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comparison output.json @ 13:7d1778f5e164 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 10:10:46 +0000
parents 0be569bd5443
children 16ccb36aa8e3
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12:556649b3f9bb 13:7d1778f5e164
1 { 1 {
2 "summary": { 2 "summary": {
3 "num_errors": 0, 3 "num_errors": 0,
4 "num_failures": 0, 4 "num_failures": 1,
5 "num_skips": 0, 5 "num_skips": 0,
6 "num_tests": 7 6 "num_tests": 7
7 }, 7 },
8 "tests": [ 8 "tests": [
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": "7a37f3397bf88665", 14 "id": "41ca6db0600d7999",
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": "b5f519d254c4f536", 19 "id": "66f8380583c086e1",
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/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'", 25 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpy2ysv6tn/files/1/a/1/dataset_1a1ee32d-eed7-47fd-b491-4f0799b44a85.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpy2ysv6tn/files/4/4/1/dataset_44129191-5531-4cc9-b37b-fec4e3c677d5.dat,/tmp/tmpy2ysv6tn/files/6/1/f/dataset_61f5f19f-147b-46fd-8900-a8530f311835.dat,/tmp/tmpy2ysv6tn/files/4/4/0/dataset_440b34e7-490e-49bd-9b29-6afcabe5f6f6.dat,/tmp/tmpy2ysv6tn/files/a/3/f/dataset_a3fca212-b8dc-4579-901c-612b806241af.dat,/tmp/tmpy2ysv6tn/files/5/3/9/dataset_5398f2cb-1a25-45e5-9ba0-cd79a88b6e88.dat,/tmp/tmpy2ysv6tn/files/f/5/0/dataset_f505293a-8223-4da2-a22c-aa261d4955ec.dat,/tmp/tmpy2ysv6tn/files/c/5/0/dataset_c50e4b1f-c72a-4272-b324-e1c2c7d50293.dat,/tmp/tmpy2ysv6tn/files/0/0/d/dataset_00d79560-f944-4d8e-98e7-f516684a6100.dat,/tmp/tmpy2ysv6tn/files/3/d/5/dataset_3d5bb0fb-d610-4939-8fc5-999174fee5ca.dat,/tmp/tmpy2ysv6tn/files/c/7/c/dataset_c7cf96af-ab1c-4199-821f-5bb5b947752f.dat,/tmp/tmpy2ysv6tn/files/0/a/5/dataset_0a5139e7-7d83-48f1-a1c9-458a1e72685c.dat,/tmp/tmpy2ysv6tn/files/f/b/3/dataset_fb361f22-020c-4972-8661-f1f57d1a7afa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpy2ysv6tn/files/4/4/1/dataset_44129191-5531-4cc9-b37b-fec4e3c677d5.dat:part_A.gb,/tmp/tmpy2ysv6tn/files/6/1/f/dataset_61f5f19f-147b-46fd-8900-a8530f311835.dat:part_B.gb,/tmp/tmpy2ysv6tn/files/4/4/0/dataset_440b34e7-490e-49bd-9b29-6afcabe5f6f6.dat:part_C.gb,/tmp/tmpy2ysv6tn/files/a/3/f/dataset_a3fca212-b8dc-4579-901c-612b806241af.dat:part_D.gb,/tmp/tmpy2ysv6tn/files/5/3/9/dataset_5398f2cb-1a25-45e5-9ba0-cd79a88b6e88.dat:part_E.gb,/tmp/tmpy2ysv6tn/files/f/5/0/dataset_f505293a-8223-4da2-a22c-aa261d4955ec.dat:part_F.gb,/tmp/tmpy2ysv6tn/files/c/5/0/dataset_c50e4b1f-c72a-4272-b324-e1c2c7d50293.dat:part_G.gb,/tmp/tmpy2ysv6tn/files/0/0/d/dataset_00d79560-f944-4d8e-98e7-f516684a6100.dat:part_H.gb,/tmp/tmpy2ysv6tn/files/3/d/5/dataset_3d5bb0fb-d610-4939-8fc5-999174fee5ca.dat:part_I.gb,/tmp/tmpy2ysv6tn/files/c/7/c/dataset_c7cf96af-ab1c-4199-821f-5bb5b947752f.dat:part_J.gb,/tmp/tmpy2ysv6tn/files/0/a/5/dataset_0a5139e7-7d83-48f1-a1c9-458a1e72685c.dat:part_K.gb,/tmp/tmpy2ysv6tn/files/f/b/3/dataset_fb361f22-020c-4972-8661-f1f57d1a7afa.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/tmpy2ysv6tn/job_working_directory/000/14/outputs/dataset_acb064d7-2781-46fe-98df-716fee024c8d.dat'",
26 "command_version": "", 26 "command_version": "",
27 "copied_from_job_id": null, 27 "copied_from_job_id": null,
28 "create_time": "2025-05-26T09:44:56.264493", 28 "create_time": "2025-05-26T10:00:43.823779",
29 "dependencies": [], 29 "dependencies": [],
30 "exit_code": 0, 30 "exit_code": 1,
31 "external_id": "102136", 31 "external_id": "114506",
32 "galaxy_version": "24.2", 32 "galaxy_version": "24.2",
33 "handler": null, 33 "handler": null,
34 "history_id": "b5f519d254c4f536", 34 "history_id": "66f8380583c086e1",
35 "id": "dfd75d2f0da631b2", 35 "id": "7f406d9538852eeb",
36 "inputs": { 36 "inputs": {
37 "assembly_csv": { 37 "assembly_csv": {
38 "id": "7a37f3397bf88665", 38 "id": "41ca6db0600d7999",
39 "src": "hda", 39 "src": "hda",
40 "uuid": "61aa4b8a-d71a-4e9d-a878-5f0d1494b36d" 40 "uuid": "1a1ee32d-eed7-47fd-b491-4f0799b44a85"
41 }, 41 },
42 "genbank_files1": { 42 "genbank_files1": {
43 "id": "b5f519d254c4f536", 43 "id": "66f8380583c086e1",
44 "src": "hda", 44 "src": "hda",
45 "uuid": "fce5b5a1-92e2-4c39-90d5-0eddf56635f0" 45 "uuid": "44129191-5531-4cc9-b37b-fec4e3c677d5"
46 }, 46 },
47 "genbank_files10": { 47 "genbank_files10": {
48 "id": "2bdc7fcb2931f07b", 48 "id": "d3a48cfe9e5a1f02",
49 "src": "hda", 49 "src": "hda",
50 "uuid": "387ad7a6-1931-4a46-99d5-4513ba93a999" 50 "uuid": "c7cf96af-ab1c-4199-821f-5bb5b947752f"
51 }, 51 },
52 "genbank_files11": { 52 "genbank_files11": {
53 "id": "dc7e3ab6a421767b", 53 "id": "4fffd7776804f395",
54 "src": "hda", 54 "src": "hda",
55 "uuid": "6829a587-673a-44a6-8bcf-ec6334a9184f" 55 "uuid": "0a5139e7-7d83-48f1-a1c9-458a1e72685c"
56 }, 56 },
57 "genbank_files12": { 57 "genbank_files12": {
58 "id": "b1d9a1d43e36b679", 58 "id": "193b12b5837c3789",
59 "src": "hda", 59 "src": "hda",
60 "uuid": "40405cee-d70a-45d6-ac91-05616fe798b9" 60 "uuid": "fb361f22-020c-4972-8661-f1f57d1a7afa"
61 }, 61 },
62 "genbank_files2": { 62 "genbank_files2": {
63 "id": "c5accd210dc5c9dd", 63 "id": "afa012b5b55ac394",
64 "src": "hda", 64 "src": "hda",
65 "uuid": "a6400a83-e4fd-488b-94e8-5ec1f44db9ca" 65 "uuid": "61f5f19f-147b-46fd-8900-a8530f311835"
66 }, 66 },
67 "genbank_files3": { 67 "genbank_files3": {
68 "id": "10fbf206fb2087c4", 68 "id": "c1bc3f2cd94aab77",
69 "src": "hda", 69 "src": "hda",
70 "uuid": "a66c7ac9-f828-405d-9a49-842e978b00af" 70 "uuid": "440b34e7-490e-49bd-9b29-6afcabe5f6f6"
71 }, 71 },
72 "genbank_files4": { 72 "genbank_files4": {
73 "id": "27fa0815bff520f2", 73 "id": "f1661b71781d8acc",
74 "src": "hda", 74 "src": "hda",
75 "uuid": "54b878ab-05e6-4212-b399-ab1f62c59e16" 75 "uuid": "a3fca212-b8dc-4579-901c-612b806241af"
76 }, 76 },
77 "genbank_files5": { 77 "genbank_files5": {
78 "id": "f825d543d1b9cf39", 78 "id": "e1129f30c30438be",
79 "src": "hda", 79 "src": "hda",
80 "uuid": "39021efe-6a4f-4b7f-ba0d-f87c2b436a0f" 80 "uuid": "5398f2cb-1a25-45e5-9ba0-cd79a88b6e88"
81 }, 81 },
82 "genbank_files6": { 82 "genbank_files6": {
83 "id": "24f234959abeadac", 83 "id": "abbaf1e2c3c282ad",
84 "src": "hda", 84 "src": "hda",
85 "uuid": "be26c9ab-28e8-449a-bd01-2047af0dfa5d" 85 "uuid": "f505293a-8223-4da2-a22c-aa261d4955ec"
86 }, 86 },
87 "genbank_files7": { 87 "genbank_files7": {
88 "id": "67e443cb5516c0e0", 88 "id": "18bb6cd07b986e37",
89 "src": "hda", 89 "src": "hda",
90 "uuid": "f7fd1975-81bc-4a4f-89c6-d946d59782ee" 90 "uuid": "c50e4b1f-c72a-4272-b324-e1c2c7d50293"
91 }, 91 },
92 "genbank_files8": { 92 "genbank_files8": {
93 "id": "5180b1a726879d60", 93 "id": "82689942017f4326",
94 "src": "hda", 94 "src": "hda",
95 "uuid": "fb1f0888-2487-4f14-bcdd-fa06923d4cd9" 95 "uuid": "00d79560-f944-4d8e-98e7-f516684a6100"
96 }, 96 },
97 "genbank_files9": { 97 "genbank_files9": {
98 "id": "c3b441e1ed1e9870", 98 "id": "ecc2b8a59c690090",
99 "src": "hda", 99 "src": "hda",
100 "uuid": "250500a7-25ca-4cba-8d71-7d16053afcaa" 100 "uuid": "3d5bb0fb-d610-4939-8fc5-999174fee5ca"
101 } 101 }
102 }, 102 },
103 "job_messages": [], 103 "job_messages": [
104 {
105 "code_desc": "",
106 "desc": "Fatal error: Exit code 1 ()",
107 "error_level": 3,
108 "exit_code": 1,
109 "type": "exit_code"
110 }
111 ],
104 "job_metrics": [], 112 "job_metrics": [],
105 "job_runner_name": null, 113 "job_runner_name": null,
106 "job_stderr": "", 114 "job_stderr": "",
107 "job_stdout": "", 115 "job_stdout": "",
108 "model_class": "Job", 116 "model_class": "Job",
109 "output_collections": { 117 "output_collections": {
110 "construct_gb": { 118 "construct_gb": {
111 "id": "c5accd210dc5c9dd", 119 "id": "afa012b5b55ac394",
112 "src": "hdca" 120 "src": "hdca"
113 } 121 }
114 }, 122 },
115 "outputs": { 123 "outputs": {
116 "__new_primary_file_construct_gb|construct_1__": {
117 "id": "cecf675ce2a554e8",
118 "src": "hda",
119 "uuid": "3f70ca65-7fb8-4f83-b6e7-3f9893b1db5e"
120 },
121 "__new_primary_file_construct_gb|construct_2__": {
122 "id": "9cc1fc667f1eccc7",
123 "src": "hda",
124 "uuid": "723df0ab-a674-4b94-b805-15e38f56cbd5"
125 },
126 "__new_primary_file_construct_gb|construct_3__": {
127 "id": "0b28ef6dfa05b9a4",
128 "src": "hda",
129 "uuid": "0225d884-89af-4b29-bf0c-d27e776614a3"
130 },
131 "__new_primary_file_construct_gb|construct_4__": {
132 "id": "dd0a4ddfadd2b33c",
133 "src": "hda",
134 "uuid": "2495d80c-1c1d-4aa7-af8c-eac0dd199af2"
135 },
136 "output_zip": { 124 "output_zip": {
137 "id": "dfd75d2f0da631b2", 125 "id": "7f406d9538852eeb",
138 "src": "hda", 126 "src": "hda",
139 "uuid": "a840b0de-7374-4fc2-bc9c-eec0f6615e2f" 127 "uuid": "acb064d7-2781-46fe-98df-716fee024c8d"
140 } 128 }
141 }, 129 },
142 "params": { 130 "params": {
143 "__input_ext": "\"input\"", 131 "__input_ext": "\"input\"",
144 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 132 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
145 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", 133 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
146 "chromInfo": "\"/tmp/tmphxxoceah/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 134 "chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
147 "dbkey": "\"?\"", 135 "dbkey": "\"?\"",
148 "domesticated_input": null, 136 "domesticated_input": null,
149 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", 137 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
150 "topology": "\"circular\"" 138 "topology": "\"circular\""
151 }, 139 },
152 "state": "ok", 140 "state": "error",
