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comparison output.json @ 8:07e902da89ad draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 26 May 2025 09:23:51 +0000
parents 296e5145a862
children 0be569bd5443
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7:296e5145a862 8:07e902da89ad
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": "106ff655f8a511fe", 14 "id": "0a696a8b22798e06",
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": "8094a24bdbd328fd", 19 "id": "cb6d3fbb91be6861",
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' && cp '/tmp/tmpulb7kecp/files/b/1/1/dataset_b114952d-795f-4872-a508-1b68f71f6843.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/7/7/2/dataset_7728392b-6cec-4864-bb21-79c5330f34db.dat,/tmp/tmpulb7kecp/files/f/9/6/dataset_f96a1c6f-cc5b-4969-947e-d0c5d9bc1861.dat,/tmp/tmpulb7kecp/files/5/d/9/dataset_5d9fa39d-58a0-4385-a52a-cff566ab6569.dat,/tmp/tmpulb7kecp/files/9/2/d/dataset_92d74dbb-3200-4182-b1c1-b916d8b9636a.dat,/tmp/tmpulb7kecp/files/4/e/7/dataset_4e7f3975-e0c4-4043-a1d6-e798d43c88bd.dat,/tmp/tmpulb7kecp/files/9/6/5/dataset_965d5a1c-5b11-44c4-b1bc-392cb2e34bda.dat,/tmp/tmpulb7kecp/files/b/2/9/dataset_b29b6ede-fd7d-4db7-812a-e4719848c9d9.dat,/tmp/tmpulb7kecp/files/d/0/b/dataset_d0b8b55e-d329-4566-b8a2-8708f23d57d2.dat,/tmp/tmpulb7kecp/files/b/c/1/dataset_bc107665-0e38-42fe-8183-edb3b3f22248.dat,/tmp/tmpulb7kecp/files/f/7/e/dataset_f7e084da-7abc-4b0b-a75a-d7be088e30ee.dat,/tmp/tmpulb7kecp/files/6/2/e/dataset_62ece79d-c0cc-454a-bbd8-1c943ff0bcce.dat,/tmp/tmpulb7kecp/files/2/4/7/dataset_2476887f-77e7-4955-8e73-a0b57b50009d.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/7/7/2/dataset_7728392b-6cec-4864-bb21-79c5330f34db.dat:part_A.gb,/tmp/tmpulb7kecp/files/f/9/6/dataset_f96a1c6f-cc5b-4969-947e-d0c5d9bc1861.dat:part_B.gb,/tmp/tmpulb7kecp/files/5/d/9/dataset_5d9fa39d-58a0-4385-a52a-cff566ab6569.dat:part_C.gb,/tmp/tmpulb7kecp/files/9/2/d/dataset_92d74dbb-3200-4182-b1c1-b916d8b9636a.dat:part_D.gb,/tmp/tmpulb7kecp/files/4/e/7/dataset_4e7f3975-e0c4-4043-a1d6-e798d43c88bd.dat:part_E.gb,/tmp/tmpulb7kecp/files/9/6/5/dataset_965d5a1c-5b11-44c4-b1bc-392cb2e34bda.dat:part_F.gb,/tmp/tmpulb7kecp/files/b/2/9/dataset_b29b6ede-fd7d-4db7-812a-e4719848c9d9.dat:part_G.gb,/tmp/tmpulb7kecp/files/d/0/b/dataset_d0b8b55e-d329-4566-b8a2-8708f23d57d2.dat:part_H.gb,/tmp/tmpulb7kecp/files/b/c/1/dataset_bc107665-0e38-42fe-8183-edb3b3f22248.dat:part_I.gb,/tmp/tmpulb7kecp/files/f/7/e/dataset_f7e084da-7abc-4b0b-a75a-d7be088e30ee.dat:part_J.gb,/tmp/tmpulb7kecp/files/6/2/e/dataset_62ece79d-c0cc-454a-bbd8-1c943ff0bcce.dat:part_K.gb,/tmp/tmpulb7kecp/files/2/4/7/dataset_2476887f-77e7-4955-8e73-a0b57b50009d.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/tmpulb7kecp/job_working_directory/000/14/outputs/dataset_531b5c74-8577-4ba2-86cf-d8f25f16e169.dat'", 25 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/b/a/a/dataset_baa59b14-7fb5-4efc-a75d-228d26b70adc.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/f/7/b/dataset_f7bde375-2c6b-4e23-9117-e96bb4c3f6e6.dat,/tmp/tmp_ibkdcj0/files/b/a/5/dataset_ba5c9d10-e47e-4ced-9aaf-a51bf18e7932.dat,/tmp/tmp_ibkdcj0/files/b/f/6/dataset_bf6e6482-afaa-4790-ac74-23f532fa48ad.dat,/tmp/tmp_ibkdcj0/files/1/b/8/dataset_1b8c7b47-fdba-4046-953a-89dc0c07ae14.dat,/tmp/tmp_ibkdcj0/files/5/f/5/dataset_5f5321b9-fa9a-4a73-9573-890d0c00209d.dat,/tmp/tmp_ibkdcj0/files/8/5/5/dataset_8557a762-7c36-4111-a015-2b61caad4e5b.dat,/tmp/tmp_ibkdcj0/files/f/7/0/dataset_f7000fc2-7e04-4561-875c-b84614f51966.dat,/tmp/tmp_ibkdcj0/files/3/d/f/dataset_3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09.dat,/tmp/tmp_ibkdcj0/files/e/3/b/dataset_e3b26d77-5d05-4a0f-adf7-016bf86c5eb3.dat,/tmp/tmp_ibkdcj0/files/3/2/1/dataset_3217492e-bc97-4d61-87fd-b9d1f2e4534d.dat,/tmp/tmp_ibkdcj0/files/f/8/f/dataset_f8f04302-598c-4596-99a1-6c7d84b613d6.dat,/tmp/tmp_ibkdcj0/files/9/f/6/dataset_9f67cbfd-ca06-4926-b042-74a0d43b585a.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/f/7/b/dataset_f7bde375-2c6b-4e23-9117-e96bb4c3f6e6.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/b/a/5/dataset_ba5c9d10-e47e-4ced-9aaf-a51bf18e7932.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/b/f/6/dataset_bf6e6482-afaa-4790-ac74-23f532fa48ad.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/1/b/8/dataset_1b8c7b47-fdba-4046-953a-89dc0c07ae14.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/5/f/5/dataset_5f5321b9-fa9a-4a73-9573-890d0c00209d.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/8/5/5/dataset_8557a762-7c36-4111-a015-2b61caad4e5b.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/f/7/0/dataset_f7000fc2-7e04-4561-875c-b84614f51966.dat:part_G.gb,/tmp/tmp_ibkdcj0/files/3/d/f/dataset_3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/e/3/b/dataset_e3b26d77-5d05-4a0f-adf7-016bf86c5eb3.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/3/2/1/dataset_3217492e-bc97-4d61-87fd-b9d1f2e4534d.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/f/8/f/dataset_f8f04302-598c-4596-99a1-6c7d84b613d6.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/9/f/6/dataset_9f67cbfd-ca06-4926-b042-74a0d43b585a.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/tmp_ibkdcj0/job_working_directory/000/14/outputs/dataset_49164d85-9bff-47f5-b8ee-de001d155fd3.dat'",
26 "command_version": "", 26 "command_version": "",
27 "copied_from_job_id": null, 27 "copied_from_job_id": null,
28 "create_time": "2025-05-23T12:13:12.978945", 28 "create_time": "2025-05-26T08:56:03.115650",
29 "dependencies": [], 29 "dependencies": [],
30 "exit_code": 0, 30 "exit_code": 0,
31 "external_id": "178458", 31 "external_id": "78665",
32 "galaxy_version": "24.2", 32 "galaxy_version": "24.2",
33 "handler": null, 33 "handler": null,
34 "history_id": "8094a24bdbd328fd", 34 "history_id": "cb6d3fbb91be6861",
35 "id": "a843aa6880d39864", 35 "id": "2ff5b0f6b4cfbb73",
36 "inputs": { 36 "inputs": {
37 "assembly_csv": { 37 "assembly_csv": {
38 "id": "106ff655f8a511fe", 38 "id": "0a696a8b22798e06",
39 "src": "hda", 39 "src": "hda",
40 "uuid": "b114952d-795f-4872-a508-1b68f71f6843" 40 "uuid": "baa59b14-7fb5-4efc-a75d-228d26b70adc"
41 }, 41 },
42 "genbank_files1": { 42 "genbank_files1": {
43 "id": "8094a24bdbd328fd", 43 "id": "cb6d3fbb91be6861",
44 "src": "hda", 44 "src": "hda",
45 "uuid": "7728392b-6cec-4864-bb21-79c5330f34db" 45 "uuid": "f7bde375-2c6b-4e23-9117-e96bb4c3f6e6"
46 }, 46 },
47 "genbank_files10": { 47 "genbank_files10": {
48 "id": "54ed1ed3b165c7b4", 48 "id": "7ede2556a40dc9ba",
49 "src": "hda", 49 "src": "hda",
50 "uuid": "f7e084da-7abc-4b0b-a75a-d7be088e30ee" 50 "uuid": "3217492e-bc97-4d61-87fd-b9d1f2e4534d"
51 }, 51 },
52 "genbank_files11": { 52 "genbank_files11": {
53 "id": "aa441ebc75addcb0", 53 "id": "76608081d307dc20",
54 "src": "hda", 54 "src": "hda",
55 "uuid": "62ece79d-c0cc-454a-bbd8-1c943ff0bcce" 55 "uuid": "f8f04302-598c-4596-99a1-6c7d84b613d6"
56 }, 56 },
57 "genbank_files12": { 57 "genbank_files12": {
58 "id": "41108ccf3c813abd", 58 "id": "0551bf01e3dbca02",
59 "src": "hda", 59 "src": "hda",
60 "uuid": "2476887f-77e7-4955-8e73-a0b57b50009d" 60 "uuid": "9f67cbfd-ca06-4926-b042-74a0d43b585a"
61 }, 61 },
62 "genbank_files2": { 62 "genbank_files2": {
63 "id": "6c2020bf7be1ec65", 63 "id": "18a1e53d7b8ec0fa",
64 "src": "hda", 64 "src": "hda",
65 "uuid": "f96a1c6f-cc5b-4969-947e-d0c5d9bc1861" 65 "uuid": "ba5c9d10-e47e-4ced-9aaf-a51bf18e7932"
66 }, 66 },
67 "genbank_files3": { 67 "genbank_files3": {
68 "id": "8a7a2aba20929ed0", 68 "id": "afdf3d24f0e34eea",
69 "src": "hda", 69 "src": "hda",
70 "uuid": "5d9fa39d-58a0-4385-a52a-cff566ab6569" 70 "uuid": "bf6e6482-afaa-4790-ac74-23f532fa48ad"
71 }, 71 },
