cloning_simulation: output.json comparison

comparison output.json @ 14:16ccb36aa8e3 draft

planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae

author	tduigou
date	Mon, 26 May 2025 11:29:13 +0000
parents	7d1778f5e164
children	074a76e84b80

comparison

equal deleted inserted replaced

-:7d1778f5e164
+:16ccb36aa8e3
 {
 "summary": {
 "num_errors": 0,
-"num_failures": 1,
+"num_failures": 0,
 "num_skips": 0,
 "num_tests": 7
 },
 "tests": [
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "41ca6db0600d7999",
+"id": "c173cff58a987f8f",
 "src": "hda"
 },
 "assembly_plan_name": "Type2sRestrictionAssembly",
 "genbank_files": {
-"id": "66f8380583c086e1",
+"id": "fcc5b7d13a1328f6",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"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'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/2/b/d/dataset_2bdf436f-52cc-4c6e-afdb-3f051629900f.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/4/6/5/dataset_465a53ab-8770-4514-a9b3-227f79646eb7.dat,/tmp/tmpc6lic4p9/files/a/e/2/dataset_ae22d5d2-cde0-45b5-9e8e-67b5cbd586fa.dat,/tmp/tmpc6lic4p9/files/e/6/4/dataset_e64057b1-43b3-4788-8891-77bcd297223c.dat,/tmp/tmpc6lic4p9/files/1/d/1/dataset_1d1f9832-b58e-48c2-b1b3-6c3fb18e9890.dat,/tmp/tmpc6lic4p9/files/6/7/3/dataset_6732fc79-081e-4edf-bccc-a0087520172a.dat,/tmp/tmpc6lic4p9/files/b/1/7/dataset_b17c7a49-3121-4292-95ff-51891aa066d1.dat,/tmp/tmpc6lic4p9/files/2/8/1/dataset_2811f816-8532-4ddd-8e29-9a6ed7dad54e.dat,/tmp/tmpc6lic4p9/files/e/7/4/dataset_e74d0182-807e-40a8-b67a-ac088fc2e02c.dat,/tmp/tmpc6lic4p9/files/9/d/c/dataset_9dc55c98-4ab9-4272-a680-9b3129954367.dat,/tmp/tmpc6lic4p9/files/9/5/6/dataset_95699db9-77cf-4ae1-8454-4f255f3cb62a.dat,/tmp/tmpc6lic4p9/files/1/1/9/dataset_11979c28-82ee-43c4-9e43-f34cb541f96b.dat,/tmp/tmpc6lic4p9/files/3/f/5/dataset_3f53cb86-2d2b-429a-bf51-e276bbe393fa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/4/6/5/dataset_465a53ab-8770-4514-a9b3-227f79646eb7.dat:part_A.gb,/tmp/tmpc6lic4p9/files/a/e/2/dataset_ae22d5d2-cde0-45b5-9e8e-67b5cbd586fa.dat:part_B.gb,/tmp/tmpc6lic4p9/files/e/6/4/dataset_e64057b1-43b3-4788-8891-77bcd297223c.dat:part_C.gb,/tmp/tmpc6lic4p9/files/1/d/1/dataset_1d1f9832-b58e-48c2-b1b3-6c3fb18e9890.dat:part_D.gb,/tmp/tmpc6lic4p9/files/6/7/3/dataset_6732fc79-081e-4edf-bccc-a0087520172a.dat:part_E.gb,/tmp/tmpc6lic4p9/files/b/1/7/dataset_b17c7a49-3121-4292-95ff-51891aa066d1.dat:part_F.gb,/tmp/tmpc6lic4p9/files/2/8/1/dataset_2811f816-8532-4ddd-8e29-9a6ed7dad54e.dat:part_G.gb,/tmp/tmpc6lic4p9/files/e/7/4/dataset_e74d0182-807e-40a8-b67a-ac088fc2e02c.dat:part_H.gb,/tmp/tmpc6lic4p9/files/9/d/c/dataset_9dc55c98-4ab9-4272-a680-9b3129954367.dat:part_I.gb,/tmp/tmpc6lic4p9/files/9/5/6/dataset_95699db9-77cf-4ae1-8454-4f255f3cb62a.dat:part_J.gb,/tmp/tmpc6lic4p9/files/1/1/9/dataset_11979c28-82ee-43c4-9e43-f34cb541f96b.dat:part_K.gb,/tmp/tmpc6lic4p9/files/3/f/5/dataset_3f53cb86-2d2b-429a-bf51-e276bbe393fa.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/tmpc6lic4p9/job_working_directory/000/14/outputs/dataset_ac2d98e7-ff55-4a94-9e79-861b07d63528.dat' && echo DEBUG && ls 'outdir_gb'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T10:00:43.823779",
+"create_time": "2025-05-26T11:24:01.275241",
 "dependencies": [],
-"exit_code": 1,
+"exit_code": 0,
-"external_id": "114506",
+"external_id": "151844",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "66f8380583c086e1",
+"history_id": "fcc5b7d13a1328f6",
-"id": "7f406d9538852eeb",
+"id": "c9445e550eef23d0",
 "inputs": {
 "assembly_csv": {
-"id": "41ca6db0600d7999",
+"id": "c173cff58a987f8f",
 "src": "hda",
-"uuid": "1a1ee32d-eed7-47fd-b491-4f0799b44a85"
+"uuid": "2bdf436f-52cc-4c6e-afdb-3f051629900f"