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", 141 "stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 171, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 97, in cloning_simulation\n simulation = assembly_plan.simulate(sequence_repository=repository)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/AssemblyPlan/AssemblyPlan.py\", line 251, in simulate\n simulation_result = assembly.simulate(sequence_repository)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/Assembly/builtin_assembly_classes/Type2sRestrictionAssembly.py\", line 181, in simulate\n records = sequence_repository.get_records(self.parts)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 120, in get_records\n raise NotInRepositoryError(not_in_repository, repository=self)\ndnacauldron.SequenceRepository.NotInRepositoryError: Parts not found in repo: part1, part2, part3, part4, part5, part6\n\r \r",
154 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", 142 "stdout": " 1 2 3 4 5 6\n0 \nID part1 part2 part3 part4 part5 part6\nconstruct_3 construct_1 part_L part_J part_K NaN NaN\nconstruct_4 construct_2 part_L part_J part_K NaN NaN\nconstruct_1 part_A part_B part_C part_D part_E part_F\nconstruct_2 part_A part_G part_H part_I part_F NaN\nSimulating assembly plan assambly...\n",
155 "tool_id": "cloning_simulation", 143 "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, 2.42it/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", 144 "tool_stderr": "\rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 171, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 97, in cloning_simulation\n simulation = assembly_plan.simulate(sequence_repository=repository)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/AssemblyPlan/AssemblyPlan.py\", line 251, in simulate\n simulation_result = assembly.simulate(sequence_repository)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/Assembly/builtin_assembly_classes/Type2sRestrictionAssembly.py\", line 181, in simulate\n records = sequence_repository.get_records(self.parts)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 120, in get_records\n raise NotInRepositoryError(not_in_repository, repository=self)\ndnacauldron.SequenceRepository.NotInRepositoryError: Parts not found in repo: part1, part2, part3, part4, part5, part6\n\r \r",
157 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", 145 "tool_stdout": " 1 2 3 4 5 6\n0 \nID part1 part2 part3 part4 part5 part6\nconstruct_3 construct_1 part_L part_J part_K NaN NaN\nconstruct_4 construct_2 part_L part_J part_K NaN NaN\nconstruct_1 part_A part_B part_C part_D part_E part_F\nconstruct_2 part_A part_G part_H part_I part_F NaN\nSimulating assembly plan assambly...\n",
158 "update_time": "2025-05-26T09:45:09.253153", 146 "update_time": "2025-05-26T10:00:52.817543",
159 "user_email": "planemo@galaxyproject.org", 147 "user_email": "planemo@galaxyproject.org",
160 "user_id": "b5f519d254c4f536" 148 "user_id": "66f8380583c086e1"
161 }, 149 },
162 "status": "success", 150 "output_problems": [
151 "Job in error state.. tool_id: cloning_simulation, exit_code: 1, stderr: \rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 171, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 97, in cloning_simulation\n simulation = assembly_plan.simulate(sequence_repository=repository)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/AssemblyPlan/AssemblyPlan.py\", line 251, in simulate\n simulation_result = assembly.simulate(sequence_repository)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/Assembly/builtin_assembly_classes/Type2sRestrictionAssembly.py\", line 181, in simulate\n records = sequence_repository.get_records(self.parts)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 120, in get_records\n raise NotInRepositoryError(not_in_repository, repository=self)\ndnacauldron.SequenceRepository.NotInRepositoryError: Parts not found in repo: part1, part2, part3, part4, part5, part6\n\r \r.",
152 "Job in error state.. tool_id: cloning_simulation, exit_code: 1, stderr: \rassembly: 0%| | 0/5 [00:00<?, ?it/s, now=None]Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 171, in <module>\n cloning_simulation(\n ~~~~~~~~~~~~~~~~~~^\n args.parts_files, args.domesticated_seq,\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n ...<3 lines>...\n args.output_simulation, args.enzyme, args.outdir_gb\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 97, in cloning_simulation\n simulation = assembly_plan.simulate(sequence_repository=repository)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/AssemblyPlan/AssemblyPlan.py\", line 251, in simulate\n simulation_result = assembly.simulate(sequence_repository)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/Assembly/builtin_assembly_classes/Type2sRestrictionAssembly.py\", line 181, in simulate\n records = sequence_repository.get_records(self.parts)\n File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 120, in get_records\n raise NotInRepositoryError(not_in_repository, repository=self)\ndnacauldron.SequenceRepository.NotInRepositoryError: Parts not found in repo: part1, part2, part3, part4, part5, part6\n\r \r.",
153 "Output collection 'construct_gb': expected to have 4 elements, but it had 0."
154 ],
155 "status": "failure",
163 "test_index": 0, 156 "test_index": 0,
164 "time_seconds": 53.940672636032104, 157 "time_seconds": 51.33188271522522,
165 "tool_id": "cloning_simulation", 158 "tool_id": "cloning_simulation",
166 "tool_version": "0.1.0+galaxy0" 159 "tool_version": "0.1.0+galaxy0"
167 }, 160 },
168 "has_data": true, 161 "has_data": true,
169 "id": "cloning_simulation-0" 162 "id": "cloning_simulation-0"
171 { 164 {
172 "data": { 165 "data": {
173 "inputs": { 166 "inputs": {
174 "adv|use_file_names_as_ids": true, 167 "adv|use_file_names_as_ids": true,
175 "assembly_csv": { 168 "assembly_csv": {
176 "id": "191f29e52861c771", 169 "id": "3abc48ca4f3e8d37",
177 "src": "hda" 170 "src": "hda"
178 }, 171 },
179 "assembly_plan_name": "GibsonAssembly", 172 "assembly_plan_name": "GibsonAssembly",
180 "genbank_files": { 173 "genbank_files": {
181 "id": "10fbf206fb2087c4", 174 "id": "c1bc3f2cd94aab77",
182 "src": "hdca" 175 "src": "hdca"
183 }, 176 },
184 "topology": "circular" 177 "topology": "circular"
185 }, 178 },
186 "job": { 179 "job": {
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'", 180 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpy2ysv6tn/files/6/e/b/dataset_6eb20de3-662c-4428-907f-29cbe0a5cc20.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpy2ysv6tn/files/b/6/f/dataset_b6fe141d-f27d-475d-95fd-501e032f0c3b.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpy2ysv6tn/files/b/6/f/dataset_b6fe141d-f27d-475d-95fd-501e032f0c3b.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/tmpy2ysv6tn/job_working_directory/000/17/outputs/dataset_41d853b4-adb6-4605-bbaf-d7178b962d92.dat'",
188 "command_version": "", 181 "command_version": "",
189 "copied_from_job_id": null, 182 "copied_from_job_id": null,
190 "create_time": "2025-05-26T09:45:19.833949", 183 "create_time": "2025-05-26T10:01:03.681089",
191 "dependencies": [ 184 "dependencies": [
192 { 185 {
193 "cacheable": false, 186 "cacheable": false,
194 "dependency_resolver": { 187 "dependency_resolver": {
195 "auto_init": true, 188 "auto_init": true,
365 "name": "dna_features_viewer", 358 "name": "dna_features_viewer",
366 "version": "3.1.5" 359 "version": "3.1.5"
367 } 360 }
368 ], 361 ],
369 "exit_code": 0, 362 "exit_code": 0,
370 "external_id": "102481", 363 "external_id": "114833",
371 "galaxy_version": "24.2", 364 "galaxy_version": "24.2",
372 "handler": null, 365 "handler": null,
373 "history_id": "c5accd210dc5c9dd", 366 "history_id": "afa012b5b55ac394",
374 "id": "0b28ef6dfa05b9a4", 367 "id": "991084752433b654",
375 "inputs": { 368 "inputs": {
376 "assembly_csv": { 369 "assembly_csv": {
377 "id": "191f29e52861c771", 370 "id": "3abc48ca4f3e8d37",
378 "src": "hda", 371 "src": "hda",
379 "uuid": "ae19b93d-96dc-4575-922e-1c1b13cdda00" 372 "uuid": "6eb20de3-662c-4428-907f-29cbe0a5cc20"
380 }, 373 },
381 "genbank_files1": { 374 "genbank_files1": {
382 "id": "1bd551c439d3389f", 375 "id": "9677ca5db33658a1",
383 "src": "hda", 376 "src": "hda",
384 "uuid": "66becc5b-d90e-4bca-8456-82d9f7c209ea" 377 "uuid": "b6fe141d-f27d-475d-95fd-501e032f0c3b"
385 } 378 }
386 }, 379 },
387 "job_messages": [], 380 "job_messages": [],
388 "job_metrics": [], 381 "job_metrics": [],
389 "job_runner_name": null, 382 "job_runner_name": null,
390 "job_stderr": "", 383 "job_stderr": "",
391 "job_stdout": "", 384 "job_stdout": "",
392 "model_class": "Job", 385 "model_class": "Job",
393 "output_collections": { 386 "output_collections": {
394 "construct_gb": { 387 "construct_gb": {
395 "id": "27fa0815bff520f2", 388 "id": "f1661b71781d8acc",
396 "src": "hdca" 389 "src": "hdca"
397 } 390 }
398 }, 391 },
399 "outputs": { 392 "outputs": {
400 "__new_primary_file_construct_gb|construct_1__": { 393 "__new_primary_file_construct_gb|construct_1__": {
401 "id": "a74d82facdf691d6", 394 "id": "400090ecd3303f56",
402 "src": "hda", 395 "src": "hda",
403 "uuid": "d06a3b4e-424a-4af4-b067-8426c2170c90" 396 "uuid": "e24f4e4b-a2c0-4ebc-ac8a-e80cb0ce1266"
404 }, 397 },
405 "__new_primary_file_construct_gb|construct_2__": { 398 "__new_primary_file_construct_gb|construct_2__": {
406 "id": "7d2e9c5805bbd6ea", 399 "id": "974cc872eaa7d6a0",
407 "src": "hda", 400 "src": "hda",
408 "uuid": "1f95f8b0-5fc6-4b06-9550-06dd8233e6bd" 401 "uuid": "baec54da-c9df-4fb2-a156-7aaaabc3ee2d"
409 }, 402 },
410 "__new_primary_file_construct_gb|construct_3__": { 403 "__new_primary_file_construct_gb|construct_3__": {
411 "id": "6c4aee794b3972b4", 404 "id": "8586d482e8f05e33",
412 "src": "hda", 405 "src": "hda",
413 "uuid": "cfd50000-e85e-4b17-985e-f137dc59b08b" 406 "uuid": "8649dd5f-afe7-44fa-b07c-aba6fdb3c6fc"
414 }, 407 },
415 "output_zip": { 408 "output_zip": {
416 "id": "e670fc59d69da207", 409 "id": "991084752433b654",
417 "src": "hda", 410 "src": "hda",
