assembly_csv": { 376 "assembly_csv": {
377 "id": "13b114ac662002c6", 377 "id": "e820aa9b959ea863",
378 "src": "hda", 378 "src": "hda",
379 "uuid": "579b13e6-f14d-401c-88ee-b25ed3bf42dc" 379 "uuid": "3d1a91ee-d9ba-41fc-bd79-f012ae654250"
380 }, 380 },
381 "genbank_files1": { 381 "genbank_files1": {
382 "id": "16385471cc722641", 382 "id": "82720a2239e02ea4",
383 "src": "hda", 383 "src": "hda",
384 "uuid": "f2e8406c-fdb7-4b30-aa74-202b93292a26" 384 "uuid": "069f9137-705b-4e17-b931-1ebd547a7fe4"
385 } 385 }
386 }, 386 },
387 "job_messages": [], 387 "job_messages": [],
388 "job_metrics": [], 388 "job_metrics": [],
389 "job_runner_name": null, 389 "job_runner_name": null,
390 "job_stderr": "", 390 "job_stderr": "",
391 "job_stdout": "", 391 "job_stdout": "",
392 "model_class": "Job", 392 "model_class": "Job",
393 "output_collections": { 393 "output_collections": {
394 "construct_gb": { 394 "construct_gb": {
395 "id": "4dd0eedec5562f6e", 395 "id": "543bb64c618cca80",
396 "src": "hdca" 396 "src": "hdca"
397 } 397 }
398 }, 398 },
399 "outputs": { 399 "outputs": {
400 "__new_primary_file_construct_gb|construct_1__": { 400 "__new_primary_file_construct_gb|construct_1__": {
401 "id": "eb4747fb10762624", 401 "id": "4aace7d444c68122",
402 "src": "hda", 402 "src": "hda",
403 "uuid": "8b9f07c0-2a2f-49db-b0b9-e3b27b5d2102" 403 "uuid": "24381c81-ce88-4584-94dd-e84c078419f8"
404 }, 404 },
405 "__new_primary_file_construct_gb|construct_2__": { 405 "__new_primary_file_construct_gb|construct_2__": {
406 "id": "fa2c1cd7e40ca607", 406 "id": "894db8882e848d71",
407 "src": "hda", 407 "src": "hda",
408 "uuid": "694f0f93-1c26-4a8b-91ed-bcb7fe4b3784" 408 "uuid": "9f704297-19e6-4faf-a500-b6b64578b376"
409 }, 409 },
410 "__new_primary_file_construct_gb|construct_3__": { 410 "__new_primary_file_construct_gb|construct_3__": {
411 "id": "2c9180ba70391455", 411 "id": "4d49f848d91861cd",
412 "src": "hda", 412 "src": "hda",
413 "uuid": "e57dc6e8-10e6-4527-a375-9ed583735c59" 413 "uuid": "ac0d0bab-faee-48eb-bdcf-f71f1ae7dff9"
414 }, 414 },
415 "output_zip": { 415 "output_zip": {
416 "id": "cf8958f7b0d14fa5", 416 "id": "314f9466454a965d",
417 "src": "hda", 417 "src": "hda",
418 "uuid": "36e0457f-1da8-456a-86c9-20ea242688bc" 418 "uuid": "3327e282-d219-43e3-94d7-88fd08aa6867"
419 } 419 }
420 }, 420 },
421 "params": { 421 "params": {
422 "__input_ext": "\"input\"", 422 "__input_ext": "\"input\"",
423 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 423 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
424 "assembly_plan_name": "\"GibsonAssembly\"", 424 "assembly_plan_name": "\"GibsonAssembly\"",
425 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 425 "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
426 "dbkey": "\"?\"", 426 "dbkey": "\"?\"",
427 "domesticated_input": null, 427 "domesticated_input": null,
428 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", 428 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
429 "topology": "\"circular\"" 429 "topology": "\"circular\""
430 }, 430 },
431 "state": "ok", 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, 4.71it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.79it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.60it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.70it/s, now=None]\r \r", 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, 4.20it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.12it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.34it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.62it/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", 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", 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, 4.71it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.79it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.60it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.70it/s, now=None]\r \r", 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, 4.20it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.12it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.34it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.62it/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", 436 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
437 "update_time": "2025-05-16T12:36:31.612352", 437 "update_time": "2025-05-19T13:45:38.810356",
438 "user_email": "planemo@galaxyproject.org", 438 "user_email": "planemo@galaxyproject.org",
439 "user_id": "a7025157dd5d3039" 439 "user_id": "fd8809ceca5b90d8"
440 }, 440 },
441 "status": "success", 441 "status": "success",
442 "test_index": 1, 442 "test_index": 1,
443 "time_seconds": 22.601666688919067, 443 "time_seconds": 23.490375518798828,
444 "tool_id": "cloning_simulation", 444 "tool_id": "cloning_simulation",
445 "tool_version": "0.1.0+galaxy0" 445 "tool_version": "0.1.0+galaxy0"
446 }, 446 },
447 "has_data": true, 447 "has_data": true,
448 "id": "cloning_simulation-1" 448 "id": "cloning_simulation-1"
450 { 450 {
451 "data": { 451 "data": {
452 "inputs": { 452 "inputs": {
453 "adv|use_file_names_as_ids": true, 453 "adv|use_file_names_as_ids": true,
454 "assembly_csv": { 454 "assembly_csv": {
455 "id": "84906eb14284db27", 455 "id": "675dca381201b1fe",
456 "src": "hda" 456 "src": "hda"
457 }, 457 },
458 "assembly_plan_name": "LigaseCyclingReactionAssembly", 458 "assembly_plan_name": "LigaseCyclingReactionAssembly",
459 "genbank_files": { 459 "genbank_files": {
460 "id": "d1cbd0905c1fc860", 460 "id": "e550d863bf084702",
461 "src": "hdca" 461 "src": "hdca"
462 }, 462 },