72 "genbank_files4": { 72 "genbank_files4": {
73 "id": "53ad8e2eaf8a05d9", 73 "id": "285751a21c9d1d68",
74 "src": "hda", 74 "src": "hda",
75 "uuid": "92d74dbb-3200-4182-b1c1-b916d8b9636a" 75 "uuid": "1b8c7b47-fdba-4046-953a-89dc0c07ae14"
76 }, 76 },
77 "genbank_files5": { 77 "genbank_files5": {
78 "id": "85b2c5efa0bce20f", 78 "id": "48e4779cf88cf124",
79 "src": "hda", 79 "src": "hda",
80 "uuid": "4e7f3975-e0c4-4043-a1d6-e798d43c88bd" 80 "uuid": "5f5321b9-fa9a-4a73-9573-890d0c00209d"
81 }, 81 },
82 "genbank_files6": { 82 "genbank_files6": {
83 "id": "3758c7315f184c9a", 83 "id": "2bf3ecab9316a382",
84 "src": "hda", 84 "src": "hda",
85 "uuid": "965d5a1c-5b11-44c4-b1bc-392cb2e34bda" 85 "uuid": "8557a762-7c36-4111-a015-2b61caad4e5b"
86 }, 86 },
87 "genbank_files7": { 87 "genbank_files7": {
88 "id": "cc5b73713462c207", 88 "id": "d51bf47fbc922335",
89 "src": "hda", 89 "src": "hda",
90 "uuid": "b29b6ede-fd7d-4db7-812a-e4719848c9d9" 90 "uuid": "f7000fc2-7e04-4561-875c-b84614f51966"
91 }, 91 },
92 "genbank_files8": { 92 "genbank_files8": {
93 "id": "abedd81ff2360f10", 93 "id": "590bb56cc83504dc",
94 "src": "hda", 94 "src": "hda",
95 "uuid": "d0b8b55e-d329-4566-b8a2-8708f23d57d2" 95 "uuid": "3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09"
96 }, 96 },
97 "genbank_files9": { 97 "genbank_files9": {
98 "id": "83d0643dcafc650b", 98 "id": "ff96e44e65db99f8",
99 "src": "hda", 99 "src": "hda",
100 "uuid": "bc107665-0e38-42fe-8183-edb3b3f22248" 100 "uuid": "e3b26d77-5d05-4a0f-adf7-016bf86c5eb3"
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": "6c2020bf7be1ec65", 111 "id": "18a1e53d7b8ec0fa",
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": "03b30db777cad5e1", 117 "id": "be5466d8eb2c2229",
118 "src": "hda", 118 "src": "hda",
119 "uuid": "21d43ad8-7969-4897-bade-2bde4913b7c5" 119 "uuid": "2c83aaa9-63df-43a5-b008-9a361a9fc312"
120 }, 120 },
121 "__new_primary_file_construct_gb|construct_2__": { 121 "__new_primary_file_construct_gb|construct_2__": {
122 "id": "d7483ddd36cf3921", 122 "id": "a37f81f30817f4ff",
123 "src": "hda", 123 "src": "hda",
124 "uuid": "9420de76-fe00-401e-9cef-039d76b41e8f" 124 "uuid": "8ba2ce56-ba8b-4ff8-bcc0-54d0a2ad3b09"
125 }, 125 },
126 "__new_primary_file_construct_gb|construct_3__": { 126 "__new_primary_file_construct_gb|construct_3__": {
127 "id": "2239b1a77a4b659c", 127 "id": "b4705f371a43addc",
128 "src": "hda", 128 "src": "hda",
129 "uuid": "e360b3e5-97c6-49be-9e0e-4ff44209fb03" 129 "uuid": "47741e71-6bf6-46ec-9353-25bb48d895ed"
130 }, 130 },
131 "__new_primary_file_construct_gb|construct_4__": { 131 "__new_primary_file_construct_gb|construct_4__": {
132 "id": "b9f6f443461a8e55", 132 "id": "0dc911fcb05967a3",
133 "src": "hda", 133 "src": "hda",
134 "uuid": "580f1a4e-e43c-4396-9ae5-d441a0f64d1a" 134 "uuid": "6aa740ec-6985-4d66-8427-b1652fa06f3a"
135 }, 135 },
136 "output_zip": { 136 "output_zip": {
137 "id": "a843aa6880d39864", 137 "id": "2ff5b0f6b4cfbb73",
138 "src": "hda", 138 "src": "hda",
139 "uuid": "531b5c74-8577-4ba2-86cf-d8f25f16e169" 139 "uuid": "49164d85-9bff-47f5-b8ee-de001d155fd3"
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/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 146 "chromInfo": "\"/tmp/tmp_ibkdcj0/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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.20it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.78it/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, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.20it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.78it/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, 2.41it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/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": "2025-05-23T12:13:26.150051", 158 "update_time": "2025-05-26T08:56:15.534051",
159 "user_email": "planemo@galaxyproject.org", 159 "user_email": "planemo@galaxyproject.org",
160 "user_id": "8094a24bdbd328fd" 160 "user_id": "cb6d3fbb91be6861"
161 }, 161 },
162 "status": "success", 162 "status": "success",
163 "test_index": 0, 163 "test_index": 0,
164 "time_seconds": 53.7402708530426, 164 "time_seconds": 54.95904994010925,
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": "9ebeb50920a3365f", 176 "id": "e01f0df21d75058c",
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": "8a7a2aba20929ed0", 181 "id": "afdf3d24f0e34eea",
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' && cp '/tmp/tmpulb7kecp/files/c/b/4/dataset_cb485986-3b87-4675-b3c5-cdb2d0287c2a.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/a/6/0/dataset_a609f7c2-042e-4412-98a8-2056fe698533.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/a/6/0/dataset_a609f7c2-042e-4412-98a8-2056fe698533.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/tmpulb7kecp/job_working_directory/000/17/outputs/dataset_ff63bc11-8e44-4753-a248-329fb44ee3b1.dat'", 187 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/5/b/2/dataset_5b2e01d9-e63b-45e1-8523-e88570aecbd1.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/5/6/3/dataset_5633084d-0123-48ba-b733-086550a95944.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/5/6/3/dataset_5633084d-0123-48ba-b733-086550a95944.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/tmp_ibkdcj0/job_working_directory/000/17/outputs/dataset_81c8307a-8e03-4975-b3ec-1115f4f47284.dat'",
188 "command_version": "", 188 "command_version": "",
189 "copied_from_job_id": null, 189 "copied_from_job_id": null,
190 "create_time": "2025-05-23T12:13:37.414073", 190 "create_time": "2025-05-26T08:56:26.250368",
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": "178806", 370 "external_id": "79009",
371 "galaxy_version": "24.2", 371 "galaxy_version": "24.2",
372 "handler": null, 372 "handler": null,
373 "history_id": "6c2020bf7be1ec65", 373 "history_id": "18a1e53d7b8ec0fa",
374 "id": "2239b1a77a4b659c", 374 "id": "b4705f371a43addc",
375 "inputs": { 375 "inputs": {
376 "assembly_csv": { 376 "assembly_csv": {
377 "id": "9ebeb50920a3365f", 377 "id": "e01f0df21d75058c",
378 "src": "hda", 378 "src": "hda",
379 "uuid": "cb485986-3b87-4675-b3c5-cdb2d0287c2a" 379 "uuid": "5b2e01d9-e63b-45e1-8523-e88570aecbd1"
380 }, 380 },
381 "genbank_files1": { 381 "genbank_files1": {
382 "id": "293d5da1ac833ef3", 382 "id": "bc8da7662961ae94",
383 "src": "hda", 383 "src": "hda",
384 "uuid": "a609f7c2-042e-4412-98a8-2056fe698533" 384 "uuid": "5633084d-0123-48ba-b733-086550a95944"
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": "53ad8e2eaf8a05d9", 395 "id": "285751a21c9d1d68",
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": "a21f4c8cc3b535db", 401 "id": "d8c348e4a6c18790",
402 "src": "hda", 402 "src": "hda",
403 "uuid": "0463b48d-c2d8-42a4-8b6a-ecb4dfc701c4" 403 "uuid": "39e12d2a-e4aa-491e-bb74-be0d48efaa36"
404 }, 404 },
405 "__new_primary_file_construct_gb|construct_2__": { 405 "__new_primary_file_construct_gb|construct_2__": {
406 "id": "c9bb032e1a0e8897", 406 "id": "cc98bdb1867cbf6a",
407 "src": "hda", 407 "src": "hda",
408 "uuid": "89f175c4-8e96-49e3-8c45-514b2193b29a" 408 "uuid": "dbc568c1-dd73-4973-aa7a-f33cb279cbb7"
409 }, 409 },
410 "__new_primary_file_construct_gb|construct_3__": { 410 "__new_primary_file_construct_gb|construct_3__": {
411 "id": "68281df0cf338722", 411 "id": "dd60b22cea40a264",
412 "src": "hda", 412 "src": "hda",
413 "uuid": "2a43a8fd-7b64-4f92-a483-6c716ec2f681" 413 "uuid": "3d0514f2-d798-484f-add3-d04103fef517"
414 }, 414 },
415 "output_zip": { 415 "output_zip": {
416 "id": "713969bb307bfc17", 416 "id": "cb5bc2d1019b090c",
417 "src": "hda", 417 "src": "hda",
418 "uuid": "ff63bc11-8e44-4753-a248-329fb44ee3b1" 418 "uuid": "81c8307a-8e03-4975-b3ec-1115f4f47284"