418 "uuid": "cf3ea990-c609-45fe-a823-8786fed863f9" 411 "uuid": "41d853b4-adb6-4605-bbaf-d7178b962d92"
419 } 412 }
420 }, 413 },
421 "params": { 414 "params": {
422 "__input_ext": "\"input\"", 415 "__input_ext": "\"input\"",
423 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 416 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
424 "assembly_plan_name": "\"GibsonAssembly\"", 417 "assembly_plan_name": "\"GibsonAssembly\"",
425 "chromInfo": "\"/tmp/tmphxxoceah/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 418 "chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
426 "dbkey": "\"?\"", 419 "dbkey": "\"?\"",
427 "domesticated_input": null, 420 "domesticated_input": null,
428 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", 421 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
429 "topology": "\"circular\"" 422 "topology": "\"circular\""
430 }, 423 },
431 "state": "ok", 424 "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, 4.35it/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", 425 "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, 4.32it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.24it/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, 3.63it/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", 426 "stdout": " 1 2 3 4 5\n0 \nconstruct parts NaN NaN NaN NaN\nconstruct_1 Frag_1 Frag_2 Frag_3 Frag_4 Frag_5\nconstruct_2 Frag_1 Frag_2 Frag_3 Frag_4b Frag_5\nconstruct_3 Frag_1 Frag_2 Frag_3 Frag_4c Frag_5b\nconstruct_4 Frag_1 Frag_2 Frag_3 Frag_4 NaN\nconstruct_5 Frag_1 Frag_2 Frag_3 Frag_4 Frag_4b\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
434 "tool_id": "cloning_simulation", 427 "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, 4.35it/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", 428 "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, 4.32it/s, now=None]\rassembly: 60%|\u2588\u2588\u2588\u2588\u2588\u2588 | 3/5 [00:00<00:00, 4.24it/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, 3.63it/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", 429 "tool_stdout": " 1 2 3 4 5\n0 \nconstruct parts NaN NaN NaN NaN\nconstruct_1 Frag_1 Frag_2 Frag_3 Frag_4 Frag_5\nconstruct_2 Frag_1 Frag_2 Frag_3 Frag_4b Frag_5\nconstruct_3 Frag_1 Frag_2 Frag_3 Frag_4c Frag_5b\nconstruct_4 Frag_1 Frag_2 Frag_3 Frag_4 NaN\nconstruct_5 Frag_1 Frag_2 Frag_3 Frag_4 Frag_4b\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
437 "update_time": "2025-05-26T09:45:31.869394", 430 "update_time": "2025-05-26T10:01:15.563285",
438 "user_email": "planemo@galaxyproject.org", 431 "user_email": "planemo@galaxyproject.org",
439 "user_id": "b5f519d254c4f536" 432 "user_id": "66f8380583c086e1"
440 }, 433 },
441 "status": "success", 434 "status": "success",
442 "test_index": 1, 435 "test_index": 1,
443 "time_seconds": 22.247495412826538, 436 "time_seconds": 22.980356216430664,
444 "tool_id": "cloning_simulation", 437 "tool_id": "cloning_simulation",
445 "tool_version": "0.1.0+galaxy0" 438 "tool_version": "0.1.0+galaxy0"
446 }, 439 },
447 "has_data": true, 440 "has_data": true,
448 "id": "cloning_simulation-1" 441 "id": "cloning_simulation-1"
450 { 443 {
451 "data": { 444 "data": {
452 "inputs": { 445 "inputs": {
453 "adv|use_file_names_as_ids": true, 446 "adv|use_file_names_as_ids": true,
454 "assembly_csv": { 447 "assembly_csv": {
455 "id": "83c94260ae237f16", 448 "id": "94fb43fdf96ceebf",
456 "src": "hda" 449 "src": "hda"
457 }, 450 },
458 "assembly_plan_name": "LigaseCyclingReactionAssembly", 451 "assembly_plan_name": "LigaseCyclingReactionAssembly",
459 "genbank_files": { 452 "genbank_files": {
460 "id": "f825d543d1b9cf39", 453 "id": "e1129f30c30438be",
461 "src": "hdca" 454 "src": "hdca"
462 }, 455 },
463 "topology": "circular" 456 "topology": "circular"
464 }, 457 },
465 "job": { 458 "job": {
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'", 459 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpy2ysv6tn/files/4/6/9/dataset_469df048-1608-4e28-a8c3-576433c72c7f.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpy2ysv6tn/files/1/8/9/dataset_18952cef-c715-4776-9f53-69156da89d01.dat,/tmp/tmpy2ysv6tn/files/8/1/3/dataset_81322056-69eb-4dcd-88ee-6cb78ff617db.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpy2ysv6tn/files/1/8/9/dataset_18952cef-c715-4776-9f53-69156da89d01.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpy2ysv6tn/files/8/1/3/dataset_81322056-69eb-4dcd-88ee-6cb78ff617db.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/tmpy2ysv6tn/job_working_directory/000/21/outputs/dataset_d2df6190-9462-41aa-92d2-d4a5c1a605d3.dat'",
467 "command_version": "", 460 "command_version": "",
468 "copied_from_job_id": null, 461 "copied_from_job_id": null,
469 "create_time": "2025-05-26T09:45:42.951843", 462 "create_time": "2025-05-26T10:01:27.721793",
470 "dependencies": [ 463 "dependencies": [
471 { 464 {
472 "cacheable": false, 465 "cacheable": false,
473 "dependency_resolver": { 466 "dependency_resolver": {
474 "auto_init": true, 467 "auto_init": true,
644 "name": "dna_features_viewer", 637 "name": "dna_features_viewer",
645 "version": "3.1.5" 638 "version": "3.1.5"
646 } 639 }
647 ], 640 ],
648 "exit_code": 0, 641 "exit_code": 0,
649 "external_id": "102861", 642 "external_id": "115234",
650 "galaxy_version": "24.2", 643 "galaxy_version": "24.2",
651 "handler": null, 644 "handler": null,
652 "history_id": "10fbf206fb2087c4", 645 "history_id": "c1bc3f2cd94aab77",
653 "id": "e670fc59d69da207", 646 "id": "de23ac49d5c4a7c8",
654 "inputs": { 647 "inputs": {
655 "assembly_csv": { 648 "assembly_csv": {
656 "id": "83c94260ae237f16", 649 "id": "94fb43fdf96ceebf",
657 "src": "hda", 650 "src": "hda",
658 "uuid": "82c2d90b-0ca3-4633-915b-eaa0ab81b80f" 651 "uuid": "469df048-1608-4e28-a8c3-576433c72c7f"
659 }, 652 },
660 "genbank_files1": { 653 "genbank_files1": {
661 "id": "57b57ab024b6e67d", 654 "id": "de23ac49d5c4a7c8",
662 "src": "hda", 655 "src": "hda",
663 "uuid": "cbf24487-bf9d-469a-99cd-bccebb2bc139" 656 "uuid": "18952cef-c715-4776-9f53-69156da89d01"
664 }, 657 },
665 "genbank_files2": { 658 "genbank_files2": {
666 "id": "71d78516c0fe784e", 659 "id": "de6580a03a572321",
667 "src": "hda", 660 "src": "hda",
668 "uuid": "d3d42e4b-1982-4660-8ad4-f12c8a0599cb" 661 "uuid": "81322056-69eb-4dcd-88ee-6cb78ff617db"
669 } 662 }
670 }, 663 },
671 "job_messages": [], 664 "job_messages": [],
672 "job_metrics": [], 665 "job_metrics": [],
673 "job_runner_name": null, 666 "job_runner_name": null,
674 "job_stderr": "", 667 "job_stderr": "",
675 "job_stdout": "", 668 "job_stdout": "",
676 "model_class": "Job", 669 "model_class": "Job",
677 "output_collections": { 670 "output_collections": {
678 "construct_gb": { 671 "construct_gb": {
679 "id": "24f234959abeadac", 672 "id": "abbaf1e2c3c282ad",
680 "src": "hdca" 673 "src": "hdca"
681 } 674 }
682 }, 675 },
683 "outputs": { 676 "outputs": {
684 "output_zip": { 677 "output_zip": {
685 "id": "1211f83788e0a9a2", 678 "id": "fdc5ed0a88852c9a",
686 "src": "hda", 679 "src": "hda",
687 "uuid": "233ed98e-ee9b-468f-8145-9a8c44e8034f" 680 "uuid": "d2df6190-9462-41aa-92d2-d4a5c1a605d3"
688 } 681 }
689 }, 682 },
690 "params": { 683 "params": {
691 "__input_ext": "\"input\"", 684 "__input_ext": "\"input\"",
692 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 685 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
693 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"", 686 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"",
694 "chromInfo": "\"/tmp/tmphxxoceah/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 687 "chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
695 "dbkey": "\"?\"", 688 "dbkey": "\"?\"",
696 "domesticated_input": null, 689 "domesticated_input": null,
697 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}", 690 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}",
698 "topology": "\"circular\"" 691 "topology": "\"circular\""
699 }, 692 },
700 "state": "ok", 693 "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, 2.38it/s, now=None]\r \r", 694 "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, 2.27it/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", 695 "stdout": " 1 ... 14\n0 ... \nConstruct1 RFP_GFP_BO_10232 ... p7_backbone\nConstruct2_flawed RFP_GFP_BO_10232 ... NaN\n\n[2 rows x 14 columns]\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
703 "tool_id": "cloning_simulation", 696 "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, 2.38it/s, now=None]\r \r", 697 "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, 2.27it/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", 698 "tool_stdout": " 1 ... 14\n0 ... \nConstruct1 RFP_GFP_BO_10232 ... p7_backbone\nConstruct2_flawed RFP_GFP_BO_10232 ... NaN\n\n[2 rows x 14 columns]\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
706 "update_time": "2025-05-26T09:45:54.473182", 699 "update_time": "2025-05-26T10:01:40.416074",
707 "user_email": "planemo@galaxyproject.org", 700 "user_email": "planemo@galaxyproject.org",
708 "user_id": "b5f519d254c4f536" 701 "user_id": "66f8380583c086e1"
709 }, 702 },
710 "status": "success", 703 "status": "success",
711 "test_index": 2, 704 "test_index": 2,
712 "time_seconds": 22.476279258728027, 705 "time_seconds": 24.68060541152954,
713 "tool_id": "cloning_simulation", 706 "tool_id": "cloning_simulation",
714 "tool_version": "0.1.0+galaxy0" 707 "tool_version": "0.1.0+galaxy0"
715 }, 708 },
716 "has_data": true, 709 "has_data": true,
717 "id": "cloning_simulation-2" 710 "id": "cloning_simulation-2"
719 { 712 {
720 "data": { 713 "data": {
721 "inputs": { 714 "inputs": {
722 "adv|use_file_names_as_ids": true, 715 "adv|use_file_names_as_ids": true,
723 "assembly_csv": { 716 "assembly_csv": {
724 "id": "2aab5679a1ae5c57", 717 "id": "b07ae8db70ca0b69",