463 "topology": "circular" 463 "topology": "circular"
464 }, 464 },
465 "job": { 465 "job": {
466 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/1/5/7/dataset_15741680-9963-4b3d-979e-792be37256f2.dat,/tmp/tmph0r87skq/files/d/3/d/dataset_d3de76b3-3793-46fa-990e-970e1bcb2a72.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/2/0/e/dataset_20eb88b1-0fc5-476b-a409-da7f598780b6.dat' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/1/5/7/dataset_15741680-9963-4b3d-979e-792be37256f2.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmph0r87skq/files/d/3/d/dataset_d3de76b3-3793-46fa-990e-970e1bcb2a72.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/tmph0r87skq/job_working_directory/000/21/outputs/dataset_0ffdda24-b80f-4db5-8c10-1467d34eb3a8.dat'", 466 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/e/0/f/dataset_e0f8296e-094d-4971-976b-6e534148d1d5.dat,/tmp/tmpay0tme4v/files/6/0/8/dataset_608722d5-ead5-49fb-8736-04fa7ab027f3.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/1/d/9/dataset_1d9ed268-bc25-40c0-a67f-439accae7e40.dat' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/e/0/f/dataset_e0f8296e-094d-4971-976b-6e534148d1d5.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpay0tme4v/files/6/0/8/dataset_608722d5-ead5-49fb-8736-04fa7ab027f3.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/tmpay0tme4v/job_working_directory/000/21/outputs/dataset_b1af7192-a26f-4e6a-ba22-9aeffac2ea46.dat'",
467 "command_version": "", 467 "command_version": "",
468 "copied_from_job_id": null, 468 "copied_from_job_id": null,
469 "create_time": "2025-05-16T12:36:42.888728", 469 "create_time": "2025-05-19T13:45:50.704320",
470 "dependencies": [ 470 "dependencies": [
471 { 471 {
472 "cacheable": false, 472 "cacheable": false,
473 "dependency_resolver": { 473 "dependency_resolver": {
474 "auto_init": true, 474 "auto_init": true,
644 "name": "dna_features_viewer", 644 "name": "dna_features_viewer",
645 "version": "3.1.5" 645 "version": "3.1.5"
646 } 646 }
647 ], 647 ],
648 "exit_code": 0, 648 "exit_code": 0,
649 "external_id": "205894", 649 "external_id": "246155",
650 "galaxy_version": "24.2", 650 "galaxy_version": "24.2",
651 "handler": null, 651 "handler": null,
652 "history_id": "e52e8d0a017d5bd2", 652 "history_id": "65f48584dd2a1828",
653 "id": "cf8958f7b0d14fa5", 653 "id": "314f9466454a965d",
654 "inputs": { 654 "inputs": {
655 "assembly_csv": { 655 "assembly_csv": {
656 "id": "84906eb14284db27", 656 "id": "675dca381201b1fe",
657 "src": "hda", 657 "src": "hda",
658 "uuid": "20eb88b1-0fc5-476b-a409-da7f598780b6" 658 "uuid": "1d9ed268-bc25-40c0-a67f-439accae7e40"
659 }, 659 },
660 "genbank_files1": { 660 "genbank_files1": {
661 "id": "1fdafe0e70c0e721", 661 "id": "1b1aadbedc3f334a",
662 "src": "hda", 662 "src": "hda",
663 "uuid": "15741680-9963-4b3d-979e-792be37256f2" 663 "uuid": "e0f8296e-094d-4971-976b-6e534148d1d5"
664 }, 664 },
665 "genbank_files2": { 665 "genbank_files2": {
666 "id": "044728be18fd1186", 666 "id": "05b5deb4bb488223",
667 "src": "hda", 667 "src": "hda",
668 "uuid": "d3de76b3-3793-46fa-990e-970e1bcb2a72" 668 "uuid": "608722d5-ead5-49fb-8736-04fa7ab027f3"
669 } 669 }
670 }, 670 },
671 "job_messages": [], 671 "job_messages": [],
672 "job_metrics": [], 672 "job_metrics": [],
673 "job_runner_name": null, 673 "job_runner_name": null,
674 "job_stderr": "", 674 "job_stderr": "",
675 "job_stdout": "", 675 "job_stdout": "",
676 "model_class": "Job", 676 "model_class": "Job",
677 "output_collections": { 677 "output_collections": {
678 "construct_gb": { 678 "construct_gb": {
679 "id": "0494b81690cb2f5c", 679 "id": "6a73e15df176b356",
680 "src": "hdca" 680 "src": "hdca"
681 } 681 }
682 }, 682 },
683 "outputs": { 683 "outputs": {
684 "output_zip": { 684 "output_zip": {
685 "id": "920c0db56b0a806b", 685 "id": "499c1d005d68ae46",
686 "src": "hda", 686 "src": "hda",
687 "uuid": "0ffdda24-b80f-4db5-8c10-1467d34eb3a8" 687 "uuid": "b1af7192-a26f-4e6a-ba22-9aeffac2ea46"
688 } 688 }
689 }, 689 },
690 "params": { 690 "params": {
691 "__input_ext": "\"input\"", 691 "__input_ext": "\"input\"",
692 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 692 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
693 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", 693 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"",
694 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 694 "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
695 "dbkey": "\"?\"", 695 "dbkey": "\"?\"",
696 "domesticated_input": null, 696 "domesticated_input": null,
697 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", 697 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}",
698 "topology": "\"circular\"" 698 "topology": "\"circular\""
699 }, 699 },
700 "state": "ok", 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, 2.42it/s, now=None]\r \r", 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, 2.05it/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", 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", 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, 2.42it/s, now=None]\r \r", 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, 2.05it/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", 705 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
706 "update_time": "2025-05-16T12:36:54.097489", 706 "update_time": "2025-05-19T13:46:02.749327",
707 "user_email": "planemo@galaxyproject.org", 707 "user_email": "planemo@galaxyproject.org",
708 "user_id": "a7025157dd5d3039" 708 "user_id": "fd8809ceca5b90d8"
709 }, 709 },