 },
 "genbank_files1": {
-"id": "66f8380583c086e1",
+"id": "fcc5b7d13a1328f6",
 "src": "hda",
-"uuid": "44129191-5531-4cc9-b37b-fec4e3c677d5"
+"uuid": "465a53ab-8770-4514-a9b3-227f79646eb7"
 },
 "genbank_files10": {
-"id": "d3a48cfe9e5a1f02",
+"id": "cf75f655bb15877b",
 "src": "hda",
-"uuid": "c7cf96af-ab1c-4199-821f-5bb5b947752f"
+"uuid": "95699db9-77cf-4ae1-8454-4f255f3cb62a"
 },
 "genbank_files11": {
-"id": "4fffd7776804f395",
+"id": "744832bdd7ccd728",
 "src": "hda",
-"uuid": "0a5139e7-7d83-48f1-a1c9-458a1e72685c"
+"uuid": "11979c28-82ee-43c4-9e43-f34cb541f96b"
 },
 "genbank_files12": {
-"id": "193b12b5837c3789",
+"id": "855b83dd0dec8eab",
 "src": "hda",
-"uuid": "fb361f22-020c-4972-8661-f1f57d1a7afa"
+"uuid": "3f53cb86-2d2b-429a-bf51-e276bbe393fa"
 },
 "genbank_files2": {
-"id": "afa012b5b55ac394",
+"id": "df00a2d9def0cc87",
 "src": "hda",
-"uuid": "61f5f19f-147b-46fd-8900-a8530f311835"
+"uuid": "ae22d5d2-cde0-45b5-9e8e-67b5cbd586fa"
 },
 "genbank_files3": {
-"id": "c1bc3f2cd94aab77",
+"id": "d9e72a80becfe6e7",
 "src": "hda",
-"uuid": "440b34e7-490e-49bd-9b29-6afcabe5f6f6"
+"uuid": "e64057b1-43b3-4788-8891-77bcd297223c"
 },
 "genbank_files4": {
-"id": "f1661b71781d8acc",
+"id": "038c626e299361e9",
 "src": "hda",
-"uuid": "a3fca212-b8dc-4579-901c-612b806241af"
+"uuid": "1d1f9832-b58e-48c2-b1b3-6c3fb18e9890"
 },
 "genbank_files5": {
-"id": "e1129f30c30438be",
+"id": "c7c3cd49f3337c1a",
 "src": "hda",
-"uuid": "5398f2cb-1a25-45e5-9ba0-cd79a88b6e88"
+"uuid": "6732fc79-081e-4edf-bccc-a0087520172a"
 },
 "genbank_files6": {
-"id": "abbaf1e2c3c282ad",
+"id": "51c35891e43131e2",
 "src": "hda",
-"uuid": "f505293a-8223-4da2-a22c-aa261d4955ec"
+"uuid": "b17c7a49-3121-4292-95ff-51891aa066d1"
 },
 "genbank_files7": {
-"id": "18bb6cd07b986e37",
+"id": "84db48b219855f4d",
 "src": "hda",
-"uuid": "c50e4b1f-c72a-4272-b324-e1c2c7d50293"
+"uuid": "2811f816-8532-4ddd-8e29-9a6ed7dad54e"
 },
 "genbank_files8": {
-"id": "82689942017f4326",
+"id": "cf00b67a5455eb5a",
 "src": "hda",
-"uuid": "00d79560-f944-4d8e-98e7-f516684a6100"
+"uuid": "e74d0182-807e-40a8-b67a-ac088fc2e02c"
 },
 "genbank_files9": {
-"id": "ecc2b8a59c690090",
+"id": "a3780ecc1a00a0d8",
 "src": "hda",
-"uuid": "3d5bb0fb-d610-4939-8fc5-999174fee5ca"
+"uuid": "9dc55c98-4ab9-4272-a680-9b3129954367"
 }
 },
-"job_messages": [
+"job_messages": [],
-{
-"code_desc": "",
-"desc": "Fatal error: Exit code 1 ()",
-"error_level": 3,
-"exit_code": 1,
-"type": "exit_code"
-}
-],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "afa012b5b55ac394",
+"id": "df00a2d9def0cc87",
 "src": "hdca"
 }
 },
 "outputs": {
+"__new_primary_file_construct_gb|construct_1__": {
+"id": "fedb85639c7c80b9",
+"src": "hda",
+"uuid": "4bf90377-e4de-4d13-8ebc-39a53494ea2a"
+},
+"__new_primary_file_construct_gb|construct_2__": {
+"id": "bd75ec7b3d9705ea",
+"src": "hda",
+"uuid": "ac9bac0c-348b-46b7-a882-60f56867cc30"
+},
+"__new_primary_file_construct_gb|construct_3__": {
+"id": "7eb30039064fccdd",
+"src": "hda",
+"uuid": "48e39545-a44e-410b-859b-01fcf6189002"
+},
+"__new_primary_file_construct_gb|construct_4__": {
+"id": "61cc0a7b70456dfd",
+"src": "hda",
+"uuid": "df8aca7f-8413-430f-b35f-7dac694ee0b6"
+},
 "output_zip": {
-"id": "7f406d9538852eeb",
+"id": "c9445e550eef23d0",
 "src": "hda",
-"uuid": "acb064d7-2781-46fe-98df-716fee024c8d"
+"uuid": "ac2d98e7-ff55-4a94-9e79-861b07d63528"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
-"state": "error",
+"state": "ok",
-"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",
+"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,  2.38it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.18it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.77it/s, now=None]\r                                                                 \r",
