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comparison output.json @ 10:0be569bd5443 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 09:50:30 +0000
parents 07e902da89ad
children 7d1778f5e164
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9:eaff3028ba07 10:0be569bd5443
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": "0a696a8b22798e06", 14 "id": "7a37f3397bf88665",
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": "cb6d3fbb91be6861", 19 "id": "b5f519d254c4f536",
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/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'", 25 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/6/1/a/dataset_61aa4b8a-d71a-4e9d-a878-5f0d1494b36d.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/f/c/e/dataset_fce5b5a1-92e2-4c39-90d5-0eddf56635f0.dat,/tmp/tmphxxoceah/files/a/6/4/dataset_a6400a83-e4fd-488b-94e8-5ec1f44db9ca.dat,/tmp/tmphxxoceah/files/a/6/6/dataset_a66c7ac9-f828-405d-9a49-842e978b00af.dat,/tmp/tmphxxoceah/files/5/4/b/dataset_54b878ab-05e6-4212-b399-ab1f62c59e16.dat,/tmp/tmphxxoceah/files/3/9/0/dataset_39021efe-6a4f-4b7f-ba0d-f87c2b436a0f.dat,/tmp/tmphxxoceah/files/b/e/2/dataset_be26c9ab-28e8-449a-bd01-2047af0dfa5d.dat,/tmp/tmphxxoceah/files/f/7/f/dataset_f7fd1975-81bc-4a4f-89c6-d946d59782ee.dat,/tmp/tmphxxoceah/files/f/b/1/dataset_fb1f0888-2487-4f14-bcdd-fa06923d4cd9.dat,/tmp/tmphxxoceah/files/2/5/0/dataset_250500a7-25ca-4cba-8d71-7d16053afcaa.dat,/tmp/tmphxxoceah/files/3/8/7/dataset_387ad7a6-1931-4a46-99d5-4513ba93a999.dat,/tmp/tmphxxoceah/files/6/8/2/dataset_6829a587-673a-44a6-8bcf-ec6334a9184f.dat,/tmp/tmphxxoceah/files/4/0/4/dataset_40405cee-d70a-45d6-ac91-05616fe798b9.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/f/c/e/dataset_fce5b5a1-92e2-4c39-90d5-0eddf56635f0.dat:part_A.gb,/tmp/tmphxxoceah/files/a/6/4/dataset_a6400a83-e4fd-488b-94e8-5ec1f44db9ca.dat:part_B.gb,/tmp/tmphxxoceah/files/a/6/6/dataset_a66c7ac9-f828-405d-9a49-842e978b00af.dat:part_C.gb,/tmp/tmphxxoceah/files/5/4/b/dataset_54b878ab-05e6-4212-b399-ab1f62c59e16.dat:part_D.gb,/tmp/tmphxxoceah/files/3/9/0/dataset_39021efe-6a4f-4b7f-ba0d-f87c2b436a0f.dat:part_E.gb,/tmp/tmphxxoceah/files/b/e/2/dataset_be26c9ab-28e8-449a-bd01-2047af0dfa5d.dat:part_F.gb,/tmp/tmphxxoceah/files/f/7/f/dataset_f7fd1975-81bc-4a4f-89c6-d946d59782ee.dat:part_G.gb,/tmp/tmphxxoceah/files/f/b/1/dataset_fb1f0888-2487-4f14-bcdd-fa06923d4cd9.dat:part_H.gb,/tmp/tmphxxoceah/files/2/5/0/dataset_250500a7-25ca-4cba-8d71-7d16053afcaa.dat:part_I.gb,/tmp/tmphxxoceah/files/3/8/7/dataset_387ad7a6-1931-4a46-99d5-4513ba93a999.dat:part_J.gb,/tmp/tmphxxoceah/files/6/8/2/dataset_6829a587-673a-44a6-8bcf-ec6334a9184f.dat:part_K.gb,/tmp/tmphxxoceah/files/4/0/4/dataset_40405cee-d70a-45d6-ac91-05616fe798b9.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/tmphxxoceah/job_working_directory/000/14/outputs/dataset_a840b0de-7374-4fc2-bc9c-eec0f6615e2f.dat'",
26 "command_version": "", 26 "command_version": "",
27 "copied_from_job_id": null, 27 "copied_from_job_id": null,
28 "create_time": "2025-05-26T08:56:03.115650", 28 "create_time": "2025-05-26T09:44:56.264493",
29 "dependencies": [], 29 "dependencies": [],
30 "exit_code": 0, 30 "exit_code": 0,
31 "external_id": "78665", 31 "external_id": "102136",
32 "galaxy_version": "24.2", 32 "galaxy_version": "24.2",
33 "handler": null, 33 "handler": null,
34 "history_id": "cb6d3fbb91be6861", 34 "history_id": "b5f519d254c4f536",
35 "id": "2ff5b0f6b4cfbb73", 35 "id": "dfd75d2f0da631b2",
36 "inputs": { 36 "inputs": {
37 "assembly_csv": { 37 "assembly_csv": {
38 "id": "0a696a8b22798e06", 38 "id": "7a37f3397bf88665",
39 "src": "hda", 39 "src": "hda",
40 "uuid": "baa59b14-7fb5-4efc-a75d-228d26b70adc" 40 "uuid": "61aa4b8a-d71a-4e9d-a878-5f0d1494b36d"
41 }, 41 },
42 "genbank_files1": { 42 "genbank_files1": {
43 "id": "cb6d3fbb91be6861", 43 "id": "b5f519d254c4f536",
44 "src": "hda", 44 "src": "hda",
45 "uuid": "f7bde375-2c6b-4e23-9117-e96bb4c3f6e6" 45 "uuid": "fce5b5a1-92e2-4c39-90d5-0eddf56635f0"
46 }, 46 },
47 "genbank_files10": { 47 "genbank_files10": {
48 "id": "7ede2556a40dc9ba", 48 "id": "2bdc7fcb2931f07b",
49 "src": "hda", 49 "src": "hda",
50 "uuid": "3217492e-bc97-4d61-87fd-b9d1f2e4534d" 50 "uuid": "387ad7a6-1931-4a46-99d5-4513ba93a999"
51 }, 51 },
52 "genbank_files11": { 52 "genbank_files11": {
53 "id": "76608081d307dc20", 53 "id": "dc7e3ab6a421767b",
54 "src": "hda", 54 "src": "hda",
55 "uuid": "f8f04302-598c-4596-99a1-6c7d84b613d6" 55 "uuid": "6829a587-673a-44a6-8bcf-ec6334a9184f"
56 }, 56 },
57 "genbank_files12": { 57 "genbank_files12": {
58 "id": "0551bf01e3dbca02", 58 "id": "b1d9a1d43e36b679",
59 "src": "hda", 59 "src": "hda",
60 "uuid": "9f67cbfd-ca06-4926-b042-74a0d43b585a" 60 "uuid": "40405cee-d70a-45d6-ac91-05616fe798b9"
61 }, 61 },
62 "genbank_files2": { 62 "genbank_files2": {
63 "id": "18a1e53d7b8ec0fa", 63 "id": "c5accd210dc5c9dd",
64 "src": "hda", 64 "src": "hda",
65 "uuid": "ba5c9d10-e47e-4ced-9aaf-a51bf18e7932" 65 "uuid": "a6400a83-e4fd-488b-94e8-5ec1f44db9ca"
66 }, 66 },
67 "genbank_files3": { 67 "genbank_files3": {
68 "id": "afdf3d24f0e34eea", 68 "id": "10fbf206fb2087c4",
69 "src": "hda", 69 "src": "hda",
70 "uuid": "bf6e6482-afaa-4790-ac74-23f532fa48ad" 70 "uuid": "a66c7ac9-f828-405d-9a49-842e978b00af"
71 }, 71 },
72 "genbank_files4": { 72 "genbank_files4": {
73 "id": "285751a21c9d1d68", 73 "id": "27fa0815bff520f2",
74 "src": "hda", 74 "src": "hda",
75 "uuid": "1b8c7b47-fdba-4046-953a-89dc0c07ae14" 75 "uuid": "54b878ab-05e6-4212-b399-ab1f62c59e16"
76 }, 76 },
77 "genbank_files5": { 77 "genbank_files5": {
78 "id": "48e4779cf88cf124", 78 "id": "f825d543d1b9cf39",
79 "src": "hda", 79 "src": "hda",
80 "uuid": "5f5321b9-fa9a-4a73-9573-890d0c00209d" 80 "uuid": "39021efe-6a4f-4b7f-ba0d-f87c2b436a0f"
81 }, 81 },
82 "genbank_files6": { 82 "genbank_files6": {
83 "id": "2bf3ecab9316a382", 83 "id": "24f234959abeadac",
84 "src": "hda", 84 "src": "hda",
85 "uuid": "8557a762-7c36-4111-a015-2b61caad4e5b" 85 "uuid": "be26c9ab-28e8-449a-bd01-2047af0dfa5d"
86 }, 86 },