710 "status": "success", 710 "status": "success",
711 "test_index": 2, 711 "test_index": 2,
712 "time_seconds": 22.133039951324463, 712 "time_seconds": 23.55416440963745,
713 "tool_id": "cloning_simulation", 713 "tool_id": "cloning_simulation",
714 "tool_version": "0.1.0+galaxy0" 714 "tool_version": "0.1.0+galaxy0"
715 }, 715 },
716 "has_data": true, 716 "has_data": true,
717 "id": "cloning_simulation-2" 717 "id": "cloning_simulation-2"
719 { 719 {
720 "data": { 720 "data": {
721 "inputs": { 721 "inputs": {
722 "adv|use_file_names_as_ids": true, 722 "adv|use_file_names_as_ids": true,
723 "assembly_csv": { 723 "assembly_csv": {
724 "id": "df13d5ca39cba7c4", 724 "id": "c06583b31ad25e9f",
725 "src": "hda" 725 "src": "hda"
726 }, 726 },
727 "assembly_plan_name": "BASICAssembly", 727 "assembly_plan_name": "BASICAssembly",
728 "genbank_files": { 728 "genbank_files": {
729 "id": "edce0bc0654ca8cc", 729 "id": "7faba24a30f85c9d",
730 "src": "hdca" 730 "src": "hdca"
731 }, 731 },
732 "topology": "circular" 732 "topology": "circular"
733 }, 733 },
734 "job": { 734 "job": {
735 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/4/f/0/dataset_4f0d4258-2f50-4a4e-9271-58e8c272856e.dat,/tmp/tmph0r87skq/files/2/7/f/dataset_27f67c7a-5e38-4103-a00b-a9d8234b6686.dat,/tmp/tmph0r87skq/files/4/e/8/dataset_4e880afa-3f37-43a4-982e-36d750aab3d3.dat,/tmp/tmph0r87skq/files/3/7/4/dataset_3746bcc6-ee0c-4936-832f-ce29f808430d.dat,/tmp/tmph0r87skq/files/7/8/8/dataset_788ebd7b-6247-4f96-a3d3-3c3306c210a0.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/e/9/7/dataset_e971a6cf-b13e-4a65-a78d-aa22a0ea1fff.dat' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/4/f/0/dataset_4f0d4258-2f50-4a4e-9271-58e8c272856e.dat:GFP.gb,/tmp/tmph0r87skq/files/2/7/f/dataset_27f67c7a-5e38-4103-a00b-a9d8234b6686.dat:p15A_kan.gb,/tmp/tmph0r87skq/files/4/e/8/dataset_4e880afa-3f37-43a4-982e-36d750aab3d3.dat:promoter.gb,/tmp/tmph0r87skq/files/3/7/4/dataset_3746bcc6-ee0c-4936-832f-ce29f808430d.dat:RFP.gb,/tmp/tmph0r87skq/files/7/8/8/dataset_788ebd7b-6247-4f96-a3d3-3c3306c210a0.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/tmph0r87skq/job_working_directory/000/28/outputs/dataset_5e0faa51-141c-49d1-ba84-ca8aba27508c.dat'", 735 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/5/0/9/dataset_509fa87d-4af9-46f7-b323-48f8128675c8.dat,/tmp/tmpay0tme4v/files/0/2/b/dataset_02b8b6f2-43ab-4885-a9de-336d903edc55.dat,/tmp/tmpay0tme4v/files/9/5/a/dataset_95aa5a16-9b61-45be-94e6-35284531fcd7.dat,/tmp/tmpay0tme4v/files/1/7/c/dataset_17c94fe6-e0ce-4c72-9adc-5f8132a6df81.dat,/tmp/tmpay0tme4v/files/d/b/6/dataset_db6bb8ba-4682-476e-a688-be9e5cfb0afd.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/3/4/4/dataset_344ef380-e9d3-4729-bc6e-45a003000613.dat' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/5/0/9/dataset_509fa87d-4af9-46f7-b323-48f8128675c8.dat:GFP.gb,/tmp/tmpay0tme4v/files/0/2/b/dataset_02b8b6f2-43ab-4885-a9de-336d903edc55.dat:p15A_kan.gb,/tmp/tmpay0tme4v/files/9/5/a/dataset_95aa5a16-9b61-45be-94e6-35284531fcd7.dat:promoter.gb,/tmp/tmpay0tme4v/files/1/7/c/dataset_17c94fe6-e0ce-4c72-9adc-5f8132a6df81.dat:RFP.gb,/tmp/tmpay0tme4v/files/d/b/6/dataset_db6bb8ba-4682-476e-a688-be9e5cfb0afd.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/tmpay0tme4v/job_working_directory/000/28/outputs/dataset_cdb61cbc-c9c5-45fc-9fc8-e00c1f3d4f0f.dat'",
736 "command_version": "", 736 "command_version": "",
737 "copied_from_job_id": null, 737 "copied_from_job_id": null,
738 "create_time": "2025-05-16T12:37:15.245845", 738 "create_time": "2025-05-19T13:46:24.141767",
739 "dependencies": [ 739 "dependencies": [
740 { 740 {
741 "cacheable": false, 741 "cacheable": false,
742 "dependency_resolver": { 742 "dependency_resolver": {
743 "auto_init": true, 743 "auto_init": true,
913 "name": "dna_features_viewer", 913 "name": "dna_features_viewer",
914 "version": "3.1.5" 914 "version": "3.1.5"
915 } 915 }
916 ], 916 ],
917 "exit_code": 0, 917 "exit_code": 0,
918 "external_id": "206517", 918 "external_id": "246833",
919 "galaxy_version": "24.2", 919 "galaxy_version": "24.2",
920 "handler": null, 920 "handler": null,
921 "history_id": "4dd0eedec5562f6e", 921 "history_id": "543bb64c618cca80",
922 "id": "920c0db56b0a806b", 922 "id": "499c1d005d68ae46",
923 "inputs": { 923 "inputs": {
924 "assembly_csv": { 924 "assembly_csv": {
925 "id": "df13d5ca39cba7c4", 925 "id": "c06583b31ad25e9f",
926 "src": "hda", 926 "src": "hda",
927 "uuid": "e971a6cf-b13e-4a65-a78d-aa22a0ea1fff" 927 "uuid": "344ef380-e9d3-4729-bc6e-45a003000613"
928 }, 928 },
929 "genbank_files1": { 929 "genbank_files1": {
930 "id": "caecbbc14917ac69", 930 "id": "dcd17297edd6443c",
931 "src": "hda", 931 "src": "hda",
932 "uuid": "4f0d4258-2f50-4a4e-9271-58e8c272856e" 932 "uuid": "509fa87d-4af9-46f7-b323-48f8128675c8"
933 }, 933 },
934 "genbank_files2": { 934 "genbank_files2": {
935 "id": "10cd084c8017547c", 935 "id": "5255abeff5637f7e",
936 "src": "hda", 936 "src": "hda",
937 "uuid": "27f67c7a-5e38-4103-a00b-a9d8234b6686" 937 "uuid": "02b8b6f2-43ab-4885-a9de-336d903edc55"
938 }, 938 },
939 "genbank_files3": { 939 "genbank_files3": {
940 "id": "aa3451be0c94f76e", 940 "id": "a30c1b2be38d49df",
941 "src": "hda", 941 "src": "hda",
942 "uuid": "4e880afa-3f37-43a4-982e-36d750aab3d3" 942 "uuid": "95aa5a16-9b61-45be-94e6-35284531fcd7"
943 }, 943 },
944 "genbank_files4": { 944 "genbank_files4": {
945 "id": "a5f159065ae97d01", 945 "id": "70728511d187b46b",
946 "src": "hda", 946 "src": "hda",
947 "uuid": "3746bcc6-ee0c-4936-832f-ce29f808430d" 947 "uuid": "17c94fe6-e0ce-4c72-9adc-5f8132a6df81"