-"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",
+"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",
 "tool_id": "cloning_simulation",
-"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",
+"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,  2.38it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.18it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.77it/s, now=None]\r                                                                 \r",
-"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",
+"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",
-"update_time": "2025-05-26T10:00:52.817543",
+"update_time": "2025-05-26T11:24:14.526803",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "66f8380583c086e1"
+"user_id": "fcc5b7d13a1328f6"
 },
-"output_problems": [
+"status": "success",
-"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.",
-"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.",
-"Output collection 'construct_gb': expected to have 4 elements, but it had 0."
-],
-"status": "failure",
 "test_index": 0,
-"time_seconds": 51.33188271522522,
+"time_seconds": 53.70547914505005,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-0"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "3abc48ca4f3e8d37",
+"id": "3af58a5242e85ea6",
 "src": "hda"
 },
 "assembly_plan_name": "GibsonAssembly",
 "genbank_files": {
-"id": "c1bc3f2cd94aab77",
+"id": "d9e72a80becfe6e7",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"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'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/1/d/6/dataset_1d624c24-e864-463a-9fd3-0c63fd46cbd2.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/5/0/5/dataset_505aafa2-5e9c-44bb-9d26-3f3e6248fc9b.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/5/0/5/dataset_505aafa2-5e9c-44bb-9d26-3f3e6248fc9b.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/tmpc6lic4p9/job_working_directory/000/17/outputs/dataset_0f617192-e625-4d9e-8358-0b9b1b0aa024.dat' && echo DEBUG && ls 'outdir_gb'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T10:01:03.681089",
+"create_time": "2025-05-26T11:24:25.394299",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "114833",
+"external_id": "152204",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "afa012b5b55ac394",
+"history_id": "df00a2d9def0cc87",
-"id": "991084752433b654",
+"id": "7eb30039064fccdd",
 "inputs": {
 "assembly_csv": {
-"id": "3abc48ca4f3e8d37",
+"id": "3af58a5242e85ea6",
 "src": "hda",
-"uuid": "6eb20de3-662c-4428-907f-29cbe0a5cc20"
+"uuid": "1d624c24-e864-463a-9fd3-0c63fd46cbd2"
 },
 "genbank_files1": {
-"id": "9677ca5db33658a1",
+"id": "3b85967b9c87a1cc",
 "src": "hda",
-"uuid": "b6fe141d-f27d-475d-95fd-501e032f0c3b"
+"uuid": "505aafa2-5e9c-44bb-9d26-3f3e6248fc9b"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "f1661b71781d8acc",
+"id": "038c626e299361e9",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "400090ecd3303f56",
+"id": "9773f41fb184880d",
 "src": "hda",
-"uuid": "e24f4e4b-a2c0-4ebc-ac8a-e80cb0ce1266"
+"uuid": "0d66c887-a6a3-4fd6-978a-9c0e2ce4b317"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "974cc872eaa7d6a0",
+"id": "41b44b0c750630a6",
 "src": "hda",
-"uuid": "baec54da-c9df-4fb2-a156-7aaaabc3ee2d"
+"uuid": "be7e7183-3b0d-40dd-9908-3e8dcd7f80bf"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "8586d482e8f05e33",
+"id": "bfc60c3d9bac68ee",
 "src": "hda",
-"uuid": "8649dd5f-afe7-44fa-b07c-aba6fdb3c6fc"
+"uuid": "2c7f645c-33d1-4a91-9608-221494b22be4"
 },
 "output_zip": {
-"id": "991084752433b654",
+"id": "5c8c8c874b5b07c6",
 "src": "hda",
-"uuid": "41d853b4-adb6-4605-bbaf-d7178b962d92"