725 "src": "hda" 718 "src": "hda"
726 }, 719 },
727 "assembly_plan_name": "BASICAssembly", 720 "assembly_plan_name": "BASICAssembly",
728 "genbank_files": { 721 "genbank_files": {
729 "id": "67e443cb5516c0e0", 722 "id": "18bb6cd07b986e37",
730 "src": "hdca" 723 "src": "hdca"
731 }, 724 },
732 "topology": "circular" 725 "topology": "circular"
733 }, 726 },
734 "job": { 727 "job": {
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'", 728 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpy2ysv6tn/files/1/1/b/dataset_11b19080-d21f-4a3e-a516-77bb7f1eb8ff.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpy2ysv6tn/files/c/1/3/dataset_c13c3bb5-74f3-49b4-979e-08064cbcd96e.dat,/tmp/tmpy2ysv6tn/files/2/2/0/dataset_220d8ce3-65a2-4880-9924-e41f685e1386.dat,/tmp/tmpy2ysv6tn/files/2/6/4/dataset_264d7e95-807d-45aa-ada7-244e7896dd95.dat,/tmp/tmpy2ysv6tn/files/7/e/e/dataset_7eede81c-a796-4189-94df-82245763e19f.dat,/tmp/tmpy2ysv6tn/files/c/9/5/dataset_c9537938-db0d-4d07-9eee-2cfeec50a90d.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpy2ysv6tn/files/c/1/3/dataset_c13c3bb5-74f3-49b4-979e-08064cbcd96e.dat:GFP.gb,/tmp/tmpy2ysv6tn/files/2/2/0/dataset_220d8ce3-65a2-4880-9924-e41f685e1386.dat:p15A_kan.gb,/tmp/tmpy2ysv6tn/files/2/6/4/dataset_264d7e95-807d-45aa-ada7-244e7896dd95.dat:promoter.gb,/tmp/tmpy2ysv6tn/files/7/e/e/dataset_7eede81c-a796-4189-94df-82245763e19f.dat:RFP.gb,/tmp/tmpy2ysv6tn/files/c/9/5/dataset_c9537938-db0d-4d07-9eee-2cfeec50a90d.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/tmpy2ysv6tn/job_working_directory/000/28/outputs/dataset_b055edc9-ea72-46ca-8971-352c46db387e.dat'",
736 "command_version": "", 729 "command_version": "",
737 "copied_from_job_id": null, 730 "copied_from_job_id": null,
738 "create_time": "2025-05-26T09:46:15.589461", 731 "create_time": "2025-05-26T10:02:02.222212",
739 "dependencies": [ 732 "dependencies": [
740 { 733 {
741 "cacheable": false, 734 "cacheable": false,
742 "dependency_resolver": { 735 "dependency_resolver": {
743 "auto_init": true, 736 "auto_init": true,
913 "name": "dna_features_viewer", 906 "name": "dna_features_viewer",
914 "version": "3.1.5" 907 "version": "3.1.5"
915 } 908 }
916 ], 909 ],
917 "exit_code": 0, 910 "exit_code": 0,
918 "external_id": "103494", 911 "external_id": "115859",
919 "galaxy_version": "24.2", 912 "galaxy_version": "24.2",
920 "handler": null, 913 "handler": null,
921 "history_id": "27fa0815bff520f2", 914 "history_id": "f1661b71781d8acc",
922 "id": "1211f83788e0a9a2", 915 "id": "80951ee9dc2649e8",
923 "inputs": { 916 "inputs": {
924 "assembly_csv": { 917 "assembly_csv": {
925 "id": "2aab5679a1ae5c57", 918 "id": "b07ae8db70ca0b69",
926 "src": "hda", 919 "src": "hda",
927 "uuid": "2c3186df-93d9-4d24-8956-c6a17e7d822a" 920 "uuid": "11b19080-d21f-4a3e-a516-77bb7f1eb8ff"
928 }, 921 },
929 "genbank_files1": { 922 "genbank_files1": {
930 "id": "0164abbd74b9b05d", 923 "id": "cd28fb0d133db699",
931 "src": "hda", 924 "src": "hda",
932 "uuid": "1d824d9e-0b4f-4a81-af49-1acb506e8f4b" 925 "uuid": "c13c3bb5-74f3-49b4-979e-08064cbcd96e"
933 }, 926 },
934 "genbank_files2": { 927 "genbank_files2": {
935 "id": "f5f5feeed891820d", 928 "id": "204f425176d83e80",
936 "src": "hda", 929 "src": "hda",
937 "uuid": "57d780ae-3783-4cdf-a295-642ebc88a60e" 930 "uuid": "220d8ce3-65a2-4880-9924-e41f685e1386"
938 }, 931 },
939 "genbank_files3": { 932 "genbank_files3": {
940 "id": "b3161e3b65353042", 933 "id": "a412e91f962611fc",
941 "src": "hda", 934 "src": "hda",
942 "uuid": "b89b536e-e310-470d-bddc-cd2847c2cfff" 935 "uuid": "264d7e95-807d-45aa-ada7-244e7896dd95"
943 }, 936 },
944 "genbank_files4": { 937 "genbank_files4": {
945 "id": "292aa45e4e016cce", 938 "id": "80951ee9dc2649e8",
946 "src": "hda", 939 "src": "hda",
947 "uuid": "bbdc2ed9-f2fa-4e92-b9ac-2140a8f80ea8" 940 "uuid": "7eede81c-a796-4189-94df-82245763e19f"
948 }, 941 },
949 "genbank_files5": { 942 "genbank_files5": {
950 "id": "9318ef3621fbfa11", 943 "id": "02cc6fb051fdc602",
951 "src": "hda", 944 "src": "hda",
952 "uuid": "06587a95-951c-4c6f-bded-3df9fd38a5d1" 945 "uuid": "c9537938-db0d-4d07-9eee-2cfeec50a90d"
953 } 946 }
954 }, 947 },
955 "job_messages": [], 948 "job_messages": [],
956 "job_metrics": [], 949 "job_metrics": [],
957 "job_runner_name": null, 950 "job_runner_name": null,
958 "job_stderr": "", 951 "job_stderr": "",
959 "job_stdout": "", 952 "job_stdout": "",
960 "model_class": "Job", 953 "model_class": "Job",
961 "output_collections": { 954 "output_collections": {
962 "construct_gb": { 955 "construct_gb": {
963 "id": "5180b1a726879d60", 956 "id": "82689942017f4326",
964 "src": "hdca" 957 "src": "hdca"
965 } 958 }
966 }, 959 },
967 "outputs": { 960 "outputs": {
968 "output_zip": { 961 "output_zip": {
969 "id": "4b5a70f26b4819b4", 962 "id": "68883cc453ec32a5",
970 "src": "hda", 963 "src": "hda",
971 "uuid": "003ab152-a58f-45ab-a3c5-38a87199b77d" 964 "uuid": "b055edc9-ea72-46ca-8971-352c46db387e"
972 } 965 }
973 }, 966 },
974 "params": { 967 "params": {
975 "__input_ext": "\"input\"", 968 "__input_ext": "\"input\"",
976 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 969 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
977 "assembly_plan_name": "\"BASICAssembly\"", 970 "assembly_plan_name": "\"BASICAssembly\"",
978 "chromInfo": "\"/tmp/tmphxxoceah/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 971 "chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
979 "dbkey": "\"?\"", 972 "dbkey": "\"?\"",
980 "domesticated_input": null, 973 "domesticated_input": null,
981 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}", 974 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}",
982 "topology": "\"circular\"" 975 "topology": "\"circular\""
983 }, 976 },
984 "state": "ok", 977 "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, 49.32it/s, now=None]\r \r", 978 "stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 47.54it/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", 979 "stdout": " 1 2 3 ... 10 11 12\n0 ... \nL2RBS-1P L2RBS-1P_fwd L2RBS-1P_adapter NaN ... NaN NaN NaN\nLMA-S LMA-S_fwd LMA-S_adapter NaN ... NaN NaN NaN\nL1RBS-xS L1RBS-xS_fwd L1RBS-xS_adapter NaN ... NaN NaN NaN\nL1RBS-1P L1RBS-1P_fwd L1RBS-1P_adapter NaN ... NaN NaN NaN\nL2RBS-xS L2RBS-xS_fwd L2RBS-xS_adapter NaN ... NaN NaN NaN\nLMA-P LMA-P_fwd LMA-P_adapter NaN ... NaN NaN NaN\nLMB-S LMB-S_fwd LMB-S_adapter NaN ... NaN NaN NaN\nLMB-P LMB-P_fwd LMB-P_adapter NaN ... NaN NaN NaN\nasm_GFP_RFP LMA-P promoter L1RBS-xS ... LMB-P p15A_kan LMA-S\nasm_RFP_GFP LMA-P promoter L1RBS-xS ... LMB-P p15A_kan LMA-S\n\n[10 rows x 12 columns]\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
987 "tool_id": "cloning_simulation", 980 "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, 49.32it/s, now=None]\r \r", 981 "tool_stderr": "\rassembly: 0%| | 0/10 [00:00<?, ?it/s, now=None]\r \r\rassembly: 0%| | 0/8 [00:00<?, ?it/s, now=None]\rassembly: 62%|\u2588\u2588\u2588\u2588\u2588\u2588\u258e | 5/8 [00:00<00:00, 47.54it/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", 982 "tool_stdout": " 1 2 3 ... 10 11 12\n0 ... \nL2RBS-1P L2RBS-1P_fwd L2RBS-1P_adapter NaN ... NaN NaN NaN\nLMA-S LMA-S_fwd LMA-S_adapter NaN ... NaN NaN NaN\nL1RBS-xS L1RBS-xS_fwd L1RBS-xS_adapter NaN ... NaN NaN NaN\nL1RBS-1P L1RBS-1P_fwd L1RBS-1P_adapter NaN ... NaN NaN NaN\nL2RBS-xS L2RBS-xS_fwd L2RBS-xS_adapter NaN ... NaN NaN NaN\nLMA-P LMA-P_fwd LMA-P_adapter NaN ... NaN NaN NaN\nLMB-S LMB-S_fwd LMB-S_adapter NaN ... NaN NaN NaN\nLMB-P LMB-P_fwd LMB-P_adapter NaN ... NaN NaN NaN\nasm_GFP_RFP LMA-P promoter L1RBS-xS ... LMB-P p15A_kan LMA-S\nasm_RFP_GFP LMA-P promoter L1RBS-xS ... LMB-P p15A_kan LMA-S\n\n[10 rows x 12 columns]\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
990 "update_time": "2025-05-26T09:46:26.255886", 983 "update_time": "2025-05-26T10:02:12.965513",
991 "user_email": "planemo@galaxyproject.org", 984 "user_email": "planemo@galaxyproject.org",
992 "user_id": "b5f519d254c4f536" 985 "user_id": "66f8380583c086e1"
993 }, 986 },
994 "status": "success", 987 "status": "success",
995 "test_index": 3, 988 "test_index": 3,
996 "time_seconds": 31.84161639213562, 989 "time_seconds": 32.275617599487305,
997 "tool_id": "cloning_simulation", 990 "tool_id": "cloning_simulation",
998 "tool_version": "0.1.0+galaxy0" 991 "tool_version": "0.1.0+galaxy0"
999 }, 992 },
1000 "has_data": true, 993 "has_data": true,
1001 "id": "cloning_simulation-3" 994 "id": "cloning_simulation-3"
1003 { 996 {
1004 "data": { 997 "data": {
1005 "inputs": { 998 "inputs": {
1006 "adv|use_file_names_as_ids": true, 999 "adv|use_file_names_as_ids": true,
1007 "assembly_csv": { 1000 "assembly_csv": {
1008 "id": "6aba8bde83c91d2f", 1001 "id": "ab2d796f030478a4",
1009 "src": "hda" 1002 "src": "hda"
1010 }, 1003 },
1011 "assembly_plan_name": "BioBrickStandardAssembly", 1004 "assembly_plan_name": "BioBrickStandardAssembly",
1012 "genbank_files": { 1005 "genbank_files": {
1013 "id": "c3b441e1ed1e9870", 1006 "id": "ecc2b8a59c690090",
1014 "src": "hdca" 1007 "src": "hdca"
1015 }, 1008 },
1016 "topology": "circular" 1009 "topology": "circular"
1017 }, 1010 },
1018 "job": { 1011 "job": {