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/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 425 "chromInfo": "\"/tmp/tmp_ibkdcj0/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, 4.37it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.36it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.35it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.54it/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, 4.42it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.41it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.40it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.63it/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, 4.37it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.36it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.35it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.54it/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, 4.42it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.41it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.40it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.63it/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": "2025-05-23T12:13:49.541469", 437 "update_time": "2025-05-26T08:56:38.283009",
438 "user_email": "planemo@galaxyproject.org", 438 "user_email": "planemo@galaxyproject.org",
439 "user_id": "8094a24bdbd328fd" 439 "user_id": "cb6d3fbb91be6861"
440 }, 440 },
441 "status": "success", 441 "status": "success",
442 "test_index": 1, 442 "test_index": 1,
443 "time_seconds": 23.19603419303894, 443 "time_seconds": 22.636474609375,
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": "6ba0e4a0e82495c8", 455 "id": "c6996082322986ef",
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": "85b2c5efa0bce20f", 460 "id": "48e4779cf88cf124",
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' && cp '/tmp/tmpulb7kecp/files/b/7/7/dataset_b7713227-6c97-4684-ac9a-76650631a0a9.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/f/e/9/dataset_fe9a8ec6-5d0f-4f89-934f-a46bb9ff8db7.dat,/tmp/tmpulb7kecp/files/4/5/7/dataset_45763854-327e-472f-9cb3-a3cc72b8f76b.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/f/e/9/dataset_fe9a8ec6-5d0f-4f89-934f-a46bb9ff8db7.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpulb7kecp/files/4/5/7/dataset_45763854-327e-472f-9cb3-a3cc72b8f76b.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/tmpulb7kecp/job_working_directory/000/21/outputs/dataset_1d53129b-a396-429b-9971-2d00b993e48a.dat'", 466 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/3/6/c/dataset_36c9642c-c980-4a5f-babe-e1140450965b.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/f/d/7/dataset_fd7feec8-d839-4aac-ba59-54d4042d72d4.dat,/tmp/tmp_ibkdcj0/files/0/9/7/dataset_097d3af5-48d7-4b15-9063-19cc11585d82.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/f/d/7/dataset_fd7feec8-d839-4aac-ba59-54d4042d72d4.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmp_ibkdcj0/files/0/9/7/dataset_097d3af5-48d7-4b15-9063-19cc11585d82.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/tmp_ibkdcj0/job_working_directory/000/21/outputs/dataset_dd39a396-84ad-4350-8d9b-a0efafd5ea2a.dat'",
467 "command_version": "", 467 "command_version": "",
468 "copied_from_job_id": null, 468 "copied_from_job_id": null,
469 "create_time": "2025-05-23T12:14:01.238952", 469 "create_time": "2025-05-26T08:56:49.662294",
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": "179225", 649 "external_id": "79436",
650 "galaxy_version": "24.2", 650 "galaxy_version": "24.2",
651 "handler": null, 651 "handler": null,
652 "history_id": "8a7a2aba20929ed0", 652 "history_id": "afdf3d24f0e34eea",
653 "id": "713969bb307bfc17", 653 "id": "cb5bc2d1019b090c",
654 "inputs": { 654 "inputs": {
655 "assembly_csv": { 655 "assembly_csv": {
656 "id": "6ba0e4a0e82495c8", 656 "id": "c6996082322986ef",
657 "src": "hda", 657 "src": "hda",
658 "uuid": "b7713227-6c97-4684-ac9a-76650631a0a9" 658 "uuid": "36c9642c-c980-4a5f-babe-e1140450965b"
659 }, 659 },
660 "genbank_files1": { 660 "genbank_files1": {
661 "id": "f1fafc006c3c5be7", 661 "id": "ff6721ae641686bd",
662 "src": "hda", 662 "src": "hda",
663 "uuid": "fe9a8ec6-5d0f-4f89-934f-a46bb9ff8db7" 663 "uuid": "fd7feec8-d839-4aac-ba59-54d4042d72d4"
664 }, 664 },
665 "genbank_files2": { 665 "genbank_files2": {
666 "id": "8c1f52fe6e59f5ac", 666 "id": "898f771988549b05",
667 "src": "hda", 667 "src": "hda",
668 "uuid": "45763854-327e-472f-9cb3-a3cc72b8f76b" 668 "uuid": "097d3af5-48d7-4b15-9063-19cc11585d82"
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": "3758c7315f184c9a", 679 "id": "2bf3ecab9316a382",
680 "src": "hdca" 680 "src": "hdca"
681 } 681 }
682 }, 682 },
683 "outputs": { 683 "outputs": {
684 "output_zip": { 684 "output_zip": {
685 "id": "db12508970e81a14", 685 "id": "b995dfb8c32b92b7",
686 "src": "hda", 686 "src": "hda",
687 "uuid": "1d53129b-a396-429b-9971-2d00b993e48a" 687 "uuid": "dd39a396-84ad-4350-8d9b-a0efafd5ea2a"
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/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 694 "chromInfo": "\"/tmp/tmp_ibkdcj0/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, 2.37it/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, 2.23it/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, 2.37it/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, 2.23it/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": "2025-05-23T12:14:13.046545", 706 "update_time": "2025-05-26T08:57:02.321903",
707 "user_email": "planemo@galaxyproject.org", 707 "user_email": "planemo@galaxyproject.org",
708 "user_id": "8094a24bdbd328fd" 708 "user_id": "cb6d3fbb91be6861"
709 }, 709 },
710 "status": "success", 710 "status": "success",
711 "test_index": 2, 711 "test_index": 2,
712 "time_seconds": 23.21994924545288, 712 "time_seconds": 23.856895685195923,
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": "a9ed9e5261104c2a", 724 "id": "9d9573fdc2182066",
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": "cc5b73713462c207", 729 "id": "d51bf47fbc922335",
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' && cp '/tmp/tmpulb7kecp/files/5/1/3/dataset_513294c4-b1bf-4a02-a37d-6f4bd74436d9.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/a/7/9/dataset_a79829ef-6450-404a-8d59-fa42ddb91ca3.dat,/tmp/tmpulb7kecp/files/7/c/7/dataset_7c74d4c3-38b5-40a7-9c71-482502e6e5f8.dat,/tmp/tmpulb7kecp/files/5/1/c/dataset_51c3184d-fd7e-49a8-af51-e29bbf7a8a37.dat,/tmp/tmpulb7kecp/files/2/4/4/dataset_24493579-a703-4b94-ac09-e283f59035b0.dat,/tmp/tmpulb7kecp/files/c/b/4/dataset_cb4bfd16-db5c-47ce-98f5-a5c5065d4dd4.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/a/7/9/dataset_a79829ef-6450-404a-8d59-fa42ddb91ca3.dat:GFP.gb,/tmp/tmpulb7kecp/files/7/c/7/dataset_7c74d4c3-38b5-40a7-9c71-482502e6e5f8.dat:p15A_kan.gb,/tmp/tmpulb7kecp/files/5/1/c/dataset_51c3184d-fd7e-49a8-af51-e29bbf7a8a37.dat:promoter.gb,/tmp/tmpulb7kecp/files/2/4/4/dataset_24493579-a703-4b94-ac09-e283f59035b0.dat:RFP.gb,/tmp/tmpulb7kecp/files/c/b/4/dataset_cb4bfd16-db5c-47ce-98f5-a5c5065d4dd4.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/tmpulb7kecp/job_working_directory/000/28/outputs/dataset_47491132-901d-4249-9c1e-dfd12feae17e.dat'", 735 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/2/5/1/dataset_251d413f-0fe8-42cd-8a76-7ef77cde6f15.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/7/d/8/dataset_7d893bbf-b4e0-4d64-bafc-21ba1566237d.dat,/tmp/tmp_ibkdcj0/files/c/c/2/dataset_cc2314fa-924f-47c0-b89a-661fb78790a4.dat,/tmp/tmp_ibkdcj0/files/8/d/0/dataset_8d097c97-7bd5-48eb-9f9e-f5b92ce19458.dat,/tmp/tmp_ibkdcj0/files/5/9/1/dataset_59189305-e832-4191-be7c-496c01c8aba6.dat,/tmp/tmp_ibkdcj0/files/4/0/2/dataset_402500d7-6532-4008-9445-c0cf7fed5350.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/7/d/8/dataset_7d893bbf-b4e0-4d64-bafc-21ba1566237d.dat:GFP.gb,/tmp/tmp_ibkdcj0/files/c/c/2/dataset_cc2314fa-924f-47c0-b89a-661fb78790a4.dat:p15A_kan.gb,/tmp/tmp_ibkdcj0/files/8/d/0/dataset_8d097c97-7bd5-48eb-9f9e-f5b92ce19458.dat:promoter.gb,/tmp/tmp_ibkdcj0/files/5/9/1/dataset_59189305-e832-4191-be7c-496c01c8aba6.dat:RFP.gb,/tmp/tmp_ibkdcj0/files/4/0/2/dataset_402500d7-6532-4008-9445-c0cf7fed5350.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/tmp_ibkdcj0/job_working_directory/000/28/outputs/dataset_8e6b31eb-84b3-4184-92eb-33384ae50857.dat'",