+"uuid": "0f617192-e625-4d9e-8358-0b9b1b0aa024"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"GibsonAssembly\"",
-"chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"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",
+"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,  4.24it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.27it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.28it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.48it/s, now=None]\r                                                                 \r",
-"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",
+"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...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\n",
 "tool_id": "cloning_simulation",
-"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",
+"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,  4.24it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.27it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.28it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.48it/s, now=None]\r                                                                 \r",
-"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",
+"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...\nDEBUG\nconstruct_1.gb\nconstruct_2.gb\nconstruct_3.gb\n",
-"update_time": "2025-05-26T10:01:15.563285",
+"update_time": "2025-05-26T11:24:37.446583",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "66f8380583c086e1"
+"user_id": "fcc5b7d13a1328f6"
 },
 "status": "success",
 "test_index": 1,
-"time_seconds": 22.980356216430664,
+"time_seconds": 22.626197814941406,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-1"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "94fb43fdf96ceebf",
+"id": "48d1542b43af9171",
 "src": "hda"
 },
 "assembly_plan_name": "LigaseCyclingReactionAssembly",
 "genbank_files": {
-"id": "e1129f30c30438be",
+"id": "c7c3cd49f3337c1a",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"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'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/a/1/f/dataset_a1f989b9-e79f-4bd7-9cf3-66675c1d1e94.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/a/6/1/dataset_a617ae1f-70e3-4873-bdcc-f2268ffeaad4.dat,/tmp/tmpc6lic4p9/files/9/4/1/dataset_941b4e95-600a-485c-a3fa-1dcf0defdd76.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/a/6/1/dataset_a617ae1f-70e3-4873-bdcc-f2268ffeaad4.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpc6lic4p9/files/9/4/1/dataset_941b4e95-600a-485c-a3fa-1dcf0defdd76.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/tmpc6lic4p9/job_working_directory/000/21/outputs/dataset_827e64a1-7f84-4f9e-8468-eabb3684efa3.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T10:01:27.721793",
+"create_time": "2025-05-26T11:24:49.729783",
-"dependencies": [
+"dependencies": [],
-{
-"cacheable": false,
-"dependency_resolver": {
-"auto_init": true,
-"auto_install": true,
-"can_uninstall_dependencies": true,
-"ensure_channels": "conda-forge,bioconda",
-"model_class": "CondaDependencyResolver",
-"prefix": "/home/rkhaled/miniconda3",
-"read_only": false,
-"resolver_type": "conda",
-"resolves_simple_dependencies": true,
-"use_local": false,
-"versionless": false
-},
-"dependency_type": "conda",
-"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
-"exact": true,
-"model_class": "MergedCondaDependency",
-"name": "flametree",
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-{
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-"can_uninstall_dependencies": true,
-"ensure_channels": "conda-forge,bioconda",
-"model_class": "CondaDependencyResolver",
-"prefix": "/home/rkhaled/miniconda3",