87 "genbank_files7": { 87 "genbank_files7": {
88 "id": "d51bf47fbc922335", 88 "id": "67e443cb5516c0e0",
89 "src": "hda", 89 "src": "hda",
90 "uuid": "f7000fc2-7e04-4561-875c-b84614f51966" 90 "uuid": "f7fd1975-81bc-4a4f-89c6-d946d59782ee"
91 }, 91 },
92 "genbank_files8": { 92 "genbank_files8": {
93 "id": "590bb56cc83504dc", 93 "id": "5180b1a726879d60",
94 "src": "hda", 94 "src": "hda",
95 "uuid": "3dfdeb1b-9582-4e15-a4f8-ff002ba9bf09" 95 "uuid": "fb1f0888-2487-4f14-bcdd-fa06923d4cd9"
96 }, 96 },
97 "genbank_files9": { 97 "genbank_files9": {
98 "id": "ff96e44e65db99f8", 98 "id": "c3b441e1ed1e9870",
99 "src": "hda", 99 "src": "hda",
100 "uuid": "e3b26d77-5d05-4a0f-adf7-016bf86c5eb3" 100 "uuid": "250500a7-25ca-4cba-8d71-7d16053afcaa"
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": "18a1e53d7b8ec0fa", 111 "id": "c5accd210dc5c9dd",
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": "be5466d8eb2c2229", 117 "id": "cecf675ce2a554e8",
118 "src": "hda", 118 "src": "hda",
119 "uuid": "2c83aaa9-63df-43a5-b008-9a361a9fc312" 119 "uuid": "3f70ca65-7fb8-4f83-b6e7-3f9893b1db5e"
120 }, 120 },
121 "__new_primary_file_construct_gb|construct_2__": { 121 "__new_primary_file_construct_gb|construct_2__": {
122 "id": "a37f81f30817f4ff", 122 "id": "9cc1fc667f1eccc7",
123 "src": "hda", 123 "src": "hda",
124 "uuid": "8ba2ce56-ba8b-4ff8-bcc0-54d0a2ad3b09" 124 "uuid": "723df0ab-a674-4b94-b805-15e38f56cbd5"
125 }, 125 },
126 "__new_primary_file_construct_gb|construct_3__": { 126 "__new_primary_file_construct_gb|construct_3__": {
127 "id": "b4705f371a43addc", 127 "id": "0b28ef6dfa05b9a4",
128 "src": "hda", 128 "src": "hda",
129 "uuid": "47741e71-6bf6-46ec-9353-25bb48d895ed" 129 "uuid": "0225d884-89af-4b29-bf0c-d27e776614a3"
130 }, 130 },
131 "__new_primary_file_construct_gb|construct_4__": { 131 "__new_primary_file_construct_gb|construct_4__": {
132 "id": "0dc911fcb05967a3", 132 "id": "dd0a4ddfadd2b33c",
133 "src": "hda", 133 "src": "hda",
134 "uuid": "6aa740ec-6985-4d66-8427-b1652fa06f3a" 134 "uuid": "2495d80c-1c1d-4aa7-af8c-eac0dd199af2"
135 }, 135 },
136 "output_zip": { 136 "output_zip": {
137 "id": "2ff5b0f6b4cfbb73", 137 "id": "dfd75d2f0da631b2",
138 "src": "hda", 138 "src": "hda",
139 "uuid": "49164d85-9bff-47f5-b8ee-de001d155fd3" 139 "uuid": "a840b0de-7374-4fc2-bc9c-eec0f6615e2f"
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/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 146 "chromInfo": "\"/tmp/tmphxxoceah/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, 2.21it/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", 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, 2.42it/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, 1.83it/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, 2.21it/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", 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, 2.42it/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, 1.83it/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": "2025-05-26T08:56:15.534051", 158 "update_time": "2025-05-26T09:45:09.253153",
159 "user_email": "planemo@galaxyproject.org", 159 "user_email": "planemo@galaxyproject.org",
160 "user_id": "cb6d3fbb91be6861" 160 "user_id": "b5f519d254c4f536"
161 }, 161 },
162 "status": "success", 162 "status": "success",
163 "test_index": 0, 163 "test_index": 0,
164 "time_seconds": 54.95904994010925, 164 "time_seconds": 53.940672636032104,
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": "e01f0df21d75058c", 176 "id": "191f29e52861c771",
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": "afdf3d24f0e34eea", 181 "id": "10fbf206fb2087c4",
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/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'", 187 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/a/e/1/dataset_ae19b93d-96dc-4575-922e-1c1b13cdda00.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/6/6/b/dataset_66becc5b-d90e-4bca-8456-82d9f7c209ea.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/6/6/b/dataset_66becc5b-d90e-4bca-8456-82d9f7c209ea.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/tmphxxoceah/job_working_directory/000/17/outputs/dataset_cf3ea990-c609-45fe-a823-8786fed863f9.dat'",
188 "command_version": "", 188 "command_version": "",
189 "copied_from_job_id": null, 189 "copied_from_job_id": null,
190 "create_time": "2025-05-26T08:56:26.250368", 190 "create_time": "2025-05-26T09:45:19.833949",
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": "79009", 370 "external_id": "102481",
371 "galaxy_version": "24.2", 371 "galaxy_version": "24.2",
372 "handler": null, 372 "handler": null,
373 "history_id": "18a1e53d7b8ec0fa", 373 "history_id": "c5accd210dc5c9dd",
374 "id": "b4705f371a43addc", 374 "id": "0b28ef6dfa05b9a4",
375 "inputs": { 375 "inputs": {
376 "assembly_csv": { 376 "assembly_csv": {
377 "id": "e01f0df21d75058c", 377 "id": "191f29e52861c771",
378 "src": "hda", 378 "src": "hda",
379 "uuid": "5b2e01d9-e63b-45e1-8523-e88570aecbd1" 379 "uuid": "ae19b93d-96dc-4575-922e-1c1b13cdda00"
380 }, 380 },
381 "genbank_files1": { 381 "genbank_files1": {
382 "id": "bc8da7662961ae94", 382 "id": "1bd551c439d3389f",
383 "src": "hda", 383 "src": "hda",
384 "uuid": "5633084d-0123-48ba-b733-086550a95944" 384 "uuid": "66becc5b-d90e-4bca-8456-82d9f7c209ea"
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": "285751a21c9d1d68", 395 "id": "27fa0815bff520f2",
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": "d8c348e4a6c18790", 401 "id": "a74d82facdf691d6",
402 "src": "hda", 402 "src": "hda",
403 "uuid": "39e12d2a-e4aa-491e-bb74-be0d48efaa36" 403 "uuid": "d06a3b4e-424a-4af4-b067-8426c2170c90"
404 }, 404 },
405 "__new_primary_file_construct_gb|construct_2__": { 405 "__new_primary_file_construct_gb|construct_2__": {
406 "id": "cc98bdb1867cbf6a", 406 "id": "7d2e9c5805bbd6ea",
407 "src": "hda", 407 "src": "hda",
408 "uuid": "dbc568c1-dd73-4973-aa7a-f33cb279cbb7" 408 "uuid": "1f95f8b0-5fc6-4b06-9550-06dd8233e6bd"
409 }, 409 },