948 }, 948 },
949 "genbank_files5": { 949 "genbank_files5": {
950 "id": "a001a939426dadd1", 950 "id": "db356309fe5e8361",
951 "src": "hda", 951 "src": "hda",
952 "uuid": "788ebd7b-6247-4f96-a3d3-3c3306c210a0" 952 "uuid": "db6bb8ba-4682-476e-a688-be9e5cfb0afd"
953 } 953 }
954 }, 954 },
955 "job_messages": [], 955 "job_messages": [],
956 "job_metrics": [], 956 "job_metrics": [],
957 "job_runner_name": null, 957 "job_runner_name": null,
958 "job_stderr": "", 958 "job_stderr": "",
959 "job_stdout": "", 959 "job_stdout": "",
960 "model_class": "Job", 960 "model_class": "Job",
961 "output_collections": { 961 "output_collections": {
962 "construct_gb": { 962 "construct_gb": {
963 "id": "052d0d471d180256", 963 "id": "f121a1ae40e58e96",
964 "src": "hdca" 964 "src": "hdca"
965 } 965 }
966 }, 966 },
967 "outputs": { 967 "outputs": {
968 "output_zip": { 968 "output_zip": {
969 "id": "081ab14c99ce168b", 969 "id": "15b1f0554a03958d",
970 "src": "hda", 970 "src": "hda",
971 "uuid": "5e0faa51-141c-49d1-ba84-ca8aba27508c" 971 "uuid": "cdb61cbc-c9c5-45fc-9fc8-e00c1f3d4f0f"
972 } 972 }
973 }, 973 },
974 "params": { 974 "params": {
975 "__input_ext": "\"input\"", 975 "__input_ext": "\"input\"",
976 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 976 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
977 "assembly_plan_name": "\"BASICAssembly\"", 977 "assembly_plan_name": "\"BASICAssembly\"",
978 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 978 "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
979 "dbkey": "\"?\"", 979 "dbkey": "\"?\"",
980 "domesticated_input": null, 980 "domesticated_input": null,
981 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", 981 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}",
982 "topology": "\"circular\"" 982 "topology": "\"circular\""
983 }, 983 },
984 "state": "ok", 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, 49.70it/s, now=None]\r \r", 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, 44.90it/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", 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", 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, 49.70it/s, now=None]\r \r", 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, 44.90it/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", 989 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
990 "update_time": "2025-05-16T12:37:25.925491", 990 "update_time": "2025-05-19T13:46:34.776797",
991 "user_email": "planemo@galaxyproject.org", 991 "user_email": "planemo@galaxyproject.org",
992 "user_id": "a7025157dd5d3039" 992 "user_id": "fd8809ceca5b90d8"
993 }, 993 },
994 "status": "success", 994 "status": "success",
995 "test_index": 3, 995 "test_index": 3,
996 "time_seconds": 31.832648515701294, 996 "time_seconds": 32.1408953666687,
997 "tool_id": "cloning_simulation", 997 "tool_id": "cloning_simulation",
998 "tool_version": "0.1.0+galaxy0" 998 "tool_version": "0.1.0+galaxy0"
999 }, 999 },
1000 "has_data": true, 1000 "has_data": true,
1001 "id": "cloning_simulation-3" 1001 "id": "cloning_simulation-3"
1003 { 1003 {
1004 "data": { 1004 "data": {
1005 "inputs": { 1005 "inputs": {
1006 "adv|use_file_names_as_ids": true, 1006 "adv|use_file_names_as_ids": true,
1007 "assembly_csv": { 1007 "assembly_csv": {
1008 "id": "6af8c0d3c72d39ba", 1008 "id": "e7b347ef21d63fab",
1009 "src": "hda" 1009 "src": "hda"
1010 }, 1010 },
1011 "assembly_plan_name": "BioBrickStandardAssembly", 1011 "assembly_plan_name": "BioBrickStandardAssembly",
1012 "genbank_files": { 1012 "genbank_files": {
1013 "id": "5827a0347340e98b", 1013 "id": "fc2d53421d7989de",
1014 "src": "hdca" 1014 "src": "hdca"
1015 }, 1015 },
1016 "topology": "circular" 1016 "topology": "circular"
1017 }, 1017 },
1018 "job": { 1018 "job": {
1019 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/7/7/3/dataset_773be428-2d30-4b95-9894-d3758634a3d0.dat,/tmp/tmph0r87skq/files/b/a/c/dataset_bac673f5-074c-4810-9949-59d3b228d83c.dat,/tmp/tmph0r87skq/files/e/5/b/dataset_e5b8dfd0-6e81-47e4-b899-08976d0a1724.dat,/tmp/tmph0r87skq/files/1/5/8/dataset_158cbebb-69fc-4333-b783-e9171b5324d6.dat,/tmp/tmph0r87skq/files/a/5/b/dataset_a5b6ae8b-1068-416f-b0ac-1c44e299cb87.dat' --domesticated_seq '' --assembly_csv '/tmp/tmph0r87skq/files/4/e/d/dataset_4ed60503-3b9f-4204-a8e9-0b96f76b1e49.dat' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/7/7/3/dataset_773be428-2d30-4b95-9894-d3758634a3d0.dat:BBa_E0040_GFP.gb,/tmp/tmph0r87skq/files/b/a/c/dataset_bac673f5-074c-4810-9949-59d3b228d83c.dat:BBa_J23119_prom.gb,/tmp/tmph0r87skq/files/e/5/b/dataset_e5b8dfd0-6e81-47e4-b899-08976d0a1724.dat:BBa_J23119_prom_flawed.gb,/tmp/tmph0r87skq/files/1/5/8/dataset_158cbebb-69fc-4333-b783-e9171b5324d6.dat:BBa_J61048_term.gb,/tmp/tmph0r87skq/files/a/5/b/dataset_a5b6ae8b-1068-416f-b0ac-1c44e299cb87.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/tmph0r87skq/job_working_directory/000/35/outputs/dataset_5776ccd7-5dca-4f21-b288-9c15a0b9cdca.dat'", 1019 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/6/e/0/dataset_6e0453c4-6edd-4d76-9504-4cc4941610f6.dat,/tmp/tmpay0tme4v/files/6/d/3/dataset_6d3c24e5-73cd-4bed-95aa-d1c361c74180.dat,/tmp/tmpay0tme4v/files/7/7/9/dataset_7793541b-18cc-4f7d-a9df-12396807c368.dat,/tmp/tmpay0tme4v/files/a/e/1/dataset_ae1611ed-a5e2-46e8-b975-613ada1bb8db.dat,/tmp/tmpay0tme4v/files/9/a/d/dataset_9adfafe3-b0ad-449b-8555-286ca83e65a4.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/9/7/6/dataset_976f7d99-07e5-4d5c-ab79-a96ae42760d4.dat' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/6/e/0/dataset_6e0453c4-6edd-4d76-9504-4cc4941610f6.dat:BBa_E0040_GFP.gb,/tmp/tmpay0tme4v/files/6/d/3/dataset_6d3c24e5-73cd-4bed-95aa-d1c361c74180.dat:BBa_J23119_prom.gb,/tmp/tmpay0tme4v/files/7/7/9/dataset_7793541b-18cc-4f7d-a9df-12396807c368.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpay0tme4v/files/a/e/1/dataset_ae1611ed-a5e2-46e8-b975-613ada1bb8db.dat:BBa_J61048_term.gb,/tmp/tmpay0tme4v/files/9/a/d/dataset_9adfafe3-b0ad-449b-8555-286ca83e65a4.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/tmpay0tme4v/job_working_directory/000/35/outputs/dataset_deeb975f-4ae8-44d3-9c3c-51dc05e74f05.dat'",