736 "command_version": "", 736 "command_version": "",
737 "copied_from_job_id": null, 737 "copied_from_job_id": null,
738 "create_time": "2025-05-23T12:14:34.083682", 738 "create_time": "2025-05-26T08:57:24.342653",
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": "179816", 918 "external_id": "80040",
919 "galaxy_version": "24.2", 919 "galaxy_version": "24.2",
920 "handler": null, 920 "handler": null,
921 "history_id": "53ad8e2eaf8a05d9", 921 "history_id": "285751a21c9d1d68",
922 "id": "db12508970e81a14", 922 "id": "b995dfb8c32b92b7",
923 "inputs": { 923 "inputs": {
924 "assembly_csv": { 924 "assembly_csv": {
925 "id": "a9ed9e5261104c2a", 925 "id": "9d9573fdc2182066",
926 "src": "hda", 926 "src": "hda",
927 "uuid": "513294c4-b1bf-4a02-a37d-6f4bd74436d9" 927 "uuid": "251d413f-0fe8-42cd-8a76-7ef77cde6f15"
928 }, 928 },
929 "genbank_files1": { 929 "genbank_files1": {
930 "id": "ce8e89b55ee6d12d", 930 "id": "241cfac882733d83",
931 "src": "hda", 931 "src": "hda",
932 "uuid": "a79829ef-6450-404a-8d59-fa42ddb91ca3" 932 "uuid": "7d893bbf-b4e0-4d64-bafc-21ba1566237d"
933 }, 933 },
934 "genbank_files2": { 934 "genbank_files2": {
935 "id": "9c6b8acc292ccf30", 935 "id": "7ada2c781708b1e8",
936 "src": "hda", 936 "src": "hda",
937 "uuid": "7c74d4c3-38b5-40a7-9c71-482502e6e5f8" 937 "uuid": "cc2314fa-924f-47c0-b89a-661fb78790a4"
938 }, 938 },
939 "genbank_files3": { 939 "genbank_files3": {
940 "id": "0b252ddd8f79f3ec", 940 "id": "4deb8a541e3f0671",
941 "src": "hda", 941 "src": "hda",
942 "uuid": "51c3184d-fd7e-49a8-af51-e29bbf7a8a37" 942 "uuid": "8d097c97-7bd5-48eb-9f9e-f5b92ce19458"
943 }, 943 },
944 "genbank_files4": { 944 "genbank_files4": {
945 "id": "757270683c70cddd", 945 "id": "cdcc9004d7157de8",
946 "src": "hda", 946 "src": "hda",
947 "uuid": "24493579-a703-4b94-ac09-e283f59035b0" 947 "uuid": "59189305-e832-4191-be7c-496c01c8aba6"
948 }, 948 },
949 "genbank_files5": { 949 "genbank_files5": {
950 "id": "3932a26d59be2681", 950 "id": "33fad5084f4d4cb5",
951 "src": "hda", 951 "src": "hda",
952 "uuid": "cb4bfd16-db5c-47ce-98f5-a5c5065d4dd4" 952 "uuid": "402500d7-6532-4008-9445-c0cf7fed5350"
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": "abedd81ff2360f10", 963 "id": "590bb56cc83504dc",
964 "src": "hdca" 964 "src": "hdca"
965 } 965 }
966 }, 966 },
967 "outputs": { 967 "outputs": {
968 "output_zip": { 968 "output_zip": {
969 "id": "8c26318d49002581", 969 "id": "4f510c4214d7d568",
970 "src": "hda", 970 "src": "hda",
971 "uuid": "47491132-901d-4249-9c1e-dfd12feae17e" 971 "uuid": "8e6b31eb-84b3-4184-92eb-33384ae50857"
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/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 978 "chromInfo": "\"/tmp/tmp_ibkdcj0/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, 49.05it/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: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.38it/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, 49.05it/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: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.38it/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": "2025-05-23T12:14:44.485473", 990 "update_time": "2025-05-26T08:57:34.740635",
991 "user_email": "planemo@galaxyproject.org", 991 "user_email": "planemo@galaxyproject.org",
992 "user_id": "8094a24bdbd328fd" 992 "user_id": "cb6d3fbb91be6861"
993 }, 993 },
994 "status": "success", 994 "status": "success",
995 "test_index": 3, 995 "test_index": 3,
996 "time_seconds": 31.373873472213745, 996 "time_seconds": 32.283992767333984,
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": "723f42bbf157272d", 1008 "id": "017df84d4155fcba",
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": "83d0643dcafc650b", 1013 "id": "ff96e44e65db99f8",
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' && cp '/tmp/tmpulb7kecp/files/9/4/0/dataset_940a048a-ec9f-4cc9-9990-f0f1bb9c01db.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/d/5/9/dataset_d591902b-724d-446d-bad5-1ecf539f4193.dat,/tmp/tmpulb7kecp/files/4/5/7/dataset_457d680a-7fd5-42ce-8747-a78267083da9.dat,/tmp/tmpulb7kecp/files/1/a/9/dataset_1a9aa4c8-4387-4b65-a638-1033465060d7.dat,/tmp/tmpulb7kecp/files/3/f/e/dataset_3feea62b-c35b-4f65-937d-3233db6bf0ec.dat,/tmp/tmpulb7kecp/files/f/9/1/dataset_f917f42d-9d14-4b5e-aa4f-b04e06a56357.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/d/5/9/dataset_d591902b-724d-446d-bad5-1ecf539f4193.dat:BBa_E0040_GFP.gb,/tmp/tmpulb7kecp/files/4/5/7/dataset_457d680a-7fd5-42ce-8747-a78267083da9.dat:BBa_J23119_prom.gb,/tmp/tmpulb7kecp/files/1/a/9/dataset_1a9aa4c8-4387-4b65-a638-1033465060d7.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpulb7kecp/files/3/f/e/dataset_3feea62b-c35b-4f65-937d-3233db6bf0ec.dat:BBa_J61048_term.gb,/tmp/tmpulb7kecp/files/f/9/1/dataset_f917f42d-9d14-4b5e-aa4f-b04e06a56357.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/tmpulb7kecp/job_working_directory/000/35/outputs/dataset_332a60b5-1b7e-40d6-b4d9-a07f05bc9d4b.dat'", 1019 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/f/d/9/dataset_fd913c0f-ea98-4b8d-a170-961146c201d5.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/3/8/4/dataset_38402f39-a1d3-495e-afed-bf8335b4cdb6.dat,/tmp/tmp_ibkdcj0/files/9/c/8/dataset_9c8ea453-16b9-4b9d-b171-9d5c0322adf9.dat,/tmp/tmp_ibkdcj0/files/3/1/a/dataset_31a46fbb-0267-42e3-b9d3-c60804edd30c.dat,/tmp/tmp_ibkdcj0/files/e/2/7/dataset_e278e6ea-3146-49fa-a4f5-becf766e4f5e.dat,/tmp/tmp_ibkdcj0/files/6/a/1/dataset_6a19d37f-54e1-4c94-a2b1-1a7f37820aad.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/3/8/4/dataset_38402f39-a1d3-495e-afed-bf8335b4cdb6.dat:BBa_E0040_GFP.gb,/tmp/tmp_ibkdcj0/files/9/c/8/dataset_9c8ea453-16b9-4b9d-b171-9d5c0322adf9.dat:BBa_J23119_prom.gb,/tmp/tmp_ibkdcj0/files/3/1/a/dataset_31a46fbb-0267-42e3-b9d3-c60804edd30c.dat:BBa_J23119_prom_flawed.gb,/tmp/tmp_ibkdcj0/files/e/2/7/dataset_e278e6ea-3146-49fa-a4f5-becf766e4f5e.dat:BBa_J61048_term.gb,/tmp/tmp_ibkdcj0/files/6/a/1/dataset_6a19d37f-54e1-4c94-a2b1-1a7f37820aad.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/tmp_ibkdcj0/job_working_directory/000/35/outputs/dataset_a3f2eab1-bbe1-401e-b436-b7ffc698ee3a.dat'",
1020 "command_version": "", 1020 "command_version": "",
1021 "copied_from_job_id": null, 1021 "copied_from_job_id": null,
1022 "create_time": "2025-05-23T12:15:06.093194", 1022 "create_time": "2025-05-26T08:57:56.917009",
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": "180435", 1202 "external_id": "80672",
1203 "galaxy_version": "24.2", 1203 "galaxy_version": "24.2",
1204 "handler": null, 1204 "handler": null,
1205 "history_id": "85b2c5efa0bce20f", 1205 "history_id": "48e4779cf88cf124",
1206 "id": "8c26318d49002581", 1206 "id": "4f510c4214d7d568",
1207 "inputs": { 1207 "inputs": {
1208 "assembly_csv": { 1208 "assembly_csv": {
1209 "id": "723f42bbf157272d", 1209 "id": "017df84d4155fcba",
1210 "src": "hda", 1210 "src": "hda",
1211 "uuid": "940a048a-ec9f-4cc9-9990-f0f1bb9c01db" 1211 "uuid": "fd913c0f-ea98-4b8d-a170-961146c201d5"