410 "__new_primary_file_construct_gb|construct_3__": { 410 "__new_primary_file_construct_gb|construct_3__": {
411 "id": "dd60b22cea40a264", 411 "id": "6c4aee794b3972b4",
412 "src": "hda", 412 "src": "hda",
413 "uuid": "3d0514f2-d798-484f-add3-d04103fef517" 413 "uuid": "cfd50000-e85e-4b17-985e-f137dc59b08b"
414 }, 414 },
415 "output_zip": { 415 "output_zip": {
416 "id": "cb5bc2d1019b090c", 416 "id": "e670fc59d69da207",
417 "src": "hda", 417 "src": "hda",
418 "uuid": "81c8307a-8e03-4975-b3ec-1115f4f47284" 418 "uuid": "cf3ea990-c609-45fe-a823-8786fed863f9"
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/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 425 "chromInfo": "\"/tmp/tmphxxoceah/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, 4.42it/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", 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, 4.35it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.34it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.31it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.56it/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, 4.42it/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", 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, 4.35it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.34it/s, now=None]\rassembly: 80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588 | 4/5 [00:00<00:00, 4.31it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00, 3.56it/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": "2025-05-26T08:56:38.283009", 437 "update_time": "2025-05-26T09:45:31.869394",
438 "user_email": "planemo@galaxyproject.org", 438 "user_email": "planemo@galaxyproject.org",
439 "user_id": "cb6d3fbb91be6861" 439 "user_id": "b5f519d254c4f536"
440 }, 440 },
441 "status": "success", 441 "status": "success",
442 "test_index": 1, 442 "test_index": 1,
443 "time_seconds": 22.636474609375, 443 "time_seconds": 22.247495412826538,
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": "c6996082322986ef", 455 "id": "83c94260ae237f16",
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": "48e4779cf88cf124", 460 "id": "f825d543d1b9cf39",
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/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'", 466 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/8/2/c/dataset_82c2d90b-0ca3-4633-915b-eaa0ab81b80f.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/c/b/f/dataset_cbf24487-bf9d-469a-99cd-bccebb2bc139.dat,/tmp/tmphxxoceah/files/d/3/d/dataset_d3d42e4b-1982-4660-8ad4-f12c8a0599cb.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/c/b/f/dataset_cbf24487-bf9d-469a-99cd-bccebb2bc139.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmphxxoceah/files/d/3/d/dataset_d3d42e4b-1982-4660-8ad4-f12c8a0599cb.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/tmphxxoceah/job_working_directory/000/21/outputs/dataset_233ed98e-ee9b-468f-8145-9a8c44e8034f.dat'",
467 "command_version": "", 467 "command_version": "",
468 "copied_from_job_id": null, 468 "copied_from_job_id": null,
469 "create_time": "2025-05-26T08:56:49.662294", 469 "create_time": "2025-05-26T09:45:42.951843",
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": "79436", 649 "external_id": "102861",
650 "galaxy_version": "24.2", 650 "galaxy_version": "24.2",
651 "handler": null, 651 "handler": null,
652 "history_id": "afdf3d24f0e34eea", 652 "history_id": "10fbf206fb2087c4",
653 "id": "cb5bc2d1019b090c", 653 "id": "e670fc59d69da207",
654 "inputs": { 654 "inputs": {
655 "assembly_csv": { 655 "assembly_csv": {
656 "id": "c6996082322986ef", 656 "id": "83c94260ae237f16",
657 "src": "hda", 657 "src": "hda",
658 "uuid": "36c9642c-c980-4a5f-babe-e1140450965b" 658 "uuid": "82c2d90b-0ca3-4633-915b-eaa0ab81b80f"
659 }, 659 },
660 "genbank_files1": { 660 "genbank_files1": {
661 "id": "ff6721ae641686bd", 661 "id": "57b57ab024b6e67d",
662 "src": "hda", 662 "src": "hda",
663 "uuid": "fd7feec8-d839-4aac-ba59-54d4042d72d4" 663 "uuid": "cbf24487-bf9d-469a-99cd-bccebb2bc139"
664 }, 664 },
665 "genbank_files2": { 665 "genbank_files2": {
666 "id": "898f771988549b05", 666 "id": "71d78516c0fe784e",
667 "src": "hda", 667 "src": "hda",
668 "uuid": "097d3af5-48d7-4b15-9063-19cc11585d82" 668 "uuid": "d3d42e4b-1982-4660-8ad4-f12c8a0599cb"
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": "2bf3ecab9316a382", 679 "id": "24f234959abeadac",
680 "src": "hdca" 680 "src": "hdca"
681 } 681 }
682 }, 682 },
683 "outputs": { 683 "outputs": {
684 "output_zip": { 684 "output_zip": {
685 "id": "b995dfb8c32b92b7", 685 "id": "1211f83788e0a9a2",
686 "src": "hda", 686 "src": "hda",
687 "uuid": "dd39a396-84ad-4350-8d9b-a0efafd5ea2a" 687 "uuid": "233ed98e-ee9b-468f-8145-9a8c44e8034f"
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/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 694 "chromInfo": "\"/tmp/tmphxxoceah/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, 2.23it/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, 2.38it/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, 2.23it/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, 2.38it/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": "2025-05-26T08:57:02.321903", 706 "update_time": "2025-05-26T09:45:54.473182",
707 "user_email": "planemo@galaxyproject.org", 707 "user_email": "planemo@galaxyproject.org",
708 "user_id": "cb6d3fbb91be6861" 708 "user_id": "b5f519d254c4f536"
709 }, 709 },
710 "status": "success", 710 "status": "success",
711 "test_index": 2, 711 "test_index": 2,
712 "time_seconds": 23.856895685195923, 712 "time_seconds": 22.476279258728027,
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": "9d9573fdc2182066", 724 "id": "2aab5679a1ae5c57",
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": "d51bf47fbc922335", 729 "id": "67e443cb5516c0e0",