1020 "command_version": "", 1020 "command_version": "",
1021 "copied_from_job_id": null, 1021 "copied_from_job_id": null,
1022 "create_time": "2025-05-16T12:37:47.708969", 1022 "create_time": "2025-05-19T13:46:57.146002",
1023 "dependencies": [ 1023 "dependencies": [
1024 { 1024 {
1025 "cacheable": false, 1025 "cacheable": false,
1026 "dependency_resolver": { 1026 "dependency_resolver": {
1027 "auto_init": true, 1027 "auto_init": true,
1197 "name": "dna_features_viewer", 1197 "name": "dna_features_viewer",
1198 "version": "3.1.5" 1198 "version": "3.1.5"
1199 } 1199 }
1200 ], 1200 ],
1201 "exit_code": 0, 1201 "exit_code": 0,
1202 "external_id": "207114", 1202 "external_id": "247581",
1203 "galaxy_version": "24.2", 1203 "galaxy_version": "24.2",
1204 "handler": null, 1204 "handler": null,
1205 "history_id": "d1cbd0905c1fc860", 1205 "history_id": "e550d863bf084702",
1206 "id": "081ab14c99ce168b", 1206 "id": "15b1f0554a03958d",
1207 "inputs": { 1207 "inputs": {
1208 "assembly_csv": { 1208 "assembly_csv": {
1209 "id": "6af8c0d3c72d39ba", 1209 "id": "e7b347ef21d63fab",
1210 "src": "hda", 1210 "src": "hda",
1211 "uuid": "4ed60503-3b9f-4204-a8e9-0b96f76b1e49" 1211 "uuid": "976f7d99-07e5-4d5c-ab79-a96ae42760d4"
1212 }, 1212 },
1213 "genbank_files1": { 1213 "genbank_files1": {
1214 "id": "06bb6ed11a5684d2", 1214 "id": "0d1c6bc715df133f",
1215 "src": "hda", 1215 "src": "hda",
1216 "uuid": "773be428-2d30-4b95-9894-d3758634a3d0" 1216 "uuid": "6e0453c4-6edd-4d76-9504-4cc4941610f6"
1217 }, 1217 },
1218 "genbank_files2": { 1218 "genbank_files2": {
1219 "id": "f34ce69b933b349e", 1219 "id": "7d9d065fa6859d88",
1220 "src": "hda", 1220 "src": "hda",
1221 "uuid": "bac673f5-074c-4810-9949-59d3b228d83c" 1221 "uuid": "6d3c24e5-73cd-4bed-95aa-d1c361c74180"
1222 }, 1222 },
1223 "genbank_files3": { 1223 "genbank_files3": {
1224 "id": "c295924a5ace6ae8", 1224 "id": "28aa4b1f3fb7d62b",
1225 "src": "hda", 1225 "src": "hda",
1226 "uuid": "e5b8dfd0-6e81-47e4-b899-08976d0a1724" 1226 "uuid": "7793541b-18cc-4f7d-a9df-12396807c368"
1227 }, 1227 },
1228 "genbank_files4": { 1228 "genbank_files4": {
1229 "id": "f3a950b5ccc2e145", 1229 "id": "7423dfb808ef4761",
1230 "src": "hda", 1230 "src": "hda",
1231 "uuid": "158cbebb-69fc-4333-b783-e9171b5324d6" 1231 "uuid": "ae1611ed-a5e2-46e8-b975-613ada1bb8db"
1232 }, 1232 },
1233 "genbank_files5": { 1233 "genbank_files5": {
1234 "id": "486d488c3f12b41a", 1234 "id": "175236d72b015bf8",
1235 "src": "hda", 1235 "src": "hda",
1236 "uuid": "a5b6ae8b-1068-416f-b0ac-1c44e299cb87" 1236 "uuid": "9adfafe3-b0ad-449b-8555-286ca83e65a4"
1237 } 1237 }
1238 }, 1238 },
1239 "job_messages": [], 1239 "job_messages": [],
1240 "job_metrics": [], 1240 "job_metrics": [],
1241 "job_runner_name": null, 1241 "job_runner_name": null,
1242 "job_stderr": "", 1242 "job_stderr": "",
1243 "job_stdout": "", 1243 "job_stdout": "",
1244 "model_class": "Job", 1244 "model_class": "Job",
1245 "output_collections": { 1245 "output_collections": {
1246 "construct_gb": { 1246 "construct_gb": {
1247 "id": "26800a0030991202", 1247 "id": "171b3bd3b2ffa75e",
1248 "src": "hdca" 1248 "src": "hdca"
1249 } 1249 }
1250 }, 1250 },
1251 "outputs": { 1251 "outputs": {
1252 "__new_primary_file_construct_gb|C1_prom_barcode__": { 1252 "__new_primary_file_construct_gb|C1_prom_barcode__": {
1253 "id": "62952fe061c1d5d6", 1253 "id": "2607809b86839f90",
1254 "src": "hda", 1254 "src": "hda",
1255 "uuid": "fb185bc3-4c8e-4095-864e-edc42d8c87ab" 1255 "uuid": "4e873fda-e181-4d71-b03b-61441dad6432"
1256 }, 1256 },
1257 "__new_primary_file_construct_gb|C2_gfp_term__": { 1257 "__new_primary_file_construct_gb|C2_gfp_term__": {
1258 "id": "14c055702e438446", 1258 "id": "d61271ad2bd59452",
1259 "src": "hda", 1259 "src": "hda",
1260 "uuid": "cb6310a2-1237-4f80-9efa-f149cb896f4d" 1260 "uuid": "1c217e77-9cfa-48b2-aabb-ccdcd23275ca"
1261 }, 1261 },
1262 "__new_primary_file_construct_gb|C3_final__": { 1262 "__new_primary_file_construct_gb|C3_final__": {
1263 "id": "e9ef3e2f0e439cf2", 1263 "id": "cdfae6a044106877",
1264 "src": "hda", 1264 "src": "hda",
1265 "uuid": "13db93e9-4505-4542-845c-57029b5e9a89" 1265 "uuid": "54b8bb86-f05d-4ec1-b551-7ed8ca22aedd"
1266 }, 1266 },
1267 "output_zip": { 1267 "output_zip": {
1268 "id": "7f1cb49d27c5ee0d", 1268 "id": "451b6ce8fd13ed5c",
1269 "src": "hda", 1269 "src": "hda",
1270 "uuid": "5776ccd7-5dca-4f21-b288-9c15a0b9cdca" 1270 "uuid": "deeb975f-4ae8-44d3-9c3c-51dc05e74f05"
1271 } 1271 }
1272 }, 1272 },
1273 "params": { 1273 "params": {
1274 "__input_ext": "\"input\"", 1274 "__input_ext": "\"input\"",
1275 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 1275 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1276 "assembly_plan_name": "\"BioBrickStandardAssembly\"", 1276 "assembly_plan_name": "\"BioBrickStandardAssembly\"",
1277 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1277 "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1278 "dbkey": "\"?\"", 1278 "dbkey": "\"?\"",