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'", 1012 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpy2ysv6tn/files/5/6/e/dataset_56e880bc-1f93-495f-bfa8-0873cb8182a9.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpy2ysv6tn/files/d/d/e/dataset_dded78e6-5d3a-466d-a378-5793c801f32c.dat,/tmp/tmpy2ysv6tn/files/2/a/0/dataset_2a07a992-6527-4ac7-9c49-7fd9acbdea57.dat,/tmp/tmpy2ysv6tn/files/1/2/f/dataset_12faa3d9-c95d-4c34-9df7-6c53174d4276.dat,/tmp/tmpy2ysv6tn/files/5/8/1/dataset_581a4c55-0ce2-4c3b-a380-756448871f32.dat,/tmp/tmpy2ysv6tn/files/a/b/f/dataset_abf255f7-9841-4991-9b65-598df368ff85.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpy2ysv6tn/files/d/d/e/dataset_dded78e6-5d3a-466d-a378-5793c801f32c.dat:BBa_E0040_GFP.gb,/tmp/tmpy2ysv6tn/files/2/a/0/dataset_2a07a992-6527-4ac7-9c49-7fd9acbdea57.dat:BBa_J23119_prom.gb,/tmp/tmpy2ysv6tn/files/1/2/f/dataset_12faa3d9-c95d-4c34-9df7-6c53174d4276.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpy2ysv6tn/files/5/8/1/dataset_581a4c55-0ce2-4c3b-a380-756448871f32.dat:BBa_J61048_term.gb,/tmp/tmpy2ysv6tn/files/a/b/f/dataset_abf255f7-9841-4991-9b65-598df368ff85.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/tmpy2ysv6tn/job_working_directory/000/35/outputs/dataset_d5e2affd-9228-4b21-8e89-36a43c59ab37.dat' && echo DEBUG && ls 'outdir_gb'",
1020 "command_version": "", 1013 "command_version": "",
1021 "copied_from_job_id": null, 1014 "copied_from_job_id": null,
1022 "create_time": "2025-05-26T09:46:47.832614", 1015 "create_time": "2025-05-26T10:02:34.725504",
1023 "dependencies": [ 1016 "dependencies": [],
1024 {
1025 "cacheable": false,
1026 "dependency_resolver": {
1027 "auto_init": true,
1028 "auto_install": true,
1029 "can_uninstall_dependencies": true,
1030 "ensure_channels": "conda-forge,bioconda",
1031 "model_class": "CondaDependencyResolver",
1032 "prefix": "/home/rkhaled/miniconda3",
1033 "read_only": false,
1034 "resolver_type": "conda",
1035 "resolves_simple_dependencies": true,
1036 "use_local": false,
1037 "versionless": false
1038 },
1039 "dependency_type": "conda",
1040 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1041 "exact": true,
1042 "model_class": "MergedCondaDependency",
1043 "name": "flametree",
1044 "version": "0.1.11"
1045 },
1046 {
1047 "cacheable": false,
1048 "dependency_resolver": {
1049 "auto_init": true,
1050 "auto_install": true,
1051 "can_uninstall_dependencies": true,
1052 "ensure_channels": "conda-forge,bioconda",
1053 "model_class": "CondaDependencyResolver",
1054 "prefix": "/home/rkhaled/miniconda3",
1055 "read_only": false,
1056 "resolver_type": "conda",
1057 "resolves_simple_dependencies": true,
1058 "use_local": false,
1059 "versionless": false
1060 },
1061 "dependency_type": "conda",
1062 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1063 "exact": true,
1064 "model_class": "MergedCondaDependency",
1065 "name": "biopython",
1066 "version": "1.85"
1067 },
1068 {
1069 "cacheable": false,
1070 "dependency_resolver": {
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1072 "auto_install": true,
1073 "can_uninstall_dependencies": true,
1074 "ensure_channels": "conda-forge,bioconda",
1075 "model_class": "CondaDependencyResolver",
1076 "prefix": "/home/rkhaled/miniconda3",
1077 "read_only": false,
1078 "resolver_type": "conda",
1079 "resolves_simple_dependencies": true,
1080 "use_local": false,
1081 "versionless": false
1082 },
1083 "dependency_type": "conda",
1084 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1085 "exact": true,
1086 "model_class": "MergedCondaDependency",
1087 "name": "proglog",
1088 "version": "0.1.10"
1089 },
1090 {
1091 "cacheable": false,
1092 "dependency_resolver": {
1093 "auto_init": true,
1094 "auto_install": true,
1095 "can_uninstall_dependencies": true,
1096 "ensure_channels": "conda-forge,bioconda",
1097 "model_class": "CondaDependencyResolver",
1098 "prefix": "/home/rkhaled/miniconda3",
1099 "read_only": false,
1100 "resolver_type": "conda",
1101 "resolves_simple_dependencies": true,
1102 "use_local": false,
1103 "versionless": false
1104 },
1105 "dependency_type": "conda",
1106 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1107 "exact": true,
1108 "model_class": "MergedCondaDependency",
1109 "name": "pandas",
1110 "version": "2.2.3"
1111 },
1112 {
1113 "cacheable": false,
1114 "dependency_resolver": {
1115 "auto_init": true,
1116 "auto_install": true,
1117 "can_uninstall_dependencies": true,
1118 "ensure_channels": "conda-forge,bioconda",
1119 "model_class": "CondaDependencyResolver",
1120 "prefix": "/home/rkhaled/miniconda3",
1121 "read_only": false,
1122 "resolver_type": "conda",
1123 "resolves_simple_dependencies": true,
1124 "use_local": false,
1125 "versionless": false
1126 },
1127 "dependency_type": "conda",
1128 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1129 "exact": true,
1130 "model_class": "MergedCondaDependency",
1131 "name": "dnacauldron",
1132 "version": "2.0.12"
1133 },
1134 {
1135 "cacheable": false,
1136 "dependency_resolver": {
1137 "auto_init": true,
1138 "auto_install": true,
1139 "can_uninstall_dependencies": true,
1140 "ensure_channels": "conda-forge,bioconda",
1141 "model_class": "CondaDependencyResolver",
1142 "prefix": "/home/rkhaled/miniconda3",
1143 "read_only": false,
1144 "resolver_type": "conda",
1145 "resolves_simple_dependencies": true,
1146 "use_local": false,
1147 "versionless": false
1148 },
1149 "dependency_type": "conda",
1150 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1151 "exact": true,
1152 "model_class": "MergedCondaDependency",
1153 "name": "pdf-reports",
1154 "version": "0.3.9"
1155 },
1156 {
1157 "cacheable": false,
1158 "dependency_resolver": {
1159 "auto_init": true,
1160 "auto_install": true,
1161 "can_uninstall_dependencies": true,
1162 "ensure_channels": "conda-forge,bioconda",
1163 "model_class": "CondaDependencyResolver",
1164 "prefix": "/home/rkhaled/miniconda3",
1165 "read_only": false,
1166 "resolver_type": "conda",
1167 "resolves_simple_dependencies": true,
1168 "use_local": false,
1169 "versionless": false
1170 },
1171 "dependency_type": "conda",
1172 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1173 "exact": true,
1174 "model_class": "MergedCondaDependency",
1175 "name": "sequenticon",
1176 "version": "0.1.8"
1177 },
1178 {
1179 "cacheable": false,
1180 "dependency_resolver": {
1181 "auto_init": true,
1182 "auto_install": true,
1183 "can_uninstall_dependencies": true,
1184 "ensure_channels": "conda-forge,bioconda",
1185 "model_class": "CondaDependencyResolver",
1186 "prefix": "/home/rkhaled/miniconda3",
1187 "read_only": false,
1188 "resolver_type": "conda",
1189 "resolves_simple_dependencies": true,
1190 "use_local": false,
1191 "versionless": false
1192 },
1193 "dependency_type": "conda",
1194 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
1195 "exact": true,
1196 "model_class": "MergedCondaDependency",
1197 "name": "dna_features_viewer",
1198 "version": "3.1.5"
1199 }
1200 ],
1201 "exit_code": 0, 1017 "exit_code": 0,
1202 "external_id": "104081", 1018 "external_id": "116476",
1203 "galaxy_version": "24.2", 1019 "galaxy_version": "24.2",
1204 "handler": null, 1020 "handler": null,
1205 "history_id": "f825d543d1b9cf39", 1021 "history_id": "e1129f30c30438be",
1206 "id": "4b5a70f26b4819b4", 1022 "id": "2edb1d8c4fcdfa57",
1207 "inputs": { 1023 "inputs": {
1208 "assembly_csv": { 1024 "assembly_csv": {
1209 "id": "6aba8bde83c91d2f", 1025 "id": "ab2d796f030478a4",
1210 "src": "hda", 1026 "src": "hda",
1211 "uuid": "2ad0d873-86c6-45d9-b7d2-124dcbc1af89" 1027 "uuid": "56e880bc-1f93-495f-bfa8-0873cb8182a9"
1212 }, 1028 },
1213 "genbank_files1": { 1029 "genbank_files1": {
1214 "id": "1aae5cb645dbaceb", 1030 "id": "70033f808724210d",
1215 "src": "hda", 1031 "src": "hda",
1216 "uuid": "d293bdbb-5524-4e82-a4a0-d687a407a968" 1032 "uuid": "dded78e6-5d3a-466d-a378-5793c801f32c"
1217 }, 1033 },
1218 "genbank_files2": { 1034 "genbank_files2": {
1219 "id": "cc421d01a299ef36", 1035 "id": "e4c403c1aada23ec",
1220 "src": "hda", 1036 "src": "hda",
1221 "uuid": "ea5e46a6-144f-4c5e-b626-6bca5055f710" 1037 "uuid": "2a07a992-6527-4ac7-9c49-7fd9acbdea57"
1222 }, 1038 },
1223 "genbank_files3": { 1039 "genbank_files3": {
1224 "id": "1f0503133822f6be", 1040 "id": "afa1993aa783dac3",
1225 "src": "hda", 1041 "src": "hda",
1226 "uuid": "b491036e-78aa-4140-bca6-63462b7dbb5a" 1042 "uuid": "12faa3d9-c95d-4c34-9df7-6c53174d4276"
1227 }, 1043 },
1228 "genbank_files4": { 1044 "genbank_files4": {
1229 "id": "f7b46848b0cdcf03", 1045 "id": "2edb1d8c4fcdfa57",
1230 "src": "hda", 1046 "src": "hda",
1231 "uuid": "1cf514a1-2062-47c1-98b3-d86c408d348d" 1047 "uuid": "581a4c55-0ce2-4c3b-a380-756448871f32"
1232 }, 1048 },
1233 "genbank_files5": { 1049 "genbank_files5": {
1234 "id": "c92ddd5b8e0dfe51", 1050 "id": "cc59f77d482719ba",
1235 "src": "hda", 1051 "src": "hda",
1236 "uuid": "d0ae7d04-556d-48aa-a859-63d0efd9bc1c" 1052 "uuid": "abf255f7-9841-4991-9b65-598df368ff85"
1237 } 1053 }
1238 }, 1054 },
1239 "job_messages": [], 1055 "job_messages": [],
1240 "job_metrics": [], 1056 "job_metrics": [],
1241 "job_runner_name": null, 1057 "job_runner_name": null,
1242 "job_stderr": "", 1058 "job_stderr": "",
1243 "job_stdout": "", 1059 "job_stdout": "",
1244 "model_class": "Job", 1060 "model_class": "Job",
1245 "output_collections": { 1061 "output_collections": {
1246 "construct_gb": { 1062 "construct_gb": {
1247 "id": "2bdc7fcb2931f07b", 1063 "id": "d3a48cfe9e5a1f02",
1248 "src": "hdca" 1064 "src": "hdca"
1249 } 1065 }
1250 }, 1066 },
1251 "outputs": { 1067 "outputs": {
1252 "__new_primary_file_construct_gb|C1_prom_barcode__": { 1068 "__new_primary_file_construct_gb|C1_prom_barcode__": {
1253 "id": "4e090171f4d7129f", 1069 "id": "b5e4bb927c5912de",
1254 "src": "hda", 1070 "src": "hda",
1255 "uuid": "0541aea5-21f7-4b9b-b037-ce0b677829bb" 1071 "uuid": "1689e287-c7c5-488c-b397-a0d14018a93a"
1256 }, 1072 },
1257 "__new_primary_file_construct_gb|C2_gfp_term__": { 1073 "__new_primary_file_construct_gb|C2_gfp_term__": {
1258 "id": "4a624b810533f2ef", 1074 "id": "924199a1dc6199a2",
1259 "src": "hda", 1075 "src": "hda",
1260 "uuid": "381b158b-3536-4150-be35-d3e2b6e5dc19" 1076 "uuid": "82e60c5f-9305-4962-984c-4e667dc08972"
1261 }, 1077 },
1262 "__new_primary_file_construct_gb|C3_final__": { 1078 "__new_primary_file_construct_gb|C3_final__": {
1263 "id": "99b0b6baf442a2d9", 1079 "id": "f95eef361447e9a0",