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/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'", 735 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/2/c/3/dataset_2c3186df-93d9-4d24-8956-c6a17e7d822a.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/1/d/8/dataset_1d824d9e-0b4f-4a81-af49-1acb506e8f4b.dat,/tmp/tmphxxoceah/files/5/7/d/dataset_57d780ae-3783-4cdf-a295-642ebc88a60e.dat,/tmp/tmphxxoceah/files/b/8/9/dataset_b89b536e-e310-470d-bddc-cd2847c2cfff.dat,/tmp/tmphxxoceah/files/b/b/d/dataset_bbdc2ed9-f2fa-4e92-b9ac-2140a8f80ea8.dat,/tmp/tmphxxoceah/files/0/6/5/dataset_06587a95-951c-4c6f-bded-3df9fd38a5d1.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/1/d/8/dataset_1d824d9e-0b4f-4a81-af49-1acb506e8f4b.dat:GFP.gb,/tmp/tmphxxoceah/files/5/7/d/dataset_57d780ae-3783-4cdf-a295-642ebc88a60e.dat:p15A_kan.gb,/tmp/tmphxxoceah/files/b/8/9/dataset_b89b536e-e310-470d-bddc-cd2847c2cfff.dat:promoter.gb,/tmp/tmphxxoceah/files/b/b/d/dataset_bbdc2ed9-f2fa-4e92-b9ac-2140a8f80ea8.dat:RFP.gb,/tmp/tmphxxoceah/files/0/6/5/dataset_06587a95-951c-4c6f-bded-3df9fd38a5d1.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/tmphxxoceah/job_working_directory/000/28/outputs/dataset_003ab152-a58f-45ab-a3c5-38a87199b77d.dat'",
736 "command_version": "", 736 "command_version": "",
737 "copied_from_job_id": null, 737 "copied_from_job_id": null,
738 "create_time": "2025-05-26T08:57:24.342653", 738 "create_time": "2025-05-26T09:46:15.589461",
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": "80040", 918 "external_id": "103494",
919 "galaxy_version": "24.2", 919 "galaxy_version": "24.2",
920 "handler": null, 920 "handler": null,
921 "history_id": "285751a21c9d1d68", 921 "history_id": "27fa0815bff520f2",
922 "id": "b995dfb8c32b92b7", 922 "id": "1211f83788e0a9a2",
923 "inputs": { 923 "inputs": {
924 "assembly_csv": { 924 "assembly_csv": {
925 "id": "9d9573fdc2182066", 925 "id": "2aab5679a1ae5c57",
926 "src": "hda", 926 "src": "hda",
927 "uuid": "251d413f-0fe8-42cd-8a76-7ef77cde6f15" 927 "uuid": "2c3186df-93d9-4d24-8956-c6a17e7d822a"
928 }, 928 },
929 "genbank_files1": { 929 "genbank_files1": {
930 "id": "241cfac882733d83", 930 "id": "0164abbd74b9b05d",
931 "src": "hda", 931 "src": "hda",
932 "uuid": "7d893bbf-b4e0-4d64-bafc-21ba1566237d" 932 "uuid": "1d824d9e-0b4f-4a81-af49-1acb506e8f4b"
933 }, 933 },
934 "genbank_files2": { 934 "genbank_files2": {
935 "id": "7ada2c781708b1e8", 935 "id": "f5f5feeed891820d",
936 "src": "hda", 936 "src": "hda",
937 "uuid": "cc2314fa-924f-47c0-b89a-661fb78790a4" 937 "uuid": "57d780ae-3783-4cdf-a295-642ebc88a60e"
938 }, 938 },
939 "genbank_files3": { 939 "genbank_files3": {
940 "id": "4deb8a541e3f0671", 940 "id": "b3161e3b65353042",
941 "src": "hda", 941 "src": "hda",
942 "uuid": "8d097c97-7bd5-48eb-9f9e-f5b92ce19458" 942 "uuid": "b89b536e-e310-470d-bddc-cd2847c2cfff"
943 }, 943 },
944 "genbank_files4": { 944 "genbank_files4": {
945 "id": "cdcc9004d7157de8", 945 "id": "292aa45e4e016cce",
946 "src": "hda", 946 "src": "hda",
947 "uuid": "59189305-e832-4191-be7c-496c01c8aba6" 947 "uuid": "bbdc2ed9-f2fa-4e92-b9ac-2140a8f80ea8"
948 }, 948 },
949 "genbank_files5": { 949 "genbank_files5": {
950 "id": "33fad5084f4d4cb5", 950 "id": "9318ef3621fbfa11",
951 "src": "hda", 951 "src": "hda",
952 "uuid": "402500d7-6532-4008-9445-c0cf7fed5350" 952 "uuid": "06587a95-951c-4c6f-bded-3df9fd38a5d1"
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": "590bb56cc83504dc", 963 "id": "5180b1a726879d60",
964 "src": "hdca" 964 "src": "hdca"
965 } 965 }
966 }, 966 },
967 "outputs": { 967 "outputs": {
968 "output_zip": { 968 "output_zip": {
969 "id": "4f510c4214d7d568", 969 "id": "4b5a70f26b4819b4",
970 "src": "hda", 970 "src": "hda",
971 "uuid": "8e6b31eb-84b3-4184-92eb-33384ae50857" 971 "uuid": "003ab152-a58f-45ab-a3c5-38a87199b77d"
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/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 978 "chromInfo": "\"/tmp/tmphxxoceah/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: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.38it/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, 49.32it/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: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 6/8 [00:00<00:00, 49.38it/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, 49.32it/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": "2025-05-26T08:57:34.740635", 990 "update_time": "2025-05-26T09:46:26.255886",
991 "user_email": "planemo@galaxyproject.org", 991 "user_email": "planemo@galaxyproject.org",
992 "user_id": "cb6d3fbb91be6861" 992 "user_id": "b5f519d254c4f536"
993 }, 993 },
994 "status": "success", 994 "status": "success",
995 "test_index": 3, 995 "test_index": 3,
996 "time_seconds": 32.283992767333984, 996 "time_seconds": 31.84161639213562,
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": "017df84d4155fcba", 1008 "id": "6aba8bde83c91d2f",
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": "ff96e44e65db99f8", 1013 "id": "c3b441e1ed1e9870",
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/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'", 1019 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/2/a/d/dataset_2ad0d873-86c6-45d9-b7d2-124dcbc1af89.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/d/2/9/dataset_d293bdbb-5524-4e82-a4a0-d687a407a968.dat,/tmp/tmphxxoceah/files/e/a/5/dataset_ea5e46a6-144f-4c5e-b626-6bca5055f710.dat,/tmp/tmphxxoceah/files/b/4/9/dataset_b491036e-78aa-4140-bca6-63462b7dbb5a.dat,/tmp/tmphxxoceah/files/1/c/f/dataset_1cf514a1-2062-47c1-98b3-d86c408d348d.dat,/tmp/tmphxxoceah/files/d/0/a/dataset_d0ae7d04-556d-48aa-a859-63d0efd9bc1c.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/d/2/9/dataset_d293bdbb-5524-4e82-a4a0-d687a407a968.dat:BBa_E0040_GFP.gb,/tmp/tmphxxoceah/files/e/a/5/dataset_ea5e46a6-144f-4c5e-b626-6bca5055f710.dat:BBa_J23119_prom.gb,/tmp/tmphxxoceah/files/b/4/9/dataset_b491036e-78aa-4140-bca6-63462b7dbb5a.dat:BBa_J23119_prom_flawed.gb,/tmp/tmphxxoceah/files/1/c/f/dataset_1cf514a1-2062-47c1-98b3-d86c408d348d.dat:BBa_J61048_term.gb,/tmp/tmphxxoceah/files/d/0/a/dataset_d0ae7d04-556d-48aa-a859-63d0efd9bc1c.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/tmphxxoceah/job_working_directory/000/35/outputs/dataset_4731915b-5562-4afe-b2f2-cf88b2af3eb5.dat'",