1279 "domesticated_input": null, 1279 "domesticated_input": null,
1280 "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}", 1280 "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}",
1281 "topology": "\"circular\"" 1281 "topology": "\"circular\""
1282 }, 1282 },
1283 "state": "ok", 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, 1.94it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.58it/s, now=None]\r \r", 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, 1.74it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:02<00:00, 1.43it/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", 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", 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, 1.94it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.58it/s, now=None]\r \r", 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, 1.74it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:02<00:00, 1.43it/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", 1288 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
1289 "update_time": "2025-05-16T12:38:00.688550", 1289 "update_time": "2025-05-19T13:47:10.784667",
1290 "user_email": "planemo@galaxyproject.org", 1290 "user_email": "planemo@galaxyproject.org",
1291 "user_id": "a7025157dd5d3039" 1291 "user_id": "fd8809ceca5b90d8"
1292 }, 1292 },
1293 "status": "success", 1293 "status": "success",
1294 "test_index": 4, 1294 "test_index": 4,
1295 "time_seconds": 34.85270929336548, 1295 "time_seconds": 35.92383527755737,
1296 "tool_id": "cloning_simulation", 1296 "tool_id": "cloning_simulation",
1297 "tool_version": "0.1.0+galaxy0" 1297 "tool_version": "0.1.0+galaxy0"
1298 }, 1298 },
1299 "has_data": true, 1299 "has_data": true,
1300 "id": "cloning_simulation-4" 1300 "id": "cloning_simulation-4"
1302 { 1302 {
1303 "data": { 1303 "data": {
1304 "inputs": { 1304 "inputs": {
1305 "adv|use_file_names_as_ids": true, 1305 "adv|use_file_names_as_ids": true,
1306 "assembly_csv": { 1306 "assembly_csv": {
1307 "id": "4e0765e9771b7fbe", 1307 "id": "8970dbe72f491b25",
1308 "src": "hda" 1308 "src": "hda"
1309 }, 1309 },
1310 "assembly_plan_name": "Type2sRestrictionAssembly", 1310 "assembly_plan_name": "Type2sRestrictionAssembly",
1311 "domesticated_input": { 1311 "domesticated_input": {
1312 "id": "9e9c740782c078df", 1312 "id": "ec7f951857c74506",
1313 "src": "hdca" 1313 "src": "hdca"
1314 }, 1314 },
1315 "genbank_files": { 1315 "genbank_files": {
1316 "id": "d70a40a14f24deac", 1316 "id": "8c74660869d2dd19",
1317 "src": "hdca" 1317 "src": "hdca"
1318 }, 1318 },
1319 "topology": "circular" 1319 "topology": "circular"
1320 }, 1320 },
1321 "job": { 1321 "job": {
1322 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmph0r87skq/files/b/c/d/dataset_bcd311aa-69db-4f2a-9d04-90f34cd78a6f.dat,/tmp/tmph0r87skq/files/0/4/9/dataset_049931ba-600a-46d6-a73e-af6bd3f545e3.dat,/tmp/tmph0r87skq/files/8/6/0/dataset_860e934f-31f6-4ac6-9eac-fd3abf031b08.dat,/tmp/tmph0r87skq/files/a/a/6/dataset_aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21.dat,/tmp/tmph0r87skq/files/3/d/9/dataset_3d97e337-7388-4fab-a6c3-7cb99f371f84.dat,/tmp/tmph0r87skq/files/b/4/5/dataset_b45031f8-71da-4365-9560-b827aa1d6794.dat,/tmp/tmph0r87skq/files/9/e/2/dataset_9e21455c-b124-4c01-8524-949ff16b570e.dat' --domesticated_seq '/tmp/tmph0r87skq/files/a/f/e/dataset_afe4126c-9cc0-45ec-a7d4-37816cb2132d.dat,/tmp/tmph0r87skq/files/f/a/8/dataset_fa8a7e9a-fa40-4e9f-a508-261fd8441292.dat,/tmp/tmph0r87skq/files/7/d/d/dataset_7ddb44a7-da6d-4215-8d11-1ba01c4f6516.dat,/tmp/tmph0r87skq/files/b/f/f/dataset_bff58a1b-e69e-4cb4-b344-79ba8800ac03.dat,/tmp/tmph0r87skq/files/a/f/8/dataset_af806691-7022-4bf2-a42b-7437042cee37.dat' --assembly_csv '/tmp/tmph0r87skq/files/c/6/5/dataset_c652bef1-f073-431c-9e5b-956a58e85d22.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmph0r87skq/files/b/c/d/dataset_bcd311aa-69db-4f2a-9d04-90f34cd78a6f.dat:part_A.gb,/tmp/tmph0r87skq/files/0/4/9/dataset_049931ba-600a-46d6-a73e-af6bd3f545e3.dat:part_B.gb,/tmp/tmph0r87skq/files/8/6/0/dataset_860e934f-31f6-4ac6-9eac-fd3abf031b08.dat:part_C.gb,/tmp/tmph0r87skq/files/a/a/6/dataset_aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21.dat:part_D.gb,/tmp/tmph0r87skq/files/3/d/9/dataset_3d97e337-7388-4fab-a6c3-7cb99f371f84.dat:part_E.gb,/tmp/tmph0r87skq/files/b/4/5/dataset_b45031f8-71da-4365-9560-b827aa1d6794.dat:part_F.gb,/tmp/tmph0r87skq/files/9/e/2/dataset_9e21455c-b124-4c01-8524-949ff16b570e.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmph0r87skq/files/a/f/e/dataset_afe4126c-9cc0-45ec-a7d4-37816cb2132d.dat:part_H.gb,/tmp/tmph0r87skq/files/f/a/8/dataset_fa8a7e9a-fa40-4e9f-a508-261fd8441292.dat:part_I.gb,/tmp/tmph0r87skq/files/7/d/d/dataset_7ddb44a7-da6d-4215-8d11-1ba01c4f6516.dat:part_J.gb,/tmp/tmph0r87skq/files/b/f/f/dataset_bff58a1b-e69e-4cb4-b344-79ba8800ac03.dat:part_K.gb,/tmp/tmph0r87skq/files/a/f/8/dataset_af806691-7022-4bf2-a42b-7437042cee37.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/tmph0r87skq/job_working_directory/000/49/outputs/dataset_a88370aa-4d36-4867-b0d6-613cc59ed01a.dat'", 1322 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/1/9/3/dataset_193cbd10-4b76-46d9-b377-a7f06471d4d4.dat,/tmp/tmpay0tme4v/files/f/a/3/dataset_fa31c5f5-e678-471e-b1a3-4f8a168bbee1.dat,/tmp/tmpay0tme4v/files/6/9/7/dataset_697c83fe-168b-4319-a6e5-3db90c504c8b.dat,/tmp/tmpay0tme4v/files/0/6/d/dataset_06d4dd94-5f33-4ce0-ab0a-e6efe96ca222.dat,/tmp/tmpay0tme4v/files/7/0/1/dataset_701b72c6-ec2e-4435-b0d5-8f419811a4dd.dat,/tmp/tmpay0tme4v/files/5/a/0/dataset_5a07f059-f6f9-49de-b0fc-3cded157f44b.dat,/tmp/tmpay0tme4v/files/7/5/3/dataset_753f0297-4bff-49c8-b22a-1377e43a81f6.dat' --domesticated_seq '/tmp/tmpay0tme4v/files/f/6/d/dataset_f6d602b9-7772-4a93-969d-f0dcdad98c6a.dat,/tmp/tmpay0tme4v/files/d/4/d/dataset_d4dc3ecb-77ff-4b28-a55a-7b263416c6c7.dat,/tmp/tmpay0tme4v/files/7/d/4/dataset_7d489dbd-161e-4f04-a3df-ef5b989ad1e0.dat,/tmp/tmpay0tme4v/files/4/c/a/dataset_4ca3c222-672a-4806-b60c-081f1b7b64cb.dat,/tmp/tmpay0tme4v/files/9/0/6/dataset_906707db-b3cf-40f9-af0b-1ffc143f91e8.dat' --assembly_csv '/tmp/tmpay0tme4v/files/9/c/8/dataset_9c8ec693-02f9-4cc7-b7e3-8bfb0a4dd1dc.