1264 "src": "hda", 1080 "src": "hda",
1265 "uuid": "084415f0-529e-443f-bfa9-7ce16f75171f" 1081 "uuid": "50703365-ca24-444a-8cc2-ac9467884479"
1266 }, 1082 },
1267 "output_zip": { 1083 "output_zip": {
1268 "id": "a38ed44718641cdb", 1084 "id": "5165064d73efc2e3",
1269 "src": "hda", 1085 "src": "hda",
1270 "uuid": "4731915b-5562-4afe-b2f2-cf88b2af3eb5" 1086 "uuid": "d5e2affd-9228-4b21-8e89-36a43c59ab37"
1271 } 1087 }
1272 }, 1088 },
1273 "params": { 1089 "params": {
1274 "__input_ext": "\"input\"", 1090 "__input_ext": "\"input\"",
1275 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 1091 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1276 "assembly_plan_name": "\"BioBrickStandardAssembly\"", 1092 "assembly_plan_name": "\"BioBrickStandardAssembly\"",
1277 "chromInfo": "\"/tmp/tmphxxoceah/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1093 "chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1278 "dbkey": "\"?\"", 1094 "dbkey": "\"?\"",
1279 "domesticated_input": null, 1095 "domesticated_input": null,
1280 "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}", 1096 "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}",
1281 "topology": "\"circular\"" 1097 "topology": "\"circular\""
1282 }, 1098 },
1283 "state": "ok", 1099 "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, 1.96it/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", 1100 "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, 1.98it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.60it/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", 1101 "stdout": " 1 2\n0 \nconstruct parts NaN\nC1_prom_barcode BBa_K611094_bar BBa_J23119_prom\nC2_gfp_term BBa_E0040_GFP BBa_J61048_term\nC3_final C1_prom_barcode C2_gfp_term\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\nDEBUG\nC1_prom_barcode.gb\nC2_gfp_term.gb\nC3_final.gb\n",
1286 "tool_id": "cloning_simulation", 1102 "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, 1.96it/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", 1103 "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, 1.98it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00, 1.60it/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", 1104 "tool_stdout": " 1 2\n0 \nconstruct parts NaN\nC1_prom_barcode BBa_K611094_bar BBa_J23119_prom\nC2_gfp_term BBa_E0040_GFP BBa_J61048_term\nC3_final C1_prom_barcode C2_gfp_term\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\nDEBUG\nC1_prom_barcode.gb\nC2_gfp_term.gb\nC3_final.gb\n",
1289 "update_time": "2025-05-26T09:47:00.964337", 1105 "update_time": "2025-05-26T10:02:47.655383",
1290 "user_email": "planemo@galaxyproject.org", 1106 "user_email": "planemo@galaxyproject.org",
1291 "user_id": "b5f519d254c4f536" 1107 "user_id": "66f8380583c086e1"
1292 }, 1108 },
1293 "status": "success", 1109 "status": "success",
1294 "test_index": 4, 1110 "test_index": 4,
1295 "time_seconds": 34.59279441833496, 1111 "time_seconds": 34.81275129318237,
1296 "tool_id": "cloning_simulation", 1112 "tool_id": "cloning_simulation",
1297 "tool_version": "0.1.0+galaxy0" 1113 "tool_version": "0.1.0+galaxy0"
1298 }, 1114 },
1299 "has_data": true, 1115 "has_data": true,
1300 "id": "cloning_simulation-4" 1116 "id": "cloning_simulation-4"
1302 { 1118 {
1303 "data": { 1119 "data": {
1304 "inputs": { 1120 "inputs": {
1305 "adv|use_file_names_as_ids": true, 1121 "adv|use_file_names_as_ids": true,
1306 "assembly_csv": { 1122 "assembly_csv": {
1307 "id": "09ac55ab9704eba2", 1123 "id": "3494efe97c2aacb8",
1308 "src": "hda" 1124 "src": "hda"
1309 }, 1125 },
1310 "assembly_plan_name": "Type2sRestrictionAssembly", 1126 "assembly_plan_name": "Type2sRestrictionAssembly",
1311 "domesticated_input": { 1127 "domesticated_input": {
1312 "id": "dc7e3ab6a421767b", 1128 "id": "4fffd7776804f395",
1313 "src": "hdca" 1129 "src": "hdca"
1314 }, 1130 },
1315 "genbank_files": { 1131 "genbank_files": {
1316 "id": "b1d9a1d43e36b679", 1132 "id": "193b12b5837c3789",
1317 "src": "hdca" 1133 "src": "hdca"
1318 }, 1134 },
1319 "topology": "circular" 1135 "topology": "circular"
1320 }, 1136 },
1321 "job": { 1137 "job": {
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'", 1138 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpy2ysv6tn/files/6/c/2/dataset_6c2089de-5285-4ae6-8e08-afa38810c0ee.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpy2ysv6tn/files/b/6/8/dataset_b68d8dba-f098-4f14-ac9f-b69541a834c8.dat,/tmp/tmpy2ysv6tn/files/a/9/4/dataset_a94042d7-2d70-4257-bbc5-ac3f2be93aff.dat,/tmp/tmpy2ysv6tn/files/1/d/e/dataset_1de72341-f4c1-48df-9466-a1c80e23fdfb.dat,/tmp/tmpy2ysv6tn/files/c/1/1/dataset_c1128abd-86a1-48b9-b66c-0152d76c85c9.dat,/tmp/tmpy2ysv6tn/files/2/f/2/dataset_2f2ab7b7-d6ef-4a2e-90b8-f15cddf56eea.dat,/tmp/tmpy2ysv6tn/files/9/0/4/dataset_90485827-d839-4e32-b546-9c32f77fd264.dat,/tmp/tmpy2ysv6tn/files/7/c/5/dataset_7c56a071-e9fe-4133-8a99-8a7d58e7b1fd.dat' --domesticated_seq '/tmp/tmpy2ysv6tn/files/0/f/3/dataset_0f38d420-af2a-42ba-a6d3-f16807653402.dat,/tmp/tmpy2ysv6tn/files/0/b/6/dataset_0b653ed4-f458-4567-b9b7-074257934433.dat,/tmp/tmpy2ysv6tn/files/7/0/d/dataset_70d7c859-83f1-4aa7-b1db-fee1b4d384c0.dat,/tmp/tmpy2ysv6tn/files/c/e/2/dataset_ce2505e6-35c7-4858-a27e-6c5761a35be3.dat,/tmp/tmpy2ysv6tn/files/6/8/b/dataset_68b8d30e-6c0c-466f-a70c-0e58bcc27e0d.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpy2ysv6tn/files/b/6/8/dataset_b68d8dba-f098-4f14-ac9f-b69541a834c8.dat:part_A.gb,/tmp/tmpy2ysv6tn/files/a/9/4/dataset_a94042d7-2d70-4257-bbc5-ac3f2be93aff.dat:part_B.gb,/tmp/tmpy2ysv6tn/files/1/d/e/dataset_1de72341-f4c1-48df-9466-a1c80e23fdfb.dat:part_C.gb,/tmp/tmpy2ysv6tn/files/c/1/1/dataset_c1128abd-86a1-48b9-b66c-0152d76c85c9.dat:part_D.gb,/tmp/tmpy2ysv6tn/files/2/f/2/dataset_2f2ab7b7-d6ef-4a2e-90b8-f15cddf56eea.dat:part_E.gb,/tmp/tmpy2ysv6tn/files/9/0/4/dataset_90485827-d839-4e32-b546-9c32f77fd264.dat:part_F.gb,/tmp/tmpy2ysv6tn/files/7/c/5/dataset_7c56a071-e9fe-4133-8a99-8a7d58e7b1fd.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpy2ysv6tn/files/0/f/3/dataset_0f38d420-af2a-42ba-a6d3-f16807653402.dat:part_H.gb,/tmp/tmpy2ysv6tn/files/0/b/6/dataset_0b653ed4-f458-4567-b9b7-074257934433.dat:part_I.gb,/tmp/tmpy2ysv6tn/files/7/0/d/dataset_70d7c859-83f1-4aa7-b1db-fee1b4d384c0.dat:part_J.gb,/tmp/tmpy2ysv6tn/files/c/e/2/dataset_ce2505e6-35c7-4858-a27e-6c5761a35be3.dat:part_K.gb,/tmp/tmpy2ysv6tn/files/6/8/b/dataset_68b8d30e-6c0c-466f-a70c-0e58bcc27e0d.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/tmpy2ysv6tn/job_working_directory/000/49/outputs/dataset_445bab41-baa4-4de1-adfc-d4fd56892c5f.dat' && echo DEBUG && ls 'outdir_gb'",
1323 "command_version": "", 1139 "command_version": "",
1324 "copied_from_job_id": null, 1140 "copied_from_job_id": null,
1325 "create_time": "2025-05-26T09:47:41.246196", 1141 "create_time": "2025-05-26T10:03:29.120983",
1326 "dependencies": [ 1142 "dependencies": [
1327 { 1143 {
1328 "cacheable": false, 1144 "cacheable": false,
1329 "dependency_resolver": { 1145 "dependency_resolver": {
1330 "auto_init": true, 1146 "auto_init": true,
1500 "name": "dna_features_viewer", 1316 "name": "dna_features_viewer",
1501 "version": "3.1.5" 1317 "version": "3.1.5"
1502 } 1318 }
1503 ], 1319 ],
1504 "exit_code": 0, 1320 "exit_code": 0,
1505 "external_id": "105127", 1321 "external_id": "117561",
1506 "galaxy_version": "24.2", 1322 "galaxy_version": "24.2",
1507 "handler": null, 1323 "handler": null,
1508 "history_id": "24f234959abeadac", 1324 "history_id": "abbaf1e2c3c282ad",
1509 "id": "271c0f8150c5b24a", 1325 "id": "3494efe97c2aacb8",
1510 "inputs": { 1326 "inputs": {
1511 "assembly_csv": { 1327 "assembly_csv": {
1512 "id": "09ac55ab9704eba2", 1328 "id": "3494efe97c2aacb8",
1513 "src": "hda", 1329 "src": "hda",
1514 "uuid": "0d80ec64-7c14-49ec-bf00-8b127413b402" 1330 "uuid": "6c2089de-5285-4ae6-8e08-afa38810c0ee"
1515 }, 1331 },
1516 "domesticated_input1": { 1332 "domesticated_input1": {
1517 "id": "f1e670d3230dc49d", 1333 "id": "a4800f28d8ead13a",
1518 "src": "hda", 1334 "src": "hda",
1519 "uuid": "9073f5ed-6218-436e-9c90-40231a771418" 1335 "uuid": "0f38d420-af2a-42ba-a6d3-f16807653402"
1520 }, 1336 },
1521 "domesticated_input2": { 1337 "domesticated_input2": {
1522 "id": "d6d38b30a0e08779", 1338 "id": "73a220014461252c",
1523 "src": "hda", 1339 "src": "hda",
1524 "uuid": "1c278033-6add-4e83-92ee-ece6b30d73b2" 1340 "uuid": "0b653ed4-f458-4567-b9b7-074257934433"
1525 }, 1341 },
1526 "domesticated_input3": { 1342 "domesticated_input3": {
1527 "id": "5df6658d98901785", 1343 "id": "7d1b502fc1fb844a",
1528 "src": "hda", 1344 "src": "hda",
1529 "uuid": "68ba5566-3d5c-4aaf-9f00-a5dc3f1ec5f6" 1345 "uuid": "70d7c859-83f1-4aa7-b1db-fee1b4d384c0"
1530 }, 1346 },
1531 "domesticated_input4": { 1347 "domesticated_input4": {
1532 "id": "179c4c4e78c36c21", 1348 "id": "6a344bf502116f62",
1533 "src": "hda", 1349 "src": "hda",
1534 "uuid": "e2abf373-3268-46a0-a6bd-889fe7061984" 1350 "uuid": "ce2505e6-35c7-4858-a27e-6c5761a35be3"
1535 }, 1351 },
1536 "domesticated_input5": { 1352 "domesticated_input5": {
1537 "id": "b1ed244e949762c6", 1353 "id": "a28d730bd7e6d71e",
1538 "src": "hda", 1354 "src": "hda",
1539 "uuid": "d71d0b7d-fc98-4d97-8a6b-e92bb229582e" 1355 "uuid": "68b8d30e-6c0c-466f-a70c-0e58bcc27e0d"
1540 }, 1356 },
1541 "genbank_files1": { 1357 "genbank_files1": {
1542 "id": "faf74795de9215e4", 1358 "id": "b4c6f22fd42e2fbc",
1543 "src": "hda", 1359 "src": "hda",
1544 "uuid": "bfe6c5a0-bee9-4fcd-bc48-1030fddae94b" 1360 "uuid": "b68d8dba-f098-4f14-ac9f-b69541a834c8"
1545 }, 1361 },
1546 "genbank_files2": { 1362 "genbank_files2": {
1547 "id": "982fc2b45c634401", 1363 "id": "60c65d41f8ff0e9b",
1548 "src": "hda", 1364 "src": "hda",
1549 "uuid": "5b1e4497-7e6b-42cc-8cbb-5f538d40f7bb" 1365 "uuid": "a94042d7-2d70-4257-bbc5-ac3f2be93aff"
1550 }, 1366 },