1020 "command_version": "", 1020 "command_version": "",
1021 "copied_from_job_id": null, 1021 "copied_from_job_id": null,
1022 "create_time": "2025-05-26T08:57:56.917009", 1022 "create_time": "2025-05-26T09:46:47.832614",
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": "80672", 1202 "external_id": "104081",
1203 "galaxy_version": "24.2", 1203 "galaxy_version": "24.2",
1204 "handler": null, 1204 "handler": null,
1205 "history_id": "48e4779cf88cf124", 1205 "history_id": "f825d543d1b9cf39",
1206 "id": "4f510c4214d7d568", 1206 "id": "4b5a70f26b4819b4",
1207 "inputs": { 1207 "inputs": {
1208 "assembly_csv": { 1208 "assembly_csv": {
1209 "id": "017df84d4155fcba", 1209 "id": "6aba8bde83c91d2f",
1210 "src": "hda", 1210 "src": "hda",
1211 "uuid": "fd913c0f-ea98-4b8d-a170-961146c201d5" 1211 "uuid": "2ad0d873-86c6-45d9-b7d2-124dcbc1af89"
1212 }, 1212 },
1213 "genbank_files1": { 1213 "genbank_files1": {
1214 "id": "1745fab1994e918a", 1214 "id": "1aae5cb645dbaceb",
1215 "src": "hda", 1215 "src": "hda",
1216 "uuid": "38402f39-a1d3-495e-afed-bf8335b4cdb6" 1216 "uuid": "d293bdbb-5524-4e82-a4a0-d687a407a968"
1217 }, 1217 },
1218 "genbank_files2": { 1218 "genbank_files2": {
1219 "id": "9f4b12edd1240647", 1219 "id": "cc421d01a299ef36",
1220 "src": "hda", 1220 "src": "hda",
1221 "uuid": "9c8ea453-16b9-4b9d-b171-9d5c0322adf9" 1221 "uuid": "ea5e46a6-144f-4c5e-b626-6bca5055f710"
1222 }, 1222 },
1223 "genbank_files3": { 1223 "genbank_files3": {
1224 "id": "070cf47a9114ebf0", 1224 "id": "1f0503133822f6be",
1225 "src": "hda", 1225 "src": "hda",
1226 "uuid": "31a46fbb-0267-42e3-b9d3-c60804edd30c" 1226 "uuid": "b491036e-78aa-4140-bca6-63462b7dbb5a"
1227 }, 1227 },
1228 "genbank_files4": { 1228 "genbank_files4": {
1229 "id": "176efb58f023067c", 1229 "id": "f7b46848b0cdcf03",
1230 "src": "hda", 1230 "src": "hda",
1231 "uuid": "e278e6ea-3146-49fa-a4f5-becf766e4f5e" 1231 "uuid": "1cf514a1-2062-47c1-98b3-d86c408d348d"
1232 }, 1232 },
1233 "genbank_files5": { 1233 "genbank_files5": {
1234 "id": "2c38922866e3bd19", 1234 "id": "c92ddd5b8e0dfe51",
1235 "src": "hda", 1235 "src": "hda",
1236 "uuid": "6a19d37f-54e1-4c94-a2b1-1a7f37820aad" 1236 "uuid": "d0ae7d04-556d-48aa-a859-63d0efd9bc1c"
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": "7ede2556a40dc9ba", 1247 "id": "2bdc7fcb2931f07b",
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": "e9bea5372f4a6a20", 1253 "id": "4e090171f4d7129f",
1254 "src": "hda", 1254 "src": "hda",
1255 "uuid": "80f480c8-264d-428b-8b95-253cd89d7764" 1255 "uuid": "0541aea5-21f7-4b9b-b037-ce0b677829bb"
1256 }, 1256 },
1257 "__new_primary_file_construct_gb|C2_gfp_term__": { 1257 "__new_primary_file_construct_gb|C2_gfp_term__": {
1258 "id": "1290d6537f2937e3", 1258 "id": "4a624b810533f2ef",
1259 "src": "hda", 1259 "src": "hda",
1260 "uuid": "7b7b6524-575a-4dfc-800c-dc0d3e8ece79" 1260 "uuid": "381b158b-3536-4150-be35-d3e2b6e5dc19"
1261 }, 1261 },
1262 "__new_primary_file_construct_gb|C3_final__": { 1262 "__new_primary_file_construct_gb|C3_final__": {
1263 "id": "cd293a8cb9d8e7b5", 1263 "id": "99b0b6baf442a2d9",
1264 "src": "hda", 1264 "src": "hda",
1265 "uuid": "7be9e218-0841-46cd-ac62-5686969f6935" 1265 "uuid": "084415f0-529e-443f-bfa9-7ce16f75171f"
1266 }, 1266 },
1267 "output_zip": { 1267 "output_zip": {
1268 "id": "3651b2c7591f0e47", 1268 "id": "a38ed44718641cdb",
1269 "src": "hda", 1269 "src": "hda",
1270 "uuid": "a3f2eab1-bbe1-401e-b436-b7ffc698ee3a" 1270 "uuid": "4731915b-5562-4afe-b2f2-cf88b2af3eb5"
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/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1277 "chromInfo": "\"/tmp/tmphxxoceah/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, 1.90it/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", 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, 1.96it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.59it/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, 1.90it/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", 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, 1.96it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.59it/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": "2025-05-26T08:58:09.572798", 1289 "update_time": "2025-05-26T09:47:00.964337",
1290 "user_email": "planemo@galaxyproject.org", 1290 "user_email": "planemo@galaxyproject.org",
1291 "user_id": "cb6d3fbb91be6861" 1291 "user_id": "b5f519d254c4f536"
1292 }, 1292 },
1293 "status": "success", 1293 "status": "success",
1294 "test_index": 4, 1294 "test_index": 4,
1295 "time_seconds": 34.93839716911316, 1295 "time_seconds": 34.59279441833496,
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": "b1a8f56fe428091e", 1307 "id": "09ac55ab9704eba2",
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": "76608081d307dc20", 1312 "id": "dc7e3ab6a421767b",
1313 "src": "hdca" 1313 "src": "hdca"
1314 }, 1314 },
1315 "genbank_files": { 1315 "genbank_files": {
1316 "id": "0551bf01e3dbca02", 1316 "id": "b1d9a1d43e36b679",
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/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'", 1322 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/0/d/8/dataset_0d80ec64-7c14-49ec-bf00-8b127413b402.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/b/f/e/dataset_bfe6c5a0-bee9-4fcd-bc48-1030fddae94b.dat,/tmp/tmphxxoceah/files/5/b/1/dataset_5b1e4497-7e6b-42cc-8cbb-5f538d40f7bb.dat,/tmp/tmphxxoceah/files/b/3/e/dataset_b3ecd963-5e7a-4c86-91f3-8d8322471402.dat,/tmp/tmphxxoceah/files/6/f/8/dataset_6f8d0b94-6f0f-470c-b36a-87256aa427c6.dat,/tmp/tmphxxoceah/files/2/f/d/dataset_2fd8ba0d-a6ac-4379-a094-6dfc4b3f677e.dat,/tmp/tmphxxoceah/files/c/5/f/dataset_c5fde1d8-6078-4b1c-946d-fe58c868e1a5.dat,/tmp/tmphxxoceah/files/0/2/0/dataset_0203ce08-8c98-4dcf-a274-ac69f126eb78.dat' --domesticated_seq '/tmp/tmphxxoceah/files/9/0/7/dataset_9073f5ed-6218-436e-9c90-40231a771418.dat,/tmp/tmphxxoceah/files/1/c/2/dataset_1c278033-6add-4e83-92ee-ece6b30d73b2.dat,/tmp/tmphxxoceah/files/6/8/b/dataset_68ba5566-3d5c-4aaf-9f00-a5dc3f1ec5f6.dat,/tmp/tmphxxoceah/files/e/2/a/dataset_e2abf373-3268-46a0-a6bd-889fe7061984.dat,/tmp/tmphxxoceah/files/d/7/1/dataset_d71d0b7d-fc98-4d97-8a6b-e92bb229582e.