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/1/9/3/dataset_193cbd10-4b76-46d9-b377-a7f06471d4d4.dat:part_A.gb,/tmp/tmpay0tme4v/files/f/a/3/dataset_fa31c5f5-e678-471e-b1a3-4f8a168bbee1.dat:part_B.gb,/tmp/tmpay0tme4v/files/6/9/7/dataset_697c83fe-168b-4319-a6e5-3db90c504c8b.dat:part_C.gb,/tmp/tmpay0tme4v/files/0/6/d/dataset_06d4dd94-5f33-4ce0-ab0a-e6efe96ca222.dat:part_D.gb,/tmp/tmpay0tme4v/files/7/0/1/dataset_701b72c6-ec2e-4435-b0d5-8f419811a4dd.dat:part_E.gb,/tmp/tmpay0tme4v/files/5/a/0/dataset_5a07f059-f6f9-49de-b0fc-3cded157f44b.dat:part_F.gb,/tmp/tmpay0tme4v/files/7/5/3/dataset_753f0297-4bff-49c8-b22a-1377e43a81f6.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpay0tme4v/files/f/6/d/dataset_f6d602b9-7772-4a93-969d-f0dcdad98c6a.dat:part_H.gb,/tmp/tmpay0tme4v/files/d/4/d/dataset_d4dc3ecb-77ff-4b28-a55a-7b263416c6c7.dat:part_I.gb,/tmp/tmpay0tme4v/files/7/d/4/dataset_7d489dbd-161e-4f04-a3df-ef5b989ad1e0.dat:part_J.gb,/tmp/tmpay0tme4v/files/4/c/a/dataset_4ca3c222-672a-4806-b60c-081f1b7b64cb.dat:part_K.gb,/tmp/tmpay0tme4v/files/9/0/6/dataset_906707db-b3cf-40f9-af0b-1ffc143f91e8.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/tmpay0tme4v/job_working_directory/000/49/outputs/dataset_800320dc-d181-40bf-b1cb-541f43a838c3.dat'",
1323 "command_version": "", 1323 "command_version": "",
1324 "copied_from_job_id": null, 1324 "copied_from_job_id": null,
1325 "create_time": "2025-05-16T12:38:41.107674", 1325 "create_time": "2025-05-19T13:47:53.361341",
1326 "dependencies": [ 1326 "dependencies": [
1327 { 1327 {
1328 "cacheable": false, 1328 "cacheable": false,
1329 "dependency_resolver": { 1329 "dependency_resolver": {
1330 "auto_init": true, 1330 "auto_init": true,
1500 "name": "dna_features_viewer", 1500 "name": "dna_features_viewer",
1501 "version": "3.1.5" 1501 "version": "3.1.5"
1502 } 1502 }
1503 ], 1503 ],
1504 "exit_code": 0, 1504 "exit_code": 0,
1505 "external_id": "208235", 1505 "external_id": "248775",
1506 "galaxy_version": "24.2", 1506 "galaxy_version": "24.2",
1507 "handler": null, 1507 "handler": null,
1508 "history_id": "0494b81690cb2f5c", 1508 "history_id": "6a73e15df176b356",
1509 "id": "1ad8534b5033158f", 1509 "id": "95f3db52d6362602",
1510 "inputs": { 1510 "inputs": {
1511 "assembly_csv": { 1511 "assembly_csv": {
1512 "id": "4e0765e9771b7fbe", 1512 "id": "8970dbe72f491b25",
1513 "src": "hda", 1513 "src": "hda",
1514 "uuid": "c652bef1-f073-431c-9e5b-956a58e85d22" 1514 "uuid": "9c8ec693-02f9-4cc7-b7e3-8bfb0a4dd1dc"
1515 }, 1515 },
1516 "domesticated_input1": { 1516 "domesticated_input1": {
1517 "id": "067523cf02b98b71", 1517 "id": "e666d72d584b2f08",
1518 "src": "hda", 1518 "src": "hda",
1519 "uuid": "afe4126c-9cc0-45ec-a7d4-37816cb2132d" 1519 "uuid": "f6d602b9-7772-4a93-969d-f0dcdad98c6a"
1520 }, 1520 },
1521 "domesticated_input2": { 1521 "domesticated_input2": {
1522 "id": "2f0a34076d4435df", 1522 "id": "55c4a2e28d82e47c",
1523 "src": "hda", 1523 "src": "hda",
1524 "uuid": "fa8a7e9a-fa40-4e9f-a508-261fd8441292" 1524 "uuid": "d4dc3ecb-77ff-4b28-a55a-7b263416c6c7"
1525 }, 1525 },
1526 "domesticated_input3": { 1526 "domesticated_input3": {
1527 "id": "a12a625822f3f961", 1527 "id": "b7e1b2e4287fecf1",
1528 "src": "hda", 1528 "src": "hda",
1529 "uuid": "7ddb44a7-da6d-4215-8d11-1ba01c4f6516" 1529 "uuid": "7d489dbd-161e-4f04-a3df-ef5b989ad1e0"
1530 }, 1530 },
1531 "domesticated_input4": { 1531 "domesticated_input4": {
1532 "id": "0b82bdc4f78225f4", 1532 "id": "fc5d10a4986179ce",
1533 "src": "hda", 1533 "src": "hda",
1534 "uuid": "bff58a1b-e69e-4cb4-b344-79ba8800ac03" 1534 "uuid": "4ca3c222-672a-4806-b60c-081f1b7b64cb"
1535 }, 1535 },
1536 "domesticated_input5": { 1536 "domesticated_input5": {
1537 "id": "5c9f1017a9cfea44", 1537 "id": "34217302c7a82039",
1538 "src": "hda", 1538 "src": "hda",
1539 "uuid": "af806691-7022-4bf2-a42b-7437042cee37" 1539 "uuid": "906707db-b3cf-40f9-af0b-1ffc143f91e8"
1540 }, 1540 },
1541 "genbank_files1": { 1541 "genbank_files1": {
1542 "id": "db55fd2326eb05de", 1542 "id": "bb3a8c61045de2bc",
1543 "src": "hda", 1543 "src": "hda",
1544 "uuid": "bcd311aa-69db-4f2a-9d04-90f34cd78a6f" 1544 "uuid": "193cbd10-4b76-46d9-b377-a7f06471d4d4"
1545 }, 1545 },
1546 "genbank_files2": { 1546 "genbank_files2": {
1547 "id": "551b1ccaf842a34c", 1547 "id": "ca37518126b9f794",
1548 "src": "hda", 1548 "src": "hda",
1549 "uuid": "049931ba-600a-46d6-a73e-af6bd3f545e3" 1549 "uuid": "fa31c5f5-e678-471e-b1a3-4f8a168bbee1"
1550 }, 1550 },
1551 "genbank_files3": { 1551 "genbank_files3": {
1552 "id": "aa4b51af1d3e5956", 1552 "id": "f5318c255dfd98f3",
1553 "src": "hda", 1553 "src": "hda",
1554 "uuid": "860e934f-31f6-4ac6-9eac-fd3abf031b08" 1554 "uuid": "697c83fe-168b-4319-a6e5-3db90c504c8b"
1555 }, 1555 },
1556 "genbank_files4": { 1556 "genbank_files4": {
1557 "id": "1ad8534b5033158f", 1557 "id": "95f3db52d6362602",
1558 "src": "hda", 1558 "src": "hda",
1559 "uuid": "aa6ecd8a-10b8-416a-95ec-bfbe1fa81d21" 1559 "uuid": "06d4dd94-5f33-4ce0-ab0a-e6efe96ca222"