1212 }, 1212 },
1213 "genbank_files1": { 1213 "genbank_files1": {
1214 "id": "068bcc8e8d7a762b", 1214 "id": "1745fab1994e918a",
1215 "src": "hda", 1215 "src": "hda",
1216 "uuid": "d591902b-724d-446d-bad5-1ecf539f4193" 1216 "uuid": "38402f39-a1d3-495e-afed-bf8335b4cdb6"
1217 }, 1217 },
1218 "genbank_files2": { 1218 "genbank_files2": {
1219 "id": "9f11456f5a306175", 1219 "id": "9f4b12edd1240647",
1220 "src": "hda", 1220 "src": "hda",
1221 "uuid": "457d680a-7fd5-42ce-8747-a78267083da9" 1221 "uuid": "9c8ea453-16b9-4b9d-b171-9d5c0322adf9"
1222 }, 1222 },
1223 "genbank_files3": { 1223 "genbank_files3": {
1224 "id": "4d6d92e009725c02", 1224 "id": "070cf47a9114ebf0",
1225 "src": "hda", 1225 "src": "hda",
1226 "uuid": "1a9aa4c8-4387-4b65-a638-1033465060d7" 1226 "uuid": "31a46fbb-0267-42e3-b9d3-c60804edd30c"
1227 }, 1227 },
1228 "genbank_files4": { 1228 "genbank_files4": {
1229 "id": "ba31cade4e4f4bd8", 1229 "id": "176efb58f023067c",
1230 "src": "hda", 1230 "src": "hda",
1231 "uuid": "3feea62b-c35b-4f65-937d-3233db6bf0ec" 1231 "uuid": "e278e6ea-3146-49fa-a4f5-becf766e4f5e"
1232 }, 1232 },
1233 "genbank_files5": { 1233 "genbank_files5": {
1234 "id": "5c13ba18dcd7e71d", 1234 "id": "2c38922866e3bd19",
1235 "src": "hda", 1235 "src": "hda",
1236 "uuid": "f917f42d-9d14-4b5e-aa4f-b04e06a56357" 1236 "uuid": "6a19d37f-54e1-4c94-a2b1-1a7f37820aad"
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": "54ed1ed3b165c7b4", 1247 "id": "7ede2556a40dc9ba",
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": "165ffecff174f921", 1253 "id": "e9bea5372f4a6a20",
1254 "src": "hda", 1254 "src": "hda",
1255 "uuid": "dbf78ec4-1125-4869-b2c7-22ea1e088383" 1255 "uuid": "80f480c8-264d-428b-8b95-253cd89d7764"
1256 }, 1256 },
1257 "__new_primary_file_construct_gb|C2_gfp_term__": { 1257 "__new_primary_file_construct_gb|C2_gfp_term__": {
1258 "id": "68b55cb1abb6ffc8", 1258 "id": "1290d6537f2937e3",
1259 "src": "hda", 1259 "src": "hda",
1260 "uuid": "eefbb36b-1cb4-4159-a989-674ce4a361d9" 1260 "uuid": "7b7b6524-575a-4dfc-800c-dc0d3e8ece79"
1261 }, 1261 },
1262 "__new_primary_file_construct_gb|C3_final__": { 1262 "__new_primary_file_construct_gb|C3_final__": {
1263 "id": "be504c8d89de9ae4", 1263 "id": "cd293a8cb9d8e7b5",
1264 "src": "hda", 1264 "src": "hda",
1265 "uuid": "7c89fcf8-b98f-4719-bedc-509f7d2adbb8" 1265 "uuid": "7be9e218-0841-46cd-ac62-5686969f6935"
1266 }, 1266 },
1267 "output_zip": { 1267 "output_zip": {
1268 "id": "67dd2dff3a365063", 1268 "id": "3651b2c7591f0e47",
1269 "src": "hda", 1269 "src": "hda",
1270 "uuid": "332a60b5-1b7e-40d6-b4d9-a07f05bc9d4b" 1270 "uuid": "a3f2eab1-bbe1-401e-b436-b7ffc698ee3a"
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/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1277 "chromInfo": "\"/tmp/tmp_ibkdcj0/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, 1.89it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.55it/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, 1.90it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.54it/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, 1.89it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.55it/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, 1.90it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.54it/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": "2025-05-23T12:15:19.591969", 1289 "update_time": "2025-05-26T08:58:09.572798",
1290 "user_email": "planemo@galaxyproject.org", 1290 "user_email": "planemo@galaxyproject.org",
1291 "user_id": "8094a24bdbd328fd" 1291 "user_id": "cb6d3fbb91be6861"
1292 }, 1292 },
1293 "status": "success", 1293 "status": "success",
1294 "test_index": 4, 1294 "test_index": 4,
1295 "time_seconds": 35.12441039085388, 1295 "time_seconds": 34.93839716911316,
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": "8f56f36c2b9f0a7c", 1307 "id": "b1a8f56fe428091e",
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": "aa441ebc75addcb0", 1312 "id": "76608081d307dc20",
1313 "src": "hdca" 1313 "src": "hdca"
1314 }, 1314 },
1315 "genbank_files": { 1315 "genbank_files": {
1316 "id": "41108ccf3c813abd", 1316 "id": "0551bf01e3dbca02",
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' && cp '/tmp/tmpulb7kecp/files/c/f/a/dataset_cfa1c628-1bad-4864-97c9-f5ff8ae3bb94.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/0/9/2/dataset_092e3d69-34a0-4c02-9593-859fa17016fb.dat,/tmp/tmpulb7kecp/files/e/d/5/dataset_ed59100d-a4e7-4eb8-9965-8817a8e44000.dat,/tmp/tmpulb7kecp/files/0/1/7/dataset_0172bdce-ca49-45d4-af2d-12a5304b55ca.dat,/tmp/tmpulb7kecp/files/d/2/2/dataset_d22475f3-6c2f-4c52-9164-12248ba5d2a8.dat,/tmp/tmpulb7kecp/files/1/d/9/dataset_1d9b3d4c-eed3-444e-87e6-29c04e915c0d.dat,/tmp/tmpulb7kecp/files/2/4/c/dataset_24c555ec-1536-4ef6-a07d-20d744f3b5fc.dat,/tmp/tmpulb7kecp/files/c/2/3/dataset_c23f475b-f826-4333-8641-66e68bfad42a.dat' --domesticated_seq '/tmp/tmpulb7kecp/files/f/f/a/dataset_ffa8dfa6-df34-412b-84ae-325a3e389a88.dat,/tmp/tmpulb7kecp/files/f/3/3/dataset_f33af6b6-cce3-49b2-a17e-9a168ad065f9.dat,/tmp/tmpulb7kecp/files/2/9/7/dataset_297ec6da-4e55-4534-94c7-903e7e107632.dat,/tmp/tmpulb7kecp/files/3/0/7/dataset_30785c7f-0628-4e63-be45-77272fdedb50.dat,/tmp/tmpulb7kecp/files/f/3/2/dataset_f32a9062-9cf7-48d9-9ddb-ef0c02526564.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/0/9/2/dataset_092e3d69-34a0-4c02-9593-859fa17016fb.dat:part_A.gb,/tmp/tmpulb7kecp/files/e/d/5/dataset_ed59100d-a4e7-4eb8-9965-8817a8e44000.dat:part_B.gb,/tmp/tmpulb7kecp/files/0/1/7/dataset_0172bdce-ca49-45d4-af2d-12a5304b55ca.dat:part_C.gb,/tmp/tmpulb7kecp/files/d/2/2/dataset_d22475f3-6c2f-4c52-9164-12248ba5d2a8.dat:part_D.gb,/tmp/tmpulb7kecp/files/1/d/9/dataset_1d9b3d4c-eed3-444e-87e6-29c04e915c0d.dat:part_E.gb,/tmp/tmpulb7kecp/files/2/4/c/dataset_24c555ec-1536-4ef6-a07d-20d744f3b5fc.dat:part_F.gb,/tmp/tmpulb7kecp/files/c/2/3/dataset_c23f475b-f826-4333-8641-66e68bfad42a.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpulb7kecp/files/f/f/a/dataset_ffa8dfa6-df34-412b-84ae-325a3e389a88.dat:part_H.gb,/tmp/tmpulb7kecp/files/f/3/3/dataset_f33af6b6-cce3-49b2-a17e-9a168ad065f9.dat:part_I.gb,/tmp/tmpulb7kecp/files/2/9/7/dataset_297ec6da-4e55-4534-94c7-903e7e107632.dat:part_J.gb,/tmp/tmpulb7kecp/files/3/0/7/dataset_30785c7f-0628-4e63-be45-77272fdedb50.dat:part_K.gb,/tmp/tmpulb7kecp/files/f/3/2/dataset_f32a9062-9cf7-48d9-9ddb-ef0c02526564.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/tmpulb7kecp/job_working_directory/000/49/outputs/dataset_da6f8b92-03ba-4561-81a4-2ac510aff8c6.dat'", 1322 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/9/7/b/dataset_97b16fa9-53ab-4e65-9de7-e30112bcdd06.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/8/2/3/dataset_823cfc4c-98db-494d-a03b-5181179a3581.dat,/tmp/tmp_ibkdcj0/files/6/0/a/dataset_60a53b2c-927e-4c33-b6b0-2e927266044e.dat,/tmp/tmp_ibkdcj0/files/d/3/5/dataset_d357996d-45c3-4715-b8eb-ea6bb836b18e.dat,/tmp/tmp_ibkdcj0/files/d/a/c/dataset_dacfd7e2-f5ff-4821-8d70-f73307f7997e.dat,/tmp/tmp_ibkdcj0/files/9/b/3/dataset_9b3f9357-c1cc-43c9-a81c-c100483b3a0d.dat,/tmp/tmp_ibkdcj0/files/5/e/4/dataset_5e43150c-3c7c-4072-9720-fdc085cd6d8b.dat,/tmp/tmp_ibkdcj0/files/2/d/e/dataset_2de75a41-7673-4cef-aa63-2cf6d9466e8c.dat' --domesticated_seq '/tmp/tmp_ibkdcj0/files/e/f/3/dataset_ef3f0423-f1dd-462b-8d68-e68cd6d59d82.dat,/tmp/tmp_ibkdcj0/files/e/a/2/dataset_ea297609-87c4-4bfc-abfd-084fbcc94d5b.dat,/tmp/tmp_ibkdcj0/files/6/0/d/dataset_60d919ff-9b54-4856-b3d0-9836114c2575.dat,/tmp/tmp_ibkdcj0/files/0/8/e/dataset_08efef6d-13c4-4e1b-a155-859e0a0df989.dat,/tmp/tmp_ibkdcj0/files/e/7/2/dataset_e72facc2-0bd8-49e8-94e6-6b255853b030.