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/b/f/e/dataset_bfe6c5a0-bee9-4fcd-bc48-1030fddae94b.dat:part_A.gb,/tmp/tmphxxoceah/files/5/b/1/dataset_5b1e4497-7e6b-42cc-8cbb-5f538d40f7bb.dat:part_B.gb,/tmp/tmphxxoceah/files/b/3/e/dataset_b3ecd963-5e7a-4c86-91f3-8d8322471402.dat:part_C.gb,/tmp/tmphxxoceah/files/6/f/8/dataset_6f8d0b94-6f0f-470c-b36a-87256aa427c6.dat:part_D.gb,/tmp/tmphxxoceah/files/2/f/d/dataset_2fd8ba0d-a6ac-4379-a094-6dfc4b3f677e.dat:part_E.gb,/tmp/tmphxxoceah/files/c/5/f/dataset_c5fde1d8-6078-4b1c-946d-fe58c868e1a5.dat:part_F.gb,/tmp/tmphxxoceah/files/0/2/0/dataset_0203ce08-8c98-4dcf-a274-ac69f126eb78.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmphxxoceah/files/9/0/7/dataset_9073f5ed-6218-436e-9c90-40231a771418.dat:part_H.gb,/tmp/tmphxxoceah/files/1/c/2/dataset_1c278033-6add-4e83-92ee-ece6b30d73b2.dat:part_I.gb,/tmp/tmphxxoceah/files/6/8/b/dataset_68ba5566-3d5c-4aaf-9f00-a5dc3f1ec5f6.dat:part_J.gb,/tmp/tmphxxoceah/files/e/2/a/dataset_e2abf373-3268-46a0-a6bd-889fe7061984.dat:part_K.gb,/tmp/tmphxxoceah/files/d/7/1/dataset_d71d0b7d-fc98-4d97-8a6b-e92bb229582e.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/tmphxxoceah/job_working_directory/000/49/outputs/dataset_e791efbc-be6b-44c5-a124-a744a812b597.dat'",
1323 "command_version": "", 1323 "command_version": "",
1324 "copied_from_job_id": null, 1324 "copied_from_job_id": null,
1325 "create_time": "2025-05-26T08:58:50.541909", 1325 "create_time": "2025-05-26T09:47:41.246196",
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": "81731", 1505 "external_id": "105127",
1506 "galaxy_version": "24.2", 1506 "galaxy_version": "24.2",
1507 "handler": null, 1507 "handler": null,
1508 "history_id": "2bf3ecab9316a382", 1508 "history_id": "24f234959abeadac",
1509 "id": "aa893e5f7beb4eb8", 1509 "id": "271c0f8150c5b24a",
1510 "inputs": { 1510 "inputs": {
1511 "assembly_csv": { 1511 "assembly_csv": {
1512 "id": "b1a8f56fe428091e", 1512 "id": "09ac55ab9704eba2",
1513 "src": "hda", 1513 "src": "hda",
1514 "uuid": "97b16fa9-53ab-4e65-9de7-e30112bcdd06" 1514 "uuid": "0d80ec64-7c14-49ec-bf00-8b127413b402"
1515 }, 1515 },
1516 "domesticated_input1": { 1516 "domesticated_input1": {
1517 "id": "dbc527c8f70438a2", 1517 "id": "f1e670d3230dc49d",
1518 "src": "hda", 1518 "src": "hda",
1519 "uuid": "ef3f0423-f1dd-462b-8d68-e68cd6d59d82" 1519 "uuid": "9073f5ed-6218-436e-9c90-40231a771418"
1520 }, 1520 },
1521 "domesticated_input2": { 1521 "domesticated_input2": {
1522 "id": "a3ea165695c1e088", 1522 "id": "d6d38b30a0e08779",
1523 "src": "hda", 1523 "src": "hda",
1524 "uuid": "ea297609-87c4-4bfc-abfd-084fbcc94d5b" 1524 "uuid": "1c278033-6add-4e83-92ee-ece6b30d73b2"
1525 }, 1525 },
1526 "domesticated_input3": { 1526 "domesticated_input3": {
1527 "id": "d4fcfbec208c480f", 1527 "id": "5df6658d98901785",
1528 "src": "hda", 1528 "src": "hda",
1529 "uuid": "60d919ff-9b54-4856-b3d0-9836114c2575" 1529 "uuid": "68ba5566-3d5c-4aaf-9f00-a5dc3f1ec5f6"
1530 }, 1530 },
1531 "domesticated_input4": { 1531 "domesticated_input4": {
1532 "id": "b53993d77cff267e", 1532 "id": "179c4c4e78c36c21",
1533 "src": "hda", 1533 "src": "hda",
1534 "uuid": "08efef6d-13c4-4e1b-a155-859e0a0df989" 1534 "uuid": "e2abf373-3268-46a0-a6bd-889fe7061984"
1535 }, 1535 },
1536 "domesticated_input5": { 1536 "domesticated_input5": {
1537 "id": "e1a323c2b9a73ada", 1537 "id": "b1ed244e949762c6",
1538 "src": "hda", 1538 "src": "hda",
1539 "uuid": "e72facc2-0bd8-49e8-94e6-6b255853b030" 1539 "uuid": "d71d0b7d-fc98-4d97-8a6b-e92bb229582e"
1540 }, 1540 },
1541 "genbank_files1": { 1541 "genbank_files1": {
1542 "id": "03a53f60ebb3b30b", 1542 "id": "faf74795de9215e4",
1543 "src": "hda", 1543 "src": "hda",
1544 "uuid": "823cfc4c-98db-494d-a03b-5181179a3581" 1544 "uuid": "bfe6c5a0-bee9-4fcd-bc48-1030fddae94b"
1545 }, 1545 },
1546 "genbank_files2": { 1546 "genbank_files2": {
1547 "id": "949b6e5fb08e3b2e", 1547 "id": "982fc2b45c634401",
1548 "src": "hda", 1548 "src": "hda",
1549 "uuid": "60a53b2c-927e-4c33-b6b0-2e927266044e" 1549 "uuid": "5b1e4497-7e6b-42cc-8cbb-5f538d40f7bb"
1550 }, 1550 },
1551 "genbank_files3": { 1551 "genbank_files3": {
1552 "id": "4b14363353165bd2", 1552 "id": "d49187f9d744460f",
1553 "src": "hda", 1553 "src": "hda",
1554 "uuid": "d357996d-45c3-4715-b8eb-ea6bb836b18e" 1554 "uuid": "b3ecd963-5e7a-4c86-91f3-8d8322471402"
1555 }, 1555 },
1556 "genbank_files4": { 1556 "genbank_files4": {
1557 "id": "aa893e5f7beb4eb8", 1557 "id": "271c0f8150c5b24a",
1558 "src": "hda", 1558 "src": "hda",
1559 "uuid": "dacfd7e2-f5ff-4821-8d70-f73307f7997e" 1559 "uuid": "6f8d0b94-6f0f-470c-b36a-87256aa427c6"
1560 }, 1560 },
1561 "genbank_files5": { 1561 "genbank_files5": {
1562 "id": "e33440187009b2c6", 1562 "id": "954a11ecc737c99c",
1563 "src": "hda", 1563 "src": "hda",
1564 "uuid": "9b3f9357-c1cc-43c9-a81c-c100483b3a0d" 1564 "uuid": "2fd8ba0d-a6ac-4379-a094-6dfc4b3f677e"
1565 }, 1565 },
1566 "genbank_files6": { 1566 "genbank_files6": {
1567 "id": "ef97dc51810891e7", 1567 "id": "c90496f58e5d6dd9",
1568 "src": "hda", 1568 "src": "hda",
1569 "uuid": "5e43150c-3c7c-4072-9720-fdc085cd6d8b" 1569 "uuid": "c5fde1d8-6078-4b1c-946d-fe58c868e1a5"
1570 }, 1570 },
1571 "genbank_files7": { 1571 "genbank_files7": {
1572 "id": "16b078cfbe5cb4fb", 1572 "id": "9c66fe6132ced54b",
1573 "src": "hda", 1573 "src": "hda",
1574 "uuid": "2de75a41-7673-4cef-aa63-2cf6d9466e8c" 1574 "uuid": "0203ce08-8c98-4dcf-a274-ac69f126eb78"
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": "0a696a8b22798e06", 1585 "id": "7a37f3397bf88665",
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": "08065af9f1d51b0a", 1591 "id": "ee6560cff5429b3a",
1592 "src": "hda", 1592 "src": "hda",
1593 "uuid": "4837c85e-ba71-482d-91d1-be3e3179ee5a" 1593 "uuid": "2d9d0878-8a8e-4a76-b4c7-8b2c58007a4c"
1594 }, 1594 },