-"read_only": false,
-"resolver_type": "conda",
-"resolves_simple_dependencies": true,
-"use_local": false,
-"versionless": false
-},
-"dependency_type": "conda",
-"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
-"exact": true,
-"model_class": "MergedCondaDependency",
-"name": "biopython",
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-{
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-"auto_install": true,
-"can_uninstall_dependencies": true,
-"ensure_channels": "conda-forge,bioconda",
-"model_class": "CondaDependencyResolver",
-"prefix": "/home/rkhaled/miniconda3",
-"read_only": false,
-"resolver_type": "conda",
-"resolves_simple_dependencies": true,
-"use_local": false,
-"versionless": false
-},
-"dependency_type": "conda",
-"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
-"exact": true,
-"model_class": "MergedCondaDependency",
-"name": "proglog",
-"version": "0.1.10"
-},
-{
-"cacheable": false,
-"dependency_resolver": {
-"auto_init": true,
-"auto_install": true,
-"can_uninstall_dependencies": true,
-"ensure_channels": "conda-forge,bioconda",
-"model_class": "CondaDependencyResolver",
-"prefix": "/home/rkhaled/miniconda3",
-"read_only": false,
-"resolver_type": "conda",
-"resolves_simple_dependencies": true,
-"use_local": false,
-"versionless": false
-},
-"dependency_type": "conda",
-"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
-"exact": true,
-"model_class": "MergedCondaDependency",
-"name": "pandas",
-"version": "2.2.3"
-},
-{
-"cacheable": false,
-"dependency_resolver": {
-"auto_init": true,
-"auto_install": true,
-"can_uninstall_dependencies": true,
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-"model_class": "CondaDependencyResolver",
-"prefix": "/home/rkhaled/miniconda3",
-"read_only": false,
-"resolver_type": "conda",
-"resolves_simple_dependencies": true,
-"use_local": false,
-"versionless": false
-},
-"dependency_type": "conda",
-"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
-"exact": true,
-"model_class": "MergedCondaDependency",
-"name": "dnacauldron",
-"version": "2.0.12"
-},
-{
-"cacheable": false,
-"dependency_resolver": {
-"auto_init": true,
-"auto_install": true,
-"can_uninstall_dependencies": true,
-"ensure_channels": "conda-forge,bioconda",
-"model_class": "CondaDependencyResolver",
-"prefix": "/home/rkhaled/miniconda3",
-"read_only": false,
-"resolver_type": "conda",
-"resolves_simple_dependencies": true,
-"use_local": false,
-"versionless": false
-},
-"dependency_type": "conda",
-"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
-"exact": true,
-"model_class": "MergedCondaDependency",
-"name": "pdf-reports",
-"version": "0.3.9"
-},
-{
-"cacheable": false,
-"dependency_resolver": {
-"auto_init": true,
-"auto_install": true,
-"can_uninstall_dependencies": true,
-"ensure_channels": "conda-forge,bioconda",
-"model_class": "CondaDependencyResolver",
-"prefix": "/home/rkhaled/miniconda3",
-"read_only": false,
-"resolver_type": "conda",
-"resolves_simple_dependencies": true,
-"use_local": false,
-"versionless": false
-},
-"dependency_type": "conda",
-"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
-"exact": true,
-"model_class": "MergedCondaDependency",
-"name": "sequenticon",
-"version": "0.1.8"
-},
-{
-"cacheable": false,
-"dependency_resolver": {
-"auto_init": true,
-"auto_install": true,
-"can_uninstall_dependencies": true,
-"ensure_channels": "conda-forge,bioconda",
-"model_class": "CondaDependencyResolver",
-"prefix": "/home/rkhaled/miniconda3",
-"read_only": false,
-"resolver_type": "conda",
-"resolves_simple_dependencies": true,
-"use_local": false,
-"versionless": false
-},
-"dependency_type": "conda",
-"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