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/8/2/3/dataset_823cfc4c-98db-494d-a03b-5181179a3581.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/6/0/a/dataset_60a53b2c-927e-4c33-b6b0-2e927266044e.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/d/3/5/dataset_d357996d-45c3-4715-b8eb-ea6bb836b18e.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/d/a/c/dataset_dacfd7e2-f5ff-4821-8d70-f73307f7997e.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/9/b/3/dataset_9b3f9357-c1cc-43c9-a81c-c100483b3a0d.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/5/e/4/dataset_5e43150c-3c7c-4072-9720-fdc085cd6d8b.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/2/d/e/dataset_2de75a41-7673-4cef-aa63-2cf6d9466e8c.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmp_ibkdcj0/files/e/f/3/dataset_ef3f0423-f1dd-462b-8d68-e68cd6d59d82.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/e/a/2/dataset_ea297609-87c4-4bfc-abfd-084fbcc94d5b.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/6/0/d/dataset_60d919ff-9b54-4856-b3d0-9836114c2575.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/0/8/e/dataset_08efef6d-13c4-4e1b-a155-859e0a0df989.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/e/7/2/dataset_e72facc2-0bd8-49e8-94e6-6b255853b030.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/tmp_ibkdcj0/job_working_directory/000/49/outputs/dataset_2bca238e-5421-456d-bf98-1bd44e65fc76.dat'",
1323 "command_version": "", 1323 "command_version": "",
1324 "copied_from_job_id": null, 1324 "copied_from_job_id": null,
1325 "create_time": "2025-05-23T12:16:00.836611", 1325 "create_time": "2025-05-26T08:58:50.541909",
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": "181545", 1505 "external_id": "81731",
1506 "galaxy_version": "24.2", 1506 "galaxy_version": "24.2",
1507 "handler": null, 1507 "handler": null,
1508 "history_id": "3758c7315f184c9a", 1508 "history_id": "2bf3ecab9316a382",
1509 "id": "db168591f9c4d2a8", 1509 "id": "aa893e5f7beb4eb8",
1510 "inputs": { 1510 "inputs": {
1511 "assembly_csv": { 1511 "assembly_csv": {
1512 "id": "8f56f36c2b9f0a7c", 1512 "id": "b1a8f56fe428091e",
1513 "src": "hda", 1513 "src": "hda",
1514 "uuid": "cfa1c628-1bad-4864-97c9-f5ff8ae3bb94" 1514 "uuid": "97b16fa9-53ab-4e65-9de7-e30112bcdd06"
1515 }, 1515 },
1516 "domesticated_input1": { 1516 "domesticated_input1": {
1517 "id": "762d85be4105a0e7", 1517 "id": "dbc527c8f70438a2",
1518 "src": "hda", 1518 "src": "hda",
1519 "uuid": "ffa8dfa6-df34-412b-84ae-325a3e389a88" 1519 "uuid": "ef3f0423-f1dd-462b-8d68-e68cd6d59d82"
1520 }, 1520 },
1521 "domesticated_input2": { 1521 "domesticated_input2": {
1522 "id": "c453f926cdeee4bd", 1522 "id": "a3ea165695c1e088",
1523 "src": "hda", 1523 "src": "hda",
1524 "uuid": "f33af6b6-cce3-49b2-a17e-9a168ad065f9" 1524 "uuid": "ea297609-87c4-4bfc-abfd-084fbcc94d5b"
1525 }, 1525 },
1526 "domesticated_input3": { 1526 "domesticated_input3": {
1527 "id": "5bba4dfbf52e531c", 1527 "id": "d4fcfbec208c480f",
1528 "src": "hda", 1528 "src": "hda",
1529 "uuid": "297ec6da-4e55-4534-94c7-903e7e107632" 1529 "uuid": "60d919ff-9b54-4856-b3d0-9836114c2575"
1530 }, 1530 },
1531 "domesticated_input4": { 1531 "domesticated_input4": {
1532 "id": "58e4e52cefa9d689", 1532 "id": "b53993d77cff267e",
1533 "src": "hda", 1533 "src": "hda",
1534 "uuid": "30785c7f-0628-4e63-be45-77272fdedb50" 1534 "uuid": "08efef6d-13c4-4e1b-a155-859e0a0df989"
1535 }, 1535 },
1536 "domesticated_input5": { 1536 "domesticated_input5": {
1537 "id": "492cbe2cf83388c0", 1537 "id": "e1a323c2b9a73ada",
1538 "src": "hda", 1538 "src": "hda",
1539 "uuid": "f32a9062-9cf7-48d9-9ddb-ef0c02526564" 1539 "uuid": "e72facc2-0bd8-49e8-94e6-6b255853b030"
1540 }, 1540 },
1541 "genbank_files1": { 1541 "genbank_files1": {
1542 "id": "5b9f36df99fe7ddd", 1542 "id": "03a53f60ebb3b30b",
1543 "src": "hda", 1543 "src": "hda",
1544 "uuid": "092e3d69-34a0-4c02-9593-859fa17016fb" 1544 "uuid": "823cfc4c-98db-494d-a03b-5181179a3581"
1545 }, 1545 },
1546 "genbank_files2": { 1546 "genbank_files2": {
1547 "id": "83649da70bd4e994", 1547 "id": "949b6e5fb08e3b2e",
1548 "src": "hda", 1548 "src": "hda",
1549 "uuid": "ed59100d-a4e7-4eb8-9965-8817a8e44000" 1549 "uuid": "60a53b2c-927e-4c33-b6b0-2e927266044e"
1550 }, 1550 },
1551 "genbank_files3": { 1551 "genbank_files3": {
1552 "id": "9e3a7410afb0cd47", 1552 "id": "4b14363353165bd2",
1553 "src": "hda", 1553 "src": "hda",
1554 "uuid": "0172bdce-ca49-45d4-af2d-12a5304b55ca" 1554 "uuid": "d357996d-45c3-4715-b8eb-ea6bb836b18e"
1555 }, 1555 },
1556 "genbank_files4": { 1556 "genbank_files4": {
1557 "id": "db168591f9c4d2a8", 1557 "id": "aa893e5f7beb4eb8",
1558 "src": "hda", 1558 "src": "hda",
1559 "uuid": "d22475f3-6c2f-4c52-9164-12248ba5d2a8" 1559 "uuid": "dacfd7e2-f5ff-4821-8d70-f73307f7997e"
1560 }, 1560 },
1561 "genbank_files5": { 1561 "genbank_files5": {
1562 "id": "fbc673f3c19d4e8f", 1562 "id": "e33440187009b2c6",
1563 "src": "hda", 1563 "src": "hda",
1564 "uuid": "1d9b3d4c-eed3-444e-87e6-29c04e915c0d" 1564 "uuid": "9b3f9357-c1cc-43c9-a81c-c100483b3a0d"
1565 }, 1565 },
1566 "genbank_files6": { 1566 "genbank_files6": {
1567 "id": "612b3112dca3b89a", 1567 "id": "ef97dc51810891e7",
1568 "src": "hda", 1568 "src": "hda",
1569 "uuid": "24c555ec-1536-4ef6-a07d-20d744f3b5fc" 1569 "uuid": "5e43150c-3c7c-4072-9720-fdc085cd6d8b"
1570 }, 1570 },
1571 "genbank_files7": { 1571 "genbank_files7": {
1572 "id": "1122563bf7246535", 1572 "id": "16b078cfbe5cb4fb",
1573 "src": "hda", 1573 "src": "hda",
1574 "uuid": "c23f475b-f826-4333-8641-66e68bfad42a" 1574 "uuid": "2de75a41-7673-4cef-aa63-2cf6d9466e8c"
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": "106ff655f8a511fe", 1585 "id": "0a696a8b22798e06",
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": "4ec2fde3b391b5e9", 1591 "id": "08065af9f1d51b0a",
1592 "src": "hda", 1592 "src": "hda",
1593 "uuid": "65c06a03-7919-4203-8aa0-ee2d6c747da3" 1593 "uuid": "4837c85e-ba71-482d-91d1-be3e3179ee5a"
1594 }, 1594 },
1595 "__new_primary_file_construct_gb|construct_2__": { 1595 "__new_primary_file_construct_gb|construct_2__": {
1596 "id": "db0ab281fdd171f3", 1596 "id": "23c03036acf6de8c",
1597 "src": "hda", 1597 "src": "hda",
1598 "uuid": "00b0ee36-bed6-481a-8f87-a3ee2eb3c474" 1598 "uuid": "a898af9c-3721-4b84-8ebc-790dc376316c"
1599 }, 1599 },
1600 "__new_primary_file_construct_gb|construct_3__": { 1600 "__new_primary_file_construct_gb|construct_3__": {
1601 "id": "39bf58b498d37eb0", 1601 "id": "950510fee01c22f4",
1602 "src": "hda", 1602 "src": "hda",
1603 "uuid": "c6fb815c-ee68-4263-9e77-86d27f1f5fd9" 1603 "uuid": "be8dfa79-0421-418a-9822-af3e69e3bd0a"
1604 }, 1604 },
1605 "__new_primary_file_construct_gb|construct_4__": { 1605 "__new_primary_file_construct_gb|construct_4__": {
1606 "id": "54d1dbb833355e05", 1606 "id": "abd47de82fbecc4e",
1607 "src": "hda", 1607 "src": "hda",
1608 "uuid": "af82262d-217d-4952-8d8f-b733d902879c" 1608 "uuid": "1455799d-9a0a-46e7-8ddb-df60f983fb53"
1609 }, 1609 },
1610 "output_zip": { 1610 "output_zip": {
1611 "id": "7830aac4d222c450", 1611 "id": "b52f373b44c22024",
1612 "src": "hda", 1612 "src": "hda",
1613 "uuid": "da6f8b92-03ba-4561-81a4-2ac510aff8c6" 1613 "uuid": "2bca238e-5421-456d-bf98-1bd44e65fc76"
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/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1620 "chromInfo": "\"/tmp/tmp_ibkdcj0/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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/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, 2.44it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/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, 2.43it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/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, 2.44it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/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": "2025-05-23T12:16:13.850563", 1632 "update_time": "2025-05-26T08:59:03.629936",