1595 "__new_primary_file_construct_gb|construct_2__": { 1595 "__new_primary_file_construct_gb|construct_2__": {
1596 "id": "23c03036acf6de8c", 1596 "id": "7faeb5268234c1b7",
1597 "src": "hda", 1597 "src": "hda",
1598 "uuid": "a898af9c-3721-4b84-8ebc-790dc376316c" 1598 "uuid": "d8ead123-b416-446e-bcd7-12d88aa380d8"
1599 }, 1599 },
1600 "__new_primary_file_construct_gb|construct_3__": { 1600 "__new_primary_file_construct_gb|construct_3__": {
1601 "id": "950510fee01c22f4", 1601 "id": "71b5e767ad5c3d19",
1602 "src": "hda", 1602 "src": "hda",
1603 "uuid": "be8dfa79-0421-418a-9822-af3e69e3bd0a" 1603 "uuid": "d3370005-e04e-41fe-91ca-5ae418062a9f"
1604 }, 1604 },
1605 "__new_primary_file_construct_gb|construct_4__": { 1605 "__new_primary_file_construct_gb|construct_4__": {
1606 "id": "abd47de82fbecc4e", 1606 "id": "07cc2539cb83a207",
1607 "src": "hda", 1607 "src": "hda",
1608 "uuid": "1455799d-9a0a-46e7-8ddb-df60f983fb53" 1608 "uuid": "0a5f7883-f82b-4122-a882-76fadc52a358"
1609 }, 1609 },
1610 "output_zip": { 1610 "output_zip": {
1611 "id": "b52f373b44c22024", 1611 "id": "49de8d939dbbcfba",
1612 "src": "hda", 1612 "src": "hda",
1613 "uuid": "2bca238e-5421-456d-bf98-1bd44e65fc76" 1613 "uuid": "e791efbc-be6b-44c5-a124-a744a812b597"
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/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1620 "chromInfo": "\"/tmp/tmphxxoceah/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, 2.44it/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", 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, 2.41it/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, 1.82it/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, 2.44it/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", 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, 2.41it/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, 1.82it/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": "2025-05-26T08:59:03.629936", 1632 "update_time": "2025-05-26T09:47:53.960080",
1633 "user_email": "planemo@galaxyproject.org", 1633 "user_email": "planemo@galaxyproject.org",
1634 "user_id": "cb6d3fbb91be6861" 1634 "user_id": "b5f519d254c4f536"
1635 }, 1635 },
1636 "status": "success", 1636 "status": "success",
1637 "test_index": 5, 1637 "test_index": 5,
1638 "time_seconds": 53.84836268424988, 1638 "time_seconds": 52.97593927383423,
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": "4b6130eb686f10a7", 1650 "id": "e8ab24d23dab7d7f",
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": "2ff5b0f6b4cfbb73", 1655 "id": "dfd75d2f0da631b2",
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/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'", 1661 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmphxxoceah/files/0/1/7/dataset_017ccfd4-4d46-44c1-99ad-af18724cfa9c.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmphxxoceah/files/c/2/6/dataset_c26ad39f-1237-4c04-8f7f-73d2c5d9ad58.dat,/tmp/tmphxxoceah/files/c/6/8/dataset_c68beeb3-949a-4a3e-ab43-987831504001.dat,/tmp/tmphxxoceah/files/8/f/6/dataset_8f6a4bdd-c6c0-4b79-8dfd-7a2e5f0e8c72.dat,/tmp/tmphxxoceah/files/1/0/6/dataset_1069bd61-49fb-492a-8eaf-d98e496576a8.dat,/tmp/tmphxxoceah/files/3/1/1/dataset_311db06e-881c-4a38-9fe9-a13712004ece.dat,/tmp/tmphxxoceah/files/7/8/1/dataset_781cdd92-6baf-451e-8e72-f05961154dae.dat,/tmp/tmphxxoceah/files/7/1/7/dataset_717f7fe8-1fbf-4394-aeff-14d7aa430193.dat,/tmp/tmphxxoceah/files/3/a/8/dataset_3a883d96-6381-4569-a872-6490a47980b2.dat,/tmp/tmphxxoceah/files/c/1/d/dataset_c1d48747-8d18-4249-8b11-60a73ad7446f.dat,/tmp/tmphxxoceah/files/0/e/4/dataset_0e4a4a05-7265-4844-9d70-1ad96facfdf9.dat,/tmp/tmphxxoceah/files/9/f/7/dataset_9f72d140-3946-4567-8ecb-056458d7bb70.dat,/tmp/tmphxxoceah/files/b/6/a/dataset_b6a06ac7-2240-4f68-9e75-63de3f5d10f2.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmphxxoceah/files/c/2/6/dataset_c26ad39f-1237-4c04-8f7f-73d2c5d9ad58.dat:part_A.gb,/tmp/tmphxxoceah/files/c/6/8/dataset_c68beeb3-949a-4a3e-ab43-987831504001.dat:part_B.gb,/tmp/tmphxxoceah/files/8/f/6/dataset_8f6a4bdd-c6c0-4b79-8dfd-7a2e5f0e8c72.dat:part_C.gb,/tmp/tmphxxoceah/files/1/0/6/dataset_1069bd61-49fb-492a-8eaf-d98e496576a8.dat:part_D.gb,/tmp/tmphxxoceah/files/3/1/1/dataset_311db06e-881c-4a38-9fe9-a13712004ece.dat:part_E.gb,/tmp/tmphxxoceah/files/7/8/1/dataset_781cdd92-6baf-451e-8e72-f05961154dae.dat:part_F.gb,/tmp/tmphxxoceah/files/7/1/7/dataset_717f7fe8-1fbf-4394-aeff-14d7aa430193.dat:part_G.gb,/tmp/tmphxxoceah/files/3/a/8/dataset_3a883d96-6381-4569-a872-6490a47980b2.dat:part_H.gb,/tmp/tmphxxoceah/files/c/1/d/dataset_c1d48747-8d18-4249-8b11-60a73ad7446f.dat:part_I.gb,/tmp/tmphxxoceah/files/0/e/4/dataset_0e4a4a05-7265-4844-9d70-1ad96facfdf9.dat:part_J.gb,/tmp/tmphxxoceah/files/9/f/7/dataset_9f72d140-3946-4567-8ecb-056458d7bb70.dat:part_K.gb,/tmp/tmphxxoceah/files/b/6/a/dataset_b6a06ac7-2240-4f68-9e75-63de3f5d10f2.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/tmphxxoceah/job_working_directory/000/63/outputs/dataset_9593abfa-a9bc-4a45-8334-5203050a6ca5.dat'",
1662 "command_version": "", 1662 "command_version": "",
1663 "copied_from_job_id": null, 1663 "copied_from_job_id": null,
1664 "create_time": "2025-05-26T08:59:44.629082", 1664 "create_time": "2025-05-26T09:48:34.329479",
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": "82808", 1844 "external_id": "106213",
1845 "galaxy_version": "24.2", 1845 "galaxy_version": "24.2",
1846 "handler": null, 1846 "handler": null,
1847 "history_id": "d51bf47fbc922335", 1847 "history_id": "67e443cb5516c0e0",
1848 "id": "abd47de82fbecc4e", 1848 "id": "07cc2539cb83a207",
1849 "inputs": { 1849 "inputs": {
1850 "assembly_csv": { 1850 "assembly_csv": {
1851 "id": "4b6130eb686f10a7", 1851 "id": "e8ab24d23dab7d7f",
1852 "src": "hda", 1852 "src": "hda",
1853 "uuid": "5042213c-8bb6-48e0-9501-070e55a9a8c0" 1853 "uuid": "017ccfd4-4d46-44c1-99ad-af18724cfa9c"
1854 }, 1854 },
1855 "domesticated_input1": { 1855 "domesticated_input1": {
1856 "id": "7c76f7472621b5d0", 1856 "id": "548eebef94e3a53d",