1551 "genbank_files3": { 1367 "genbank_files3": {
1552 "id": "d49187f9d744460f", 1368 "id": "554995f2d7672bb2",
1553 "src": "hda", 1369 "src": "hda",
1554 "uuid": "b3ecd963-5e7a-4c86-91f3-8d8322471402" 1370 "uuid": "1de72341-f4c1-48df-9466-a1c80e23fdfb"
1555 }, 1371 },
1556 "genbank_files4": { 1372 "genbank_files4": {
1557 "id": "271c0f8150c5b24a", 1373 "id": "9450471e42664058",
1558 "src": "hda", 1374 "src": "hda",
1559 "uuid": "6f8d0b94-6f0f-470c-b36a-87256aa427c6" 1375 "uuid": "c1128abd-86a1-48b9-b66c-0152d76c85c9"
1560 }, 1376 },
1561 "genbank_files5": { 1377 "genbank_files5": {
1562 "id": "954a11ecc737c99c", 1378 "id": "9a370553f77d6a31",
1563 "src": "hda", 1379 "src": "hda",
1564 "uuid": "2fd8ba0d-a6ac-4379-a094-6dfc4b3f677e" 1380 "uuid": "2f2ab7b7-d6ef-4a2e-90b8-f15cddf56eea"
1565 }, 1381 },
1566 "genbank_files6": { 1382 "genbank_files6": {
1567 "id": "c90496f58e5d6dd9", 1383 "id": "cecfeefdcb127887",
1568 "src": "hda", 1384 "src": "hda",
1569 "uuid": "c5fde1d8-6078-4b1c-946d-fe58c868e1a5" 1385 "uuid": "90485827-d839-4e32-b546-9c32f77fd264"
1570 }, 1386 },
1571 "genbank_files7": { 1387 "genbank_files7": {
1572 "id": "9c66fe6132ced54b", 1388 "id": "88bfe38878128ef9",
1573 "src": "hda", 1389 "src": "hda",
1574 "uuid": "0203ce08-8c98-4dcf-a274-ac69f126eb78" 1390 "uuid": "7c56a071-e9fe-4133-8a99-8a7d58e7b1fd"
1575 } 1391 }
1576 }, 1392 },
1577 "job_messages": [], 1393 "job_messages": [],
1578 "job_metrics": [], 1394 "job_metrics": [],
1579 "job_runner_name": null, 1395 "job_runner_name": null,
1580 "job_stderr": "", 1396 "job_stderr": "",
1581 "job_stdout": "", 1397 "job_stdout": "",
1582 "model_class": "Job", 1398 "model_class": "Job",
1583 "output_collections": { 1399 "output_collections": {
1584 "construct_gb": { 1400 "construct_gb": {
1585 "id": "7a37f3397bf88665", 1401 "id": "41ca6db0600d7999",
1586 "src": "hdca" 1402 "src": "hdca"
1587 } 1403 }
1588 }, 1404 },
1589 "outputs": { 1405 "outputs": {
1590 "__new_primary_file_construct_gb|construct_1__": { 1406 "__new_primary_file_construct_gb|construct_1__": {
1591 "id": "ee6560cff5429b3a", 1407 "id": "1750f123cc89cd74",
1592 "src": "hda", 1408 "src": "hda",
1593 "uuid": "2d9d0878-8a8e-4a76-b4c7-8b2c58007a4c" 1409 "uuid": "2402ee1c-8048-48aa-9180-d84ffbac4c0d"
1594 }, 1410 },
1595 "__new_primary_file_construct_gb|construct_2__": { 1411 "__new_primary_file_construct_gb|construct_2__": {
1596 "id": "7faeb5268234c1b7", 1412 "id": "0a1a12a9af9d8d2a",
1597 "src": "hda", 1413 "src": "hda",
1598 "uuid": "d8ead123-b416-446e-bcd7-12d88aa380d8" 1414 "uuid": "4f5260cc-c112-4966-83c6-f3cd6f9cdd09"
1599 }, 1415 },
1600 "__new_primary_file_construct_gb|construct_3__": { 1416 "__new_primary_file_construct_gb|construct_3__": {
1601 "id": "71b5e767ad5c3d19", 1417 "id": "a7850a538357f009",
1602 "src": "hda", 1418 "src": "hda",
1603 "uuid": "d3370005-e04e-41fe-91ca-5ae418062a9f" 1419 "uuid": "d2eb027d-9f28-4cf0-bd60-f8856220a681"
1604 }, 1420 },
1605 "__new_primary_file_construct_gb|construct_4__": { 1421 "__new_primary_file_construct_gb|construct_4__": {
1606 "id": "07cc2539cb83a207", 1422 "id": "eeb0994ae957c814",
1607 "src": "hda", 1423 "src": "hda",
1608 "uuid": "0a5f7883-f82b-4122-a882-76fadc52a358" 1424 "uuid": "df9e0b45-10c1-46a2-a1bf-fccc2817a77e"
1609 }, 1425 },
1610 "output_zip": { 1426 "output_zip": {
1611 "id": "49de8d939dbbcfba", 1427 "id": "4d7f94dc70c8b750",
1612 "src": "hda", 1428 "src": "hda",
1613 "uuid": "e791efbc-be6b-44c5-a124-a744a812b597" 1429 "uuid": "445bab41-baa4-4de1-adfc-d4fd56892c5f"
1614 } 1430 }
1615 }, 1431 },
1616 "params": { 1432 "params": {
1617 "__input_ext": "\"input\"", 1433 "__input_ext": "\"input\"",
1618 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 1434 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1619 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", 1435 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
1620 "chromInfo": "\"/tmp/tmphxxoceah/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1436 "chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1621 "dbkey": "\"?\"", 1437 "dbkey": "\"?\"",
1622 "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}", 1438 "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}",
1623 "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}", 1439 "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}",
1624 "topology": "\"circular\"" 1440 "topology": "\"circular\""
1625 }, 1441 },
1626 "state": "ok", 1442 "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, 2.41it/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", 1443 "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, 2.20it/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",
1628 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", 1444 "stdout": " 1 2 3 4 5 6\n0 \nconstruct_3 construct_1 part_L part_J part_K NaN NaN\nconstruct_4 construct_2 part_L part_J part_K NaN NaN\nconstruct_1 part_A part_B part_C part_D part_E part_F\nconstruct_2 part_A part_G part_H part_I part_F NaN\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\nconstruct_4.gb\n",
1629 "tool_id": "cloning_simulation", 1445 "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, 2.41it/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", 1446 "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, 2.20it/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",
1631 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", 1447 "tool_stdout": " 1 2 3 4 5 6\n0 \nconstruct_3 construct_1 part_L part_J part_K NaN NaN\nconstruct_4 construct_2 part_L part_J part_K NaN NaN\nconstruct_1 part_A part_B part_C part_D part_E part_F\nconstruct_2 part_A part_G part_H part_I part_F NaN\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\nconstruct_4.gb\n",
1632 "update_time": "2025-05-26T09:47:53.960080", 1448 "update_time": "2025-05-26T10:03:41.864270",
1633 "user_email": "planemo@galaxyproject.org", 1449 "user_email": "planemo@galaxyproject.org",
1634 "user_id": "b5f519d254c4f536" 1450 "user_id": "66f8380583c086e1"
1635 }, 1451 },
1636 "status": "success", 1452 "status": "success",
1637 "test_index": 5, 1453 "test_index": 5,
1638 "time_seconds": 52.97593927383423, 1454 "time_seconds": 53.94194722175598,
1639 "tool_id": "cloning_simulation", 1455 "tool_id": "cloning_simulation",
1640 "tool_version": "0.1.0+galaxy0" 1456 "tool_version": "0.1.0+galaxy0"
1641 }, 1457 },
1642 "has_data": true, 1458 "has_data": true,
1643 "id": "cloning_simulation-5" 1459 "id": "cloning_simulation-5"
1645 { 1461 {
1646 "data": { 1462 "data": {
1647 "inputs": { 1463 "inputs": {
1648 "adv|use_file_names_as_ids": true, 1464 "adv|use_file_names_as_ids": true,
1649 "assembly_csv": { 1465 "assembly_csv": {
1650 "id": "e8ab24d23dab7d7f", 1466 "id": "6fb8fb3f063f475d",
1651 "src": "hda" 1467 "src": "hda"
1652 }, 1468 },
1653 "assembly_plan_name": "Type2sRestrictionAssembly", 1469 "assembly_plan_name": "Type2sRestrictionAssembly",
1654 "domesticated_input": { 1470 "domesticated_input": {
1655 "id": "dfd75d2f0da631b2", 1471 "id": "7f406d9538852eeb",
1656 "src": "hdca" 1472 "src": "hdca"
1657 }, 1473 },
1658 "topology": "circular" 1474 "topology": "circular"
1659 }, 1475 },
1660 "job": { 1476 "job": {
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'", 1477 "command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpy2ysv6tn/files/a/a/d/dataset_aadc2ac5-b92d-4489-ba9c-9e30c79da207.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpy2ysv6tn/files/3/8/8/dataset_388674d2-24fe-4e76-b0b8-2db6463e788f.dat,/tmp/tmpy2ysv6tn/files/7/5/c/dataset_75c27ee5-fd9b-46a1-be07-f0cdc4e16bc1.dat,/tmp/tmpy2ysv6tn/files/b/b/b/dataset_bbba5ff9-69e7-4d41-af82-992df5f065fb.dat,/tmp/tmpy2ysv6tn/files/d/c/9/dataset_dc982e9d-6d93-4638-b4fc-67fc8238b295.dat,/tmp/tmpy2ysv6tn/files/e/d/2/dataset_ed2d7b35-625f-429e-ae50-ce1098a20b85.dat,/tmp/tmpy2ysv6tn/files/5/a/2/dataset_5a2010cb-64cf-4ff9-8852-f883f7ab0269.dat,/tmp/tmpy2ysv6tn/files/0/f/a/dataset_0fa8ed6a-b848-4b0d-9474-13cd22d4a47e.dat,/tmp/tmpy2ysv6tn/files/a/b/e/dataset_abead413-c3d4-42d3-bd97-c02a6bd69779.dat,/tmp/tmpy2ysv6tn/files/6/a/b/dataset_6ab6c472-c672-4bdf-9814-8e069a8a07e1.dat,/tmp/tmpy2ysv6tn/files/b/0/e/dataset_b0e2ce07-ccf0-4805-958c-8de174c3d4c1.dat,/tmp/tmpy2ysv6tn/files/3/3/a/dataset_33ad2072-fb76-47c4-b3f7-60a2a097ab87.dat,/tmp/tmpy2ysv6tn/files/9/d/1/dataset_9d13c418-bbb1-457e-bdaf-0f2bf5232f78.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpy2ysv6tn/files/3/8/8/dataset_388674d2-24fe-4e76-b0b8-2db6463e788f.dat:part_A.gb,/tmp/tmpy2ysv6tn/files/7/5/c/dataset_75c27ee5-fd9b-46a1-be07-f0cdc4e16bc1.dat:part_B.gb,/tmp/tmpy2ysv6tn/files/b/b/b/dataset_bbba5ff9-69e7-4d41-af82-992df5f065fb.dat:part_C.gb,/tmp/tmpy2ysv6tn/files/d/c/9/dataset_dc982e9d-6d93-4638-b4fc-67fc8238b295.dat:part_D.gb,/tmp/tmpy2ysv6tn/files/e/d/2/dataset_ed2d7b35-625f-429e-ae50-ce1098a20b85.dat:part_E.gb,/tmp/tmpy2ysv6tn/files/5/a/2/dataset_5a2010cb-64cf-4ff9-8852-f883f7ab0269.dat:part_F.gb,/tmp/tmpy2ysv6tn/files/0/f/a/dataset_0fa8ed6a-b848-4b0d-9474-13cd22d4a47e.dat:part_G.gb,/tmp/tmpy2ysv6tn/files/a/b/e/dataset_abead413-c3d4-42d3-bd97-c02a6bd69779.dat:part_H.gb,/tmp/tmpy2ysv6tn/files/6/a/b/dataset_6ab6c472-c672-4bdf-9814-8e069a8a07e1.dat:part_I.gb,/tmp/tmpy2ysv6tn/files/b/0/e/dataset_b0e2ce07-ccf0-4805-958c-8de174c3d4c1.dat:part_J.gb,/tmp/tmpy2ysv6tn/files/3/3/a/dataset_33ad2072-fb76-47c4-b3f7-60a2a097ab87.dat:part_K.gb,/tmp/tmpy2ysv6tn/files/9/d/1/dataset_9d13c418-bbb1-457e-bdaf-0f2bf5232f78.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/tmpy2ysv6tn/job_working_directory/000/63/outputs/dataset_fbeb57ed-1718-4d2b-a22b-5c4a5779d9ab.dat' && echo DEBUG && ls 'outdir_gb'",
1662 "command_version": "", 1478 "command_version": "",
1663 "copied_from_job_id": null, 1479 "copied_from_job_id": null,