1560 }, 1560 },
1561 "genbank_files5": { 1561 "genbank_files5": {
1562 "id": "67e60392c24a116d", 1562 "id": "22334014eeb47b8b",
1563 "src": "hda", 1563 "src": "hda",
1564 "uuid": "3d97e337-7388-4fab-a6c3-7cb99f371f84" 1564 "uuid": "701b72c6-ec2e-4435-b0d5-8f419811a4dd"
1565 }, 1565 },
1566 "genbank_files6": { 1566 "genbank_files6": {
1567 "id": "f0035bfbf96f19ca", 1567 "id": "aebcfa6b078c848c",
1568 "src": "hda", 1568 "src": "hda",
1569 "uuid": "b45031f8-71da-4365-9560-b827aa1d6794" 1569 "uuid": "5a07f059-f6f9-49de-b0fc-3cded157f44b"
1570 }, 1570 },
1571 "genbank_files7": { 1571 "genbank_files7": {
1572 "id": "d2976cafec9acf3d", 1572 "id": "63b7227f824d465f",
1573 "src": "hda", 1573 "src": "hda",
1574 "uuid": "9e21455c-b124-4c01-8524-949ff16b570e" 1574 "uuid": "753f0297-4bff-49c8-b22a-1377e43a81f6"
1575 } 1575 }
1576 }, 1576 },
1577 "job_messages": [], 1577 "job_messages": [],
1578 "job_metrics": [], 1578 "job_metrics": [],
1579 "job_runner_name": null, 1579 "job_runner_name": null,
1580 "job_stderr": "", 1580 "job_stderr": "",
1581 "job_stdout": "", 1581 "job_stdout": "",
1582 "model_class": "Job", 1582 "model_class": "Job",
1583 "output_collections": { 1583 "output_collections": {
1584 "construct_gb": { 1584 "construct_gb": {
1585 "id": "c02153e44a10e06a", 1585 "id": "40769e0726e5d2f9",
1586 "src": "hdca" 1586 "src": "hdca"
1587 } 1587 }
1588 }, 1588 },
1589 "outputs": { 1589 "outputs": {
1590 "__new_primary_file_construct_gb|construct_1__": { 1590 "__new_primary_file_construct_gb|construct_1__": {
1591 "id": "a3a16f375ef01612", 1591 "id": "00e4fea3ca53d1d5",
1592 "src": "hda", 1592 "src": "hda",
1593 "uuid": "760d3bcc-0498-4f4a-9420-511468a0b0b3" 1593 "uuid": "5cef395a-54ba-474b-b40b-1e5b3b2c4269"
1594 }, 1594 },
1595 "__new_primary_file_construct_gb|construct_2__": { 1595 "__new_primary_file_construct_gb|construct_2__": {
1596 "id": "99e6c6e9665a5a56", 1596 "id": "684375afe9650993",
1597 "src": "hda", 1597 "src": "hda",
1598 "uuid": "9836288d-70fb-464e-b565-90dc8f966379" 1598 "uuid": "77cca133-2fb3-4cf3-b4b1-a802a1f09ea3"
1599 }, 1599 },
1600 "__new_primary_file_construct_gb|construct_3__": { 1600 "__new_primary_file_construct_gb|construct_3__": {
1601 "id": "2d10fdf290562ab3", 1601 "id": "45afc15ea654e191",
1602 "src": "hda", 1602 "src": "hda",
1603 "uuid": "cf0e5bca-9446-4574-b885-ab1636310493" 1603 "uuid": "dbd53cde-61b2-4db8-b6bf-f0caaec76ace"
1604 }, 1604 },
1605 "__new_primary_file_construct_gb|construct_4__": { 1605 "__new_primary_file_construct_gb|construct_4__": {
1606 "id": "071f312ace6db7aa", 1606 "id": "8aa0c494b99ce49f",
1607 "src": "hda", 1607 "src": "hda",
1608 "uuid": "9e552d2e-e5f3-4163-b4b4-6351ec76f0d3" 1608 "uuid": "8ea5339c-3186-4886-8af7-2a2d8134e161"
1609 }, 1609 },
1610 "output_zip": { 1610 "output_zip": {
1611 "id": "72a012487a44f1a3", 1611 "id": "4d559b2811c6a30e",
1612 "src": "hda", 1612 "src": "hda",
1613 "uuid": "a88370aa-4d36-4867-b0d6-613cc59ed01a" 1613 "uuid": "800320dc-d181-40bf-b1cb-541f43a838c3"
1614 } 1614 }
1615 }, 1615 },
1616 "params": { 1616 "params": {
1617 "__input_ext": "\"input\"", 1617 "__input_ext": "\"input\"",
1618 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 1618 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1619 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", 1619 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
1620 "chromInfo": "\"/tmp/tmph0r87skq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1620 "chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1621 "dbkey": "\"?\"", 1621 "dbkey": "\"?\"",
1622 "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}", 1622 "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}",
1623 "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}", 1623 "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}",
1624 "topology": "\"circular\"" 1624 "topology": "\"circular\""
1625 }, 1625 },
1626 "state": "ok", 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, 2.46it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", 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, 2.35it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.13it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.77it/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", 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", 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, 2.46it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.25it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.84it/s, now=None]\r \r", 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, 2.35it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.13it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.77it/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", 1631 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
1632 "update_time": "2025-05-16T12:38:53.803402", 1632 "update_time": "2025-05-19T13:48:06.412363",
1633 "user_email": "planemo@galaxyproject.org", 1633 "user_email": "planemo@galaxyproject.org",
1634 "user_id": "a7025157dd5d3039" 1634 "user_id": "fd8809ceca5b90d8"
1635 }, 1635 },
1636 "status": "success", 1636 "status": "success",
1637 "test_index": 5, 1637 "test_index": 5,
1638 "time_seconds": 52.96998858451843, 1638 "time_seconds": 55.54361414909363,
1639 "tool_id": "cloning_simulation", 1639 "tool_id": "cloning_simulation",
1640 "tool_version": "0.1.0+galaxy0" 1640 "tool_version": "0.1.0+galaxy0"
1641 }, 1641 },
1642 "has_data": true, 1642 "has_data": true,
1643 "id": "cloning_simulation-5" 1643 "id": "cloning_simulation-5"