1857 "src": "hda", 1857 "src": "hda",
1858 "uuid": "dd8d9744-d7f0-46ae-b26f-de961e3f5033" 1858 "uuid": "c26ad39f-1237-4c04-8f7f-73d2c5d9ad58"
1859 }, 1859 },
1860 "domesticated_input10": { 1860 "domesticated_input10": {
1861 "id": "9bd6c123148263b6", 1861 "id": "9e9d5c19538ef8ad",
1862 "src": "hda", 1862 "src": "hda",
1863 "uuid": "d2492f3b-8ea9-40e7-8bda-a15b506a22ac" 1863 "uuid": "0e4a4a05-7265-4844-9d70-1ad96facfdf9"
1864 }, 1864 },
1865 "domesticated_input11": { 1865 "domesticated_input11": {
1866 "id": "5d3d21e362e05995", 1866 "id": "8c0e43d479b6b17a",
1867 "src": "hda", 1867 "src": "hda",
1868 "uuid": "3a857675-027c-4b28-bf69-7591db569213" 1868 "uuid": "9f72d140-3946-4567-8ecb-056458d7bb70"
1869 }, 1869 },
1870 "domesticated_input12": { 1870 "domesticated_input12": {
1871 "id": "043b0e9e9cf8c91c", 1871 "id": "b75b41451f2f7195",
1872 "src": "hda", 1872 "src": "hda",
1873 "uuid": "26df2c50-4cbe-45f5-ba07-be8fb89cfb7c" 1873 "uuid": "b6a06ac7-2240-4f68-9e75-63de3f5d10f2"
1874 }, 1874 },
1875 "domesticated_input2": { 1875 "domesticated_input2": {
1876 "id": "11e2d0eceb639139", 1876 "id": "f1612d32ca625e37",
1877 "src": "hda", 1877 "src": "hda",
1878 "uuid": "aa64d9f2-f351-4776-aab6-648a5fa5f6da" 1878 "uuid": "c68beeb3-949a-4a3e-ab43-987831504001"
1879 }, 1879 },
1880 "domesticated_input3": { 1880 "domesticated_input3": {
1881 "id": "991f793af87d39c4", 1881 "id": "bf5687b995aa6663",
1882 "src": "hda", 1882 "src": "hda",
1883 "uuid": "1dbca58c-bd12-48c7-bbfe-49ef8801f8c3" 1883 "uuid": "8f6a4bdd-c6c0-4b79-8dfd-7a2e5f0e8c72"
1884 }, 1884 },
1885 "domesticated_input4": { 1885 "domesticated_input4": {
1886 "id": "3429ba0772b9ca69", 1886 "id": "13ae5fed3f9ef282",
1887 "src": "hda", 1887 "src": "hda",
1888 "uuid": "d396d7df-8e9d-441b-b04e-abaaa0c90a7f" 1888 "uuid": "1069bd61-49fb-492a-8eaf-d98e496576a8"
1889 }, 1889 },
1890 "domesticated_input5": { 1890 "domesticated_input5": {
1891 "id": "c04c164ed0056d43", 1891 "id": "58d09772df305f7c",
1892 "src": "hda", 1892 "src": "hda",
1893 "uuid": "4130ddb4-6eb6-4fa1-bd21-33ea63dc4f2a" 1893 "uuid": "311db06e-881c-4a38-9fe9-a13712004ece"
1894 }, 1894 },
1895 "domesticated_input6": { 1895 "domesticated_input6": {
1896 "id": "b3ed12fa60bc840b", 1896 "id": "940c0a8788b53ef0",
1897 "src": "hda", 1897 "src": "hda",
1898 "uuid": "2e907739-181d-44bc-8bc4-35d252e00535" 1898 "uuid": "781cdd92-6baf-451e-8e72-f05961154dae"
1899 }, 1899 },
1900 "domesticated_input7": { 1900 "domesticated_input7": {
1901 "id": "5406c597edc1a692", 1901 "id": "5d12b487c622fea5",
1902 "src": "hda", 1902 "src": "hda",
1903 "uuid": "9d3053e2-630d-4fba-9b08-09f59013ab96" 1903 "uuid": "717f7fe8-1fbf-4394-aeff-14d7aa430193"
1904 }, 1904 },
1905 "domesticated_input8": { 1905 "domesticated_input8": {
1906 "id": "780d322efdca3fcd", 1906 "id": "7f6a5e9bab73b744",
1907 "src": "hda", 1907 "src": "hda",
1908 "uuid": "26364877-f482-4b4d-8346-61a2f50f1ccf" 1908 "uuid": "3a883d96-6381-4569-a872-6490a47980b2"
1909 }, 1909 },
1910 "domesticated_input9": { 1910 "domesticated_input9": {
1911 "id": "951610fc65ac475f", 1911 "id": "917d245d020dcffb",
1912 "src": "hda", 1912 "src": "hda",
1913 "uuid": "6f64f828-be8e-4e72-a940-87396256fe3f" 1913 "uuid": "c1d48747-8d18-4249-8b11-60a73ad7446f"
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": "be5466d8eb2c2229", 1924 "id": "cecf675ce2a554e8",
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": "6d4b50576bf02b31", 1930 "id": "6ed4cf4ef5da4ab6",
1931 "src": "hda", 1931 "src": "hda",
1932 "uuid": "d4f04f5f-16a6-4675-a892-fa6d05156592" 1932 "uuid": "77c80040-9366-4df3-8ee7-b8f5c6148b73"
1933 }, 1933 },
1934 "__new_primary_file_construct_gb|construct_2__": { 1934 "__new_primary_file_construct_gb|construct_2__": {
1935 "id": "550e95bf5471ae1d", 1935 "id": "f0c0b63c8f5e218a",
1936 "src": "hda", 1936 "src": "hda",
1937 "uuid": "845f0e19-1541-481b-a386-47135e8ebdf1" 1937 "uuid": "8a7bd174-630d-439e-a111-682129e2dbc6"
1938 }, 1938 },
1939 "__new_primary_file_construct_gb|construct_3__": { 1939 "__new_primary_file_construct_gb|construct_3__": {
1940 "id": "359048b3278e74c9", 1940 "id": "89c8871118f8304b",
1941 "src": "hda", 1941 "src": "hda",
1942 "uuid": "420b6912-da3c-4b75-ae88-b73f0c005864" 1942 "uuid": "5ee7450c-795c-4a27-8354-25ac7ab1d71f"
1943 }, 1943 },
1944 "__new_primary_file_construct_gb|construct_4__": { 1944 "__new_primary_file_construct_gb|construct_4__": {
1945 "id": "7a3e4925ca1f5f1d", 1945 "id": "57b71ad05e041af6",
1946 "src": "hda", 1946 "src": "hda",
1947 "uuid": "5b639734-e44b-415c-b347-5a702df97945" 1947 "uuid": "b3b86695-7ea9-43e6-bfbb-6a20972dec20"
1948 }, 1948 },
1949 "output_zip": { 1949 "output_zip": {
1950 "id": "40a6167ab839cf08", 1950 "id": "2ec06dcf804a9f1d",
1951 "src": "hda", 1951 "src": "hda",
1952 "uuid": "4e39f3b7-2899-410e-a32f-47270970ae14" 1952 "uuid": "9593abfa-a9bc-4a45-8334-5203050a6ca5"
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/tmp_ibkdcj0/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1959 "chromInfo": "\"/tmp/tmphxxoceah/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, 2.42it/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", 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, 2.41it/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, 1.79it/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, 2.42it/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", 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, 2.41it/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, 1.79it/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": "2025-05-26T08:59:57.832603", 1971 "update_time": "2025-05-26T09:48:47.319875",
1972 "user_email": "planemo@galaxyproject.org", 1972 "user_email": "planemo@galaxyproject.org",
1973 "user_id": "cb6d3fbb91be6861" 1973 "user_id": "b5f519d254c4f536"
1974 }, 1974 },
1975 "status": "success", 1975 "status": "success",
1976 "test_index": 6, 1976 "test_index": 6,
1977 "time_seconds": 53.99832892417908, 1977 "time_seconds": 53.241769552230835,
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"