1633 "user_email": "planemo@galaxyproject.org", 1633 "user_email": "planemo@galaxyproject.org",
1634 "user_id": "8094a24bdbd328fd" 1634 "user_id": "cb6d3fbb91be6861"
1635 }, 1635 },
1636 "status": "success", 1636 "status": "success",
1637 "test_index": 5, 1637 "test_index": 5,
1638 "time_seconds": 54.179964542388916, 1638 "time_seconds": 53.84836268424988,
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"
1645 { 1645 {
1646 "data": { 1646 "data": {
1647 "inputs": { 1647 "inputs": {
1648 "adv|use_file_names_as_ids": true, 1648 "adv|use_file_names_as_ids": true,
1649 "assembly_csv": { 1649 "assembly_csv": {
1650 "id": "a128918b334a087e", 1650 "id": "4b6130eb686f10a7",
1651 "src": "hda" 1651 "src": "hda"
1652 }, 1652 },
1653 "assembly_plan_name": "Type2sRestrictionAssembly", 1653 "assembly_plan_name": "Type2sRestrictionAssembly",
1654 "domesticated_input": { 1654 "domesticated_input": {
1655 "id": "a843aa6880d39864", 1655 "id": "2ff5b0f6b4cfbb73",
1656 "src": "hdca" 1656 "src": "hdca"
1657 }, 1657 },
1658 "topology": "circular" 1658 "topology": "circular"
1659 }, 1659 },
1660 "job": { 1660 "job": {
1661 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpulb7kecp/files/4/d/6/dataset_4d664c21-0606-48f2-a403-c970eada5469.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpulb7kecp/files/b/f/7/dataset_bf78af79-2d13-4fd5-8858-a0fcf0527125.dat,/tmp/tmpulb7kecp/files/6/c/f/dataset_6cf6f59f-3cee-4539-85e2-0b5786b42a8a.dat,/tmp/tmpulb7kecp/files/8/c/1/dataset_8c1a4509-f793-4b1a-9fc2-599b836e6d1e.dat,/tmp/tmpulb7kecp/files/3/8/1/dataset_3818afb4-1184-43b1-aa48-13efabb7ecc8.dat,/tmp/tmpulb7kecp/files/9/0/e/dataset_90e377b6-c53e-4277-8c54-c361769ee52f.dat,/tmp/tmpulb7kecp/files/4/5/9/dataset_4594442a-8d2b-4f97-a280-8deb7915da9c.dat,/tmp/tmpulb7kecp/files/6/e/9/dataset_6e9767bf-085d-48d0-9ad3-596e435224f3.dat,/tmp/tmpulb7kecp/files/1/4/b/dataset_14bd369b-8410-484e-8402-33aac9998b84.dat,/tmp/tmpulb7kecp/files/1/1/8/dataset_1180d189-8f49-4811-8e79-957c7bf319e4.dat,/tmp/tmpulb7kecp/files/4/9/1/dataset_49140292-5bb2-4b2e-bf02-87402741d120.dat,/tmp/tmpulb7kecp/files/b/4/2/dataset_b4278d16-d56d-4cbf-8fc6-100f10a5a142.dat,/tmp/tmpulb7kecp/files/1/8/0/dataset_18021752-a186-4b63-ba68-b56da64c7e9a.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpulb7kecp/files/b/f/7/dataset_bf78af79-2d13-4fd5-8858-a0fcf0527125.dat:part_A.gb,/tmp/tmpulb7kecp/files/6/c/f/dataset_6cf6f59f-3cee-4539-85e2-0b5786b42a8a.dat:part_B.gb,/tmp/tmpulb7kecp/files/8/c/1/dataset_8c1a4509-f793-4b1a-9fc2-599b836e6d1e.dat:part_C.gb,/tmp/tmpulb7kecp/files/3/8/1/dataset_3818afb4-1184-43b1-aa48-13efabb7ecc8.dat:part_D.gb,/tmp/tmpulb7kecp/files/9/0/e/dataset_90e377b6-c53e-4277-8c54-c361769ee52f.dat:part_E.gb,/tmp/tmpulb7kecp/files/4/5/9/dataset_4594442a-8d2b-4f97-a280-8deb7915da9c.dat:part_F.gb,/tmp/tmpulb7kecp/files/6/e/9/dataset_6e9767bf-085d-48d0-9ad3-596e435224f3.dat:part_G.gb,/tmp/tmpulb7kecp/files/1/4/b/dataset_14bd369b-8410-484e-8402-33aac9998b84.dat:part_H.gb,/tmp/tmpulb7kecp/files/1/1/8/dataset_1180d189-8f49-4811-8e79-957c7bf319e4.dat:part_I.gb,/tmp/tmpulb7kecp/files/4/9/1/dataset_49140292-5bb2-4b2e-bf02-87402741d120.dat:part_J.gb,/tmp/tmpulb7kecp/files/b/4/2/dataset_b4278d16-d56d-4cbf-8fc6-100f10a5a142.dat:part_K.gb,/tmp/tmpulb7kecp/files/1/8/0/dataset_18021752-a186-4b63-ba68-b56da64c7e9a.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/tmpulb7kecp/job_working_directory/000/63/outputs/dataset_5e972ac3-a1c0-48c4-9db8-648343937891.dat'", 1661 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmp_ibkdcj0/files/5/0/4/dataset_5042213c-8bb6-48e0-9501-070e55a9a8c0.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmp_ibkdcj0/files/d/d/8/dataset_dd8d9744-d7f0-46ae-b26f-de961e3f5033.dat,/tmp/tmp_ibkdcj0/files/a/a/6/dataset_aa64d9f2-f351-4776-aab6-648a5fa5f6da.dat,/tmp/tmp_ibkdcj0/files/1/d/b/dataset_1dbca58c-bd12-48c7-bbfe-49ef8801f8c3.dat,/tmp/tmp_ibkdcj0/files/d/3/9/dataset_d396d7df-8e9d-441b-b04e-abaaa0c90a7f.dat,/tmp/tmp_ibkdcj0/files/4/1/3/dataset_4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a.dat,/tmp/tmp_ibkdcj0/files/2/e/9/dataset_2e907739-181d-44bc-8bc4-35d252e00535.dat,/tmp/tmp_ibkdcj0/files/9/d/3/dataset_9d3053e2-630d-4fba-9b08-09f59013ab96.dat,/tmp/tmp_ibkdcj0/files/2/6/3/dataset_26364877-f482-4b4d-8346-61a2f50f1ccf.dat,/tmp/tmp_ibkdcj0/files/6/f/6/dataset_6f64f828-be8e-4e72-a940-87396256fe3f.dat,/tmp/tmp_ibkdcj0/files/d/2/4/dataset_d2492f3b-8ea9-40e7-8bda-a15b506a22ac.dat,/tmp/tmp_ibkdcj0/files/3/a/8/dataset_3a857675-027c-4b28-bf69-7591db569213.dat,/tmp/tmp_ibkdcj0/files/2/6/d/dataset_26df2c50-4cbe-45f5-ba07-be8fb89cfb7c.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmp_ibkdcj0/files/d/d/8/dataset_dd8d9744-d7f0-46ae-b26f-de961e3f5033.dat:part_A.gb,/tmp/tmp_ibkdcj0/files/a/a/6/dataset_aa64d9f2-f351-4776-aab6-648a5fa5f6da.dat:part_B.gb,/tmp/tmp_ibkdcj0/files/1/d/b/dataset_1dbca58c-bd12-48c7-bbfe-49ef8801f8c3.dat:part_C.gb,/tmp/tmp_ibkdcj0/files/d/3/9/dataset_d396d7df-8e9d-441b-b04e-abaaa0c90a7f.dat:part_D.gb,/tmp/tmp_ibkdcj0/files/4/1/3/dataset_4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a.dat:part_E.gb,/tmp/tmp_ibkdcj0/files/2/e/9/dataset_2e907739-181d-44bc-8bc4-35d252e00535.dat:part_F.gb,/tmp/tmp_ibkdcj0/files/9/d/3/dataset_9d3053e2-630d-4fba-9b08-09f59013ab96.dat:part_G.gb,/tmp/tmp_ibkdcj0/files/2/6/3/dataset_26364877-f482-4b4d-8346-61a2f50f1ccf.dat:part_H.gb,/tmp/tmp_ibkdcj0/files/6/f/6/dataset_6f64f828-be8e-4e72-a940-87396256fe3f.dat:part_I.gb,/tmp/tmp_ibkdcj0/files/d/2/4/dataset_d2492f3b-8ea9-40e7-8bda-a15b506a22ac.dat:part_J.gb,/tmp/tmp_ibkdcj0/files/3/a/8/dataset_3a857675-027c-4b28-bf69-7591db569213.dat:part_K.gb,/tmp/tmp_ibkdcj0/files/2/6/d/dataset_26df2c50-4cbe-45f5-ba07-be8fb89cfb7c.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/tmp_ibkdcj0/job_working_directory/000/63/outputs/dataset_4e39f3b7-2899-410e-a32f-47270970ae14.dat'",
1662 "command_version": "", 1662 "command_version": "",
1663 "copied_from_job_id": null, 1663 "copied_from_job_id": null,
1664 "create_time": "2025-05-23T12:16:53.743706", 1664 "create_time": "2025-05-26T08:59:44.629082",
1665 "dependencies": [ 1665 "dependencies": [
1666 { 1666 {
1667 "cacheable": false, 1667 "cacheable": false,
1668 "dependency_resolver": { 1668 "dependency_resolver": {
1669 "auto_init": true, 1669 "auto_init": true,
1839 "name": "dna_features_viewer", 1839 "name": "dna_features_viewer",
1840 "version": "3.1.5" 1840 "version": "3.1.5"
1841 } 1841 }
1842 ], 1842 ],
1843 "exit_code": 0, 1843 "exit_code": 0,
1844 "external_id": "182633", 1844 "external_id": "82808",
1845 "galaxy_version": "24.2", 1845 "galaxy_version": "24.2",
1846 "handler": null, 1846 "handler": null,
1847 "history_id": "cc5b73713462c207", 1847 "history_id": "d51bf47fbc922335",
1848 "id": "54d1dbb833355e05", 1848 "id": "abd47de82fbecc4e",
1849 "inputs": { 1849 "inputs": {
1850 "assembly_csv": { 1850 "assembly_csv": {
1851 "id": "a128918b334a087e", 1851 "id": "4b6130eb686f10a7",
1852 "src": "hda", 1852 "src": "hda",
1853 "uuid": "4d664c21-0606-48f2-a403-c970eada5469" 1853 "uuid": "5042213c-8bb6-48e0-9501-070e55a9a8c0"
1854 }, 1854 },
1855 "domesticated_input1": { 1855 "domesticated_input1": {
1856 "id": "7b8eadfe954993cc", 1856 "id": "7c76f7472621b5d0",
1857 "src": "hda", 1857 "src": "hda",
1858 "uuid": "bf78af79-2d13-4fd5-8858-a0fcf0527125" 1858 "uuid": "dd8d9744-d7f0-46ae-b26f-de961e3f5033"
1859 }, 1859 },
1860 "domesticated_input10": { 1860 "domesticated_input10": {