1664 "create_time": "2025-05-26T09:48:34.329479", 1480 "create_time": "2025-05-26T10:04:22.340769",
1665 "dependencies": [ 1481 "dependencies": [
1666 { 1482 {
1667 "cacheable": false, 1483 "cacheable": false,
1668 "dependency_resolver": { 1484 "dependency_resolver": {
1669 "auto_init": true, 1485 "auto_init": true,
1839 "name": "dna_features_viewer", 1655 "name": "dna_features_viewer",
1840 "version": "3.1.5" 1656 "version": "3.1.5"
1841 } 1657 }
1842 ], 1658 ],
1843 "exit_code": 0, 1659 "exit_code": 0,
1844 "external_id": "106213", 1660 "external_id": "118646",
1845 "galaxy_version": "24.2", 1661 "galaxy_version": "24.2",
1846 "handler": null, 1662 "handler": null,
1847 "history_id": "67e443cb5516c0e0", 1663 "history_id": "18bb6cd07b986e37",
1848 "id": "07cc2539cb83a207", 1664 "id": "3b86e96397860676",
1849 "inputs": { 1665 "inputs": {
1850 "assembly_csv": { 1666 "assembly_csv": {
1851 "id": "e8ab24d23dab7d7f", 1667 "id": "6fb8fb3f063f475d",
1852 "src": "hda", 1668 "src": "hda",
1853 "uuid": "017ccfd4-4d46-44c1-99ad-af18724cfa9c" 1669 "uuid": "aadc2ac5-b92d-4489-ba9c-9e30c79da207"
1854 }, 1670 },
1855 "domesticated_input1": { 1671 "domesticated_input1": {
1856 "id": "548eebef94e3a53d", 1672 "id": "3eddddb1a3bb1719",
1857 "src": "hda", 1673 "src": "hda",
1858 "uuid": "c26ad39f-1237-4c04-8f7f-73d2c5d9ad58" 1674 "uuid": "388674d2-24fe-4e76-b0b8-2db6463e788f"
1859 }, 1675 },
1860 "domesticated_input10": { 1676 "domesticated_input10": {
1861 "id": "9e9d5c19538ef8ad", 1677 "id": "6baf136e951fa3e9",
1862 "src": "hda", 1678 "src": "hda",
1863 "uuid": "0e4a4a05-7265-4844-9d70-1ad96facfdf9" 1679 "uuid": "b0e2ce07-ccf0-4805-958c-8de174c3d4c1"
1864 }, 1680 },
1865 "domesticated_input11": { 1681 "domesticated_input11": {
1866 "id": "8c0e43d479b6b17a", 1682 "id": "11a588ee1ee4e36e",
1867 "src": "hda", 1683 "src": "hda",
1868 "uuid": "9f72d140-3946-4567-8ecb-056458d7bb70" 1684 "uuid": "33ad2072-fb76-47c4-b3f7-60a2a097ab87"
1869 }, 1685 },
1870 "domesticated_input12": { 1686 "domesticated_input12": {
1871 "id": "b75b41451f2f7195", 1687 "id": "8f43de78738fc703",
1872 "src": "hda", 1688 "src": "hda",
1873 "uuid": "b6a06ac7-2240-4f68-9e75-63de3f5d10f2" 1689 "uuid": "9d13c418-bbb1-457e-bdaf-0f2bf5232f78"
1874 }, 1690 },
1875 "domesticated_input2": { 1691 "domesticated_input2": {
1876 "id": "f1612d32ca625e37", 1692 "id": "df551757dda63084",
1877 "src": "hda", 1693 "src": "hda",
1878 "uuid": "c68beeb3-949a-4a3e-ab43-987831504001" 1694 "uuid": "75c27ee5-fd9b-46a1-be07-f0cdc4e16bc1"
1879 }, 1695 },
1880 "domesticated_input3": { 1696 "domesticated_input3": {
1881 "id": "bf5687b995aa6663", 1697 "id": "3b86e96397860676",
1882 "src": "hda", 1698 "src": "hda",
1883 "uuid": "8f6a4bdd-c6c0-4b79-8dfd-7a2e5f0e8c72" 1699 "uuid": "bbba5ff9-69e7-4d41-af82-992df5f065fb"
1884 }, 1700 },
1885 "domesticated_input4": { 1701 "domesticated_input4": {
1886 "id": "13ae5fed3f9ef282", 1702 "id": "125f9d0e88ccc764",
1887 "src": "hda", 1703 "src": "hda",
1888 "uuid": "1069bd61-49fb-492a-8eaf-d98e496576a8" 1704 "uuid": "dc982e9d-6d93-4638-b4fc-67fc8238b295"
1889 }, 1705 },
1890 "domesticated_input5": { 1706 "domesticated_input5": {
1891 "id": "58d09772df305f7c", 1707 "id": "68e8d3b1610203e4",
1892 "src": "hda", 1708 "src": "hda",
1893 "uuid": "311db06e-881c-4a38-9fe9-a13712004ece" 1709 "uuid": "ed2d7b35-625f-429e-ae50-ce1098a20b85"
1894 }, 1710 },
1895 "domesticated_input6": { 1711 "domesticated_input6": {
1896 "id": "940c0a8788b53ef0", 1712 "id": "f9ce2b01423639ed",
1897 "src": "hda", 1713 "src": "hda",
1898 "uuid": "781cdd92-6baf-451e-8e72-f05961154dae" 1714 "uuid": "5a2010cb-64cf-4ff9-8852-f883f7ab0269"
1899 }, 1715 },
1900 "domesticated_input7": { 1716 "domesticated_input7": {
1901 "id": "5d12b487c622fea5", 1717 "id": "af7dc246cf57ca17",
1902 "src": "hda", 1718 "src": "hda",
1903 "uuid": "717f7fe8-1fbf-4394-aeff-14d7aa430193" 1719 "uuid": "0fa8ed6a-b848-4b0d-9474-13cd22d4a47e"
1904 }, 1720 },
1905 "domesticated_input8": { 1721 "domesticated_input8": {
1906 "id": "7f6a5e9bab73b744", 1722 "id": "73904d43e96b8397",
1907 "src": "hda", 1723 "src": "hda",
1908 "uuid": "3a883d96-6381-4569-a872-6490a47980b2" 1724 "uuid": "abead413-c3d4-42d3-bd97-c02a6bd69779"
1909 }, 1725 },
1910 "domesticated_input9": { 1726 "domesticated_input9": {
1911 "id": "917d245d020dcffb", 1727 "id": "5dd99ba27cc0c63e",
1912 "src": "hda", 1728 "src": "hda",
1913 "uuid": "c1d48747-8d18-4249-8b11-60a73ad7446f" 1729 "uuid": "6ab6c472-c672-4bdf-9814-8e069a8a07e1"
1914 } 1730 }
1915 }, 1731 },
1916 "job_messages": [], 1732 "job_messages": [],
1917 "job_metrics": [], 1733 "job_metrics": [],
1918 "job_runner_name": null, 1734 "job_runner_name": null,
1919 "job_stderr": "", 1735 "job_stderr": "",
1920 "job_stdout": "", 1736 "job_stdout": "",
1921 "model_class": "Job", 1737 "model_class": "Job",
1922 "output_collections": { 1738 "output_collections": {
1923 "construct_gb": { 1739 "construct_gb": {
1924 "id": "cecf675ce2a554e8", 1740 "id": "9677ca5db33658a1",
1925 "src": "hdca" 1741 "src": "hdca"
1926 } 1742 }
1927 }, 1743 },
1928 "outputs": { 1744 "outputs": {
1929 "__new_primary_file_construct_gb|construct_1__": { 1745 "__new_primary_file_construct_gb|construct_1__": {
1930 "id": "6ed4cf4ef5da4ab6", 1746 "id": "df1d56fe5378c54b",
1931 "src": "hda", 1747 "src": "hda",
1932 "uuid": "77c80040-9366-4df3-8ee7-b8f5c6148b73" 1748 "uuid": "c3d590de-2171-4d9a-a1c0-01110787a4ea"
1933 }, 1749 },
1934 "__new_primary_file_construct_gb|construct_2__": { 1750 "__new_primary_file_construct_gb|construct_2__": {
1935 "id": "f0c0b63c8f5e218a", 1751 "id": "a443c6a3159c515a",
1936 "src": "hda", 1752 "src": "hda",
1937 "uuid": "8a7bd174-630d-439e-a111-682129e2dbc6" 1753 "uuid": "14cde463-8656-4342-be37-c28798003a81"
1938 }, 1754 },
1939 "__new_primary_file_construct_gb|construct_3__": { 1755 "__new_primary_file_construct_gb|construct_3__": {
1940 "id": "89c8871118f8304b", 1756 "id": "4048e6cd68dc21c7",
1941 "src": "hda", 1757 "src": "hda",
1942 "uuid": "5ee7450c-795c-4a27-8354-25ac7ab1d71f" 1758 "uuid": "87c175e5-05d6-48e7-b617-e15d49a7027d"
1943 }, 1759 },
1944 "__new_primary_file_construct_gb|construct_4__": { 1760 "__new_primary_file_construct_gb|construct_4__": {
1945 "id": "57b71ad05e041af6", 1761 "id": "f601f1baaea8c27e",
1946 "src": "hda", 1762 "src": "hda",
1947 "uuid": "b3b86695-7ea9-43e6-bfbb-6a20972dec20" 1763 "uuid": "8e8367d5-caae-467d-a9d7-c681fd5497c7"
1948 }, 1764 },
1949 "output_zip": { 1765 "output_zip": {
1950 "id": "2ec06dcf804a9f1d", 1766 "id": "8c0bd3fd394dbc64",
1951 "src": "hda", 1767 "src": "hda",
1952 "uuid": "9593abfa-a9bc-4a45-8334-5203050a6ca5" 1768 "uuid": "fbeb57ed-1718-4d2b-a22b-5c4a5779d9ab"
1953 } 1769 }
1954 }, 1770 },
1955 "params": { 1771 "params": {
1956 "__input_ext": "\"input\"", 1772 "__input_ext": "\"input\"",
1957 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}", 1773 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
1958 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", 1774 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
1959 "chromInfo": "\"/tmp/tmphxxoceah/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 1775 "chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
1960 "dbkey": "\"?\"", 1776 "dbkey": "\"?\"",
1961 "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}", 1777 "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}",
1962 "genbank_files": null, 1778 "genbank_files": null,
1963 "topology": "\"circular\"" 1779 "topology": "\"circular\""
1964 }, 1780 },
1965 "state": "ok", 1781 "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, 2.41it/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", 1782 "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, 2.31it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.11it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.75it/s, now=None]\r \r",
1967 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", 1783 "stdout": " 1 2 3 4 5 6\n0 \nconstruct_3 construct_1 part_L part_J part_K NaN NaN\nconstruct_4 construct_2 part_L part_J part_K NaN NaN\nconstruct_1 part_A part_B part_C part_D part_E part_F\nconstruct_2 part_A part_G part_H part_I part_F NaN\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\nconstruct_4.gb\n",
1968 "tool_id": "cloning_simulation", 1784 "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, 2.41it/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", 1785 "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, 2.31it/s, now=None]\rassembly: 75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c | 3/4 [00:01<00:00, 2.11it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00, 1.75it/s, now=None]\r \r",
1970 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n", 1786 "tool_stdout": " 1 2 3 4 5 6\n0 \nconstruct_3 construct_1 part_L part_J part_K NaN NaN\nconstruct_4 construct_2 part_L part_J part_K NaN NaN\nconstruct_1 part_A part_B part_C part_D part_E part_F\nconstruct_2 part_A part_G part_H part_I part_F NaN\nSimulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\nconstruct_4.gb\n",
1971 "update_time": "2025-05-26T09:48:47.319875", 1787 "update_time": "2025-05-26T10:04:35.116441",
1972 "user_email": "planemo@galaxyproject.org", 1788 "user_email": "planemo@galaxyproject.org",
1973 "user_id": "b5f519d254c4f536" 1789 "user_id": "66f8380583c086e1"
1974 }, 1790 },
1975 "status": "success", 1791 "status": "success",
1976 "test_index": 6, 1792 "test_index": 6,
1977 "time_seconds": 53.241769552230835, 1793 "time_seconds": 53.07335948944092,
1978 "tool_id": "cloning_simulation", 1794 "tool_id": "cloning_simulation",
1979 "tool_version": "0.1.0+galaxy0" 1795 "tool_version": "0.1.0+galaxy0"
1980 }, 1796 },
1981 "has_data": true, 1797 "has_data": true,
1982 "id": "cloning_simulation-6" 1798 "id": "cloning_simulation-6"