1861 "id": "eadce10583f118a6", 1861 "id": "9bd6c123148263b6",
1862 "src": "hda", 1862 "src": "hda",
1863 "uuid": "49140292-5bb2-4b2e-bf02-87402741d120" 1863 "uuid": "d2492f3b-8ea9-40e7-8bda-a15b506a22ac"
1864 }, 1864 },
1865 "domesticated_input11": { 1865 "domesticated_input11": {
1866 "id": "e9b288c32babea6b", 1866 "id": "5d3d21e362e05995",
1867 "src": "hda", 1867 "src": "hda",
1868 "uuid": "b4278d16-d56d-4cbf-8fc6-100f10a5a142" 1868 "uuid": "3a857675-027c-4b28-bf69-7591db569213"
1869 }, 1869 },
1870 "domesticated_input12": { 1870 "domesticated_input12": {
1871 "id": "e756934e84f08dfa", 1871 "id": "043b0e9e9cf8c91c",
1872 "src": "hda", 1872 "src": "hda",
1873 "uuid": "18021752-a186-4b63-ba68-b56da64c7e9a" 1873 "uuid": "26df2c50-4cbe-45f5-ba07-be8fb89cfb7c"
1874 }, 1874 },
1875 "domesticated_input2": { 1875 "domesticated_input2": {
1876 "id": "8437c985b2f2555c", 1876 "id": "11e2d0eceb639139",
1877 "src": "hda", 1877 "src": "hda",
1878 "uuid": "6cf6f59f-3cee-4539-85e2-0b5786b42a8a" 1878 "uuid": "aa64d9f2-f351-4776-aab6-648a5fa5f6da"
1879 }, 1879 },
1880 "domesticated_input3": { 1880 "domesticated_input3": {
1881 "id": "15bf1fabbf77770e", 1881 "id": "991f793af87d39c4",
1882 "src": "hda", 1882 "src": "hda",
1883 "uuid": "8c1a4509-f793-4b1a-9fc2-599b836e6d1e" 1883 "uuid": "1dbca58c-bd12-48c7-bbfe-49ef8801f8c3"
1884 }, 1884 },
1885 "domesticated_input4": { 1885 "domesticated_input4": {
1886 "id": "0892281234ec1188", 1886 "id": "3429ba0772b9ca69",
1887 "src": "hda", 1887 "src": "hda",
1888 "uuid": "3818afb4-1184-43b1-aa48-13efabb7ecc8" 1888 "uuid": "d396d7df-8e9d-441b-b04e-abaaa0c90a7f"
1889 }, 1889 },
1890 "domesticated_input5": { 1890 "domesticated_input5": {
1891 "id": "d9fb2dd412cb550f", 1891 "id": "c04c164ed0056d43",
1892 "src": "hda", 1892 "src": "hda",
1893 "uuid": "90e377b6-c53e-4277-8c54-c361769ee52f" 1893 "uuid": "4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a"
1894 }, 1894 },
1895 "domesticated_input6": { 1895 "domesticated_input6": {
1896 "id": "5448650c849fc11a", 1896 "id": "b3ed12fa60bc840b",
1897 "src": "hda", 1897 "src": "hda",
1898 "uuid": "4594442a-8d2b-4f97-a280-8deb7915da9c" 1898 "uuid": "2e907739-181d-44bc-8bc4-35d252e00535"
1899 }, 1899 },
1900 "domesticated_input7": { 1900 "domesticated_input7": {
1901 "id": "2f883fbbd5083370", 1901 "id": "5406c597edc1a692",
1902 "src": "hda", 1902 "src": "hda",
1903 "uuid": "6e9767bf-085d-48d0-9ad3-596e435224f3" 1903 "uuid": "9d3053e2-630d-4fba-9b08-09f59013ab96"
1904 }, 1904 },
1905 "domesticated_input8": { 1905 "domesticated_input8": {
1906 "id": "24d06ab2f2a935eb", 1906 "id": "780d322efdca3fcd",
1907 "src": "hda", 1907 "src": "hda",
1908 "uuid": "14bd369b-8410-484e-8402-33aac9998b84" 1908 "uuid": "26364877-f482-4b4d-8346-61a2f50f1ccf"
1909 }, 1909 },
1910 "domesticated_input9": { 1910 "domesticated_input9": {
1911 "id": "e5bc5fc4cffa052a", 1911 "id": "951610fc65ac475f",
1912 "src": "hda", 1912 "src": "hda",
1913 "uuid": "1180d189-8f49-4811-8e79-957c7bf319e4" 1913 "uuid": "6f64f828-be8e-4e72-a940-87396256fe3f"
1914 } 1914 }
1915 }, 1915 },
1916 "job_messages": [], 1916 "job_messages": [],
1917 "job_metrics": [], 1917 "job_metrics": [],
1918 "job_runner_name": null, 1918 "job_runner_name": null,
1919 "job_stderr": "", 1919 "job_stderr": "",
1920 "job_stdout": "", 1920 "job_stdout": "",
1921 "model_class": "Job", 1921 "model_class": "Job",
1922 "output_collections": { 1922 "output_collections": {
1923 "construct_gb": { 1923 "construct_gb": {
1924 "id": "03b30db777cad5e1", 1924 "id": "be5466d8eb2c2229",
1925 "src": "hdca" 1925 "src": "hdca"
1926 } 1926 }
1927 }, 1927 },
1928 "outputs": { 1928 "outputs": {
1929 "__new_primary_file_construct_gb|construct_1__": { 1929 "__new_primary_file_construct_gb|construct_1__": {
1930 "id": "a0ee6696f34ccc35", 1930 "id": "6d4b50576bf02b31",
1931 "src": "hda", 1931 "src": "hda",
1932 "uuid": "f59b0877-3920-4bb4-b968-f7ae54e3bec8" 1932 "uuid": "d4f04f5f-16a6-4675-a892-fa6d05156592"
1933 }, 1933 },
1934 "__new_primary_file_construct_gb|construct_2__": { 1934 "__new_primary_file_construct_gb|construct_2__": {
1935 "id": "f468d17a6d2490da", 1935 "id": "550e95bf5471ae1d",
1936 "src": "hda", 1936 "src": "hda",
1937 "uuid": "b52ac80b-d674-4da6-8ff1-24842aac56e9" 1937 "uuid": "845f0e19-1541-481b-a386-47135e8ebdf1"
1938 }, 1938 },
1939 "__new_primary_file_construct_gb|construct_3__": { 1939 "__new_primary_file_construct_gb|construct_3__": {
1940 "id": "5d3f1c2fed018315", 1940 "id": "359048b3278e74c9",
1941 "src": "hda", 1941 "src": "hda",
1942 "uuid": "400e46dc-92e4-418b-8f71-30a8ce7e1de7" 1942 "uuid": "420b6912-da3c-4b75-ae88-b73f0c005864"
1943 }, 1943 },
1944 "__new_primary_file_construct_gb|construct_4__": { 1944 "__new_primary_file_construct_gb|construct_4__": {
1945 "id": "b40e1d6349e0d9ca", 1945 "id": "7a3e4925ca1f5f1d",
1946 "src": "hda", 1946 "src": "hda",
1947 "uuid": "03c7f474-9652-4786-954f-bd38c4f6b887" 1947 "uuid": "5b639734-e44b-415c-b347-5a702df97945"
1948 }, 1948 },
1949 "output_zip": { 1949 "output_zip": {
1950 "id": "652ce7490abe3672", 1950 "id": "40a6167ab839cf08",
1951 "src": "hda", 1951 "src": "hda",
1952 "uuid": "5e972ac3-a1c0-48c4-9db8-648343937891" 1952 "uuid": "4e39f3b7-2899-410e-a32f-47270970ae14"
1953 } 1953 }
1954 }, 1954 },
1955 "params": { 1955 "params": {
1956 "__input_ext": "\"input\"", 1956 "__input_ext": "\"input\"",
1957 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 1957 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1958 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", 1958 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
1959 "chromInfo": "\"/tmp/tmpulb7kecp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1959 "chromInfo": "\"/tmp/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1960 "dbkey": "\"?\"", 1960 "dbkey": "\"?\"",
1961 "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", 1961 "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}",
1962 "genbank_files": null, 1962 "genbank_files": null,
1963 "topology": "\"circular\"" 1963 "topology": "\"circular\""
1964 }, 1964 },
1965 "state": "ok", 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, 2.39it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.19it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.79it/s, now=None]\r \r", 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, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/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", 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", 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, 2.39it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.19it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.79it/s, now=None]\r \r", 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, 2.42it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.81it/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", 1970 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
1971 "update_time": "2025-05-23T12:17:07.008117", 1971 "update_time": "2025-05-26T08:59:57.832603",
1972 "user_email": "planemo@galaxyproject.org", 1972 "user_email": "planemo@galaxyproject.org",
1973 "user_id": "8094a24bdbd328fd" 1973 "user_id": "cb6d3fbb91be6861"
1974 }, 1974 },
1975 "status": "success", 1975 "status": "success",
1976 "test_index": 6, 1976 "test_index": 6,
1977 "time_seconds": 53.04504728317261, 1977 "time_seconds": 53.99832892417908,
1978 "tool_id": "cloning_simulation", 1978 "tool_id": "cloning_simulation",
1979 "tool_version": "0.1.0+galaxy0" 1979 "tool_version": "0.1.0+galaxy0"
1980 }, 1980 },
1981 "has_data": true, 1981 "has_data": true,
1982 "id": "cloning_simulation-6" 1982 "id": "cloning_simulation-6"