-"exact": true,
-"model_class": "MergedCondaDependency",
-"name": "dna_features_viewer",
-"version": "3.1.5"
-}
-],
 "exit_code": 0,
-"external_id": "115234",
+"external_id": "152654",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "c1bc3f2cd94aab77",
+"history_id": "d9e72a80becfe6e7",
-"id": "de23ac49d5c4a7c8",
+"id": "5c8c8c874b5b07c6",
 "inputs": {
 "assembly_csv": {
-"id": "94fb43fdf96ceebf",
+"id": "48d1542b43af9171",
 "src": "hda",
-"uuid": "469df048-1608-4e28-a8c3-576433c72c7f"
+"uuid": "a1f989b9-e79f-4bd7-9cf3-66675c1d1e94"
 },
 "genbank_files1": {
-"id": "de23ac49d5c4a7c8",
+"id": "b8df5ed9fe071f18",
 "src": "hda",
-"uuid": "18952cef-c715-4776-9f53-69156da89d01"
+"uuid": "a617ae1f-70e3-4873-bdcc-f2268ffeaad4"
 },
 "genbank_files2": {
-"id": "de6580a03a572321",
+"id": "6de9142d4b5ca725",
 "src": "hda",
-"uuid": "81322056-69eb-4dcd-88ee-6cb78ff617db"
+"uuid": "941b4e95-600a-485c-a3fa-1dcf0defdd76"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "abbaf1e2c3c282ad",
+"id": "51c35891e43131e2",
 "src": "hdca"
 }
 },
 "outputs": {
 "output_zip": {
-"id": "fdc5ed0a88852c9a",
+"id": "56521fbfdcb4ef20",
 "src": "hda",
-"uuid": "d2df6190-9462-41aa-92d2-d4a5c1a605d3"
+"uuid": "827e64a1-7f84-4f9e-8468-eabb3684efa3"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"",
-"chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"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",
+"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,  2.16it/s, now=None]\r                                                                 \r",
 "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",
 "tool_id": "cloning_simulation",
-"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",
+"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,  2.16it/s, now=None]\r                                                                 \r",
 "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",
-"update_time": "2025-05-26T10:01:40.416074",
+"update_time": "2025-05-26T11:25:02.028309",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "66f8380583c086e1"
+"user_id": "fcc5b7d13a1328f6"
 },
 "status": "success",
 "test_index": 2,
-"time_seconds": 24.68060541152954,
+"time_seconds": 24.395533084869385,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-2"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "b07ae8db70ca0b69",
+"id": "2b17a3fa18c23b8a",
 "src": "hda"
 },
 "assembly_plan_name": "BASICAssembly",
 "genbank_files": {
-"id": "18bb6cd07b986e37",
+"id": "84db48b219855f4d",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"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'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/6/b/e/dataset_6be38f7d-b5c4-4308-85d1-3bd6b4dae4fc.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/c/b/a/dataset_cba9b297-4dfe-4063-8510-6c48a1b6b7a1.dat,/tmp/tmpc6lic4p9/files/3/e/8/dataset_3e8dfce1-7a05-4665-9277-388e3aa42581.dat,/tmp/tmpc6lic4p9/files/a/5/d/dataset_a5d093c2-0087-453e-b7d1-d94a7cb664e0.dat,/tmp/tmpc6lic4p9/files/0/e/c/dataset_0ec72cc0-2a95-474b-aa77-7a436dad6a9b.dat,/tmp/tmpc6lic4p9/files/d/2/7/dataset_d272199f-2e1b-49e1-a597-5ffa11507e83.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/c/b/a/dataset_cba9b297-4dfe-4063-8510-6c48a1b6b7a1.dat:GFP.gb,/tmp/tmpc6lic4p9/files/3/e/8/dataset_3e8dfce1-7a05-4665-9277-388e3aa42581.dat:p15A_kan.gb,/tmp/tmpc6lic4p9/files/a/5/d/dataset_a5d093c2-0087-453e-b7d1-d94a7cb664e0.dat:promoter.gb,/tmp/tmpc6lic4p9/files/0/e/c/dataset_0ec72cc0-2a95-474b-aa77-7a436dad6a9b.dat:RFP.gb,/tmp/tmpc6lic4p9/files/d/2/7/dataset_d272199f-2e1b-49e1-a597-5ffa11507e83.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/tmpc6lic4p9/job_working_directory/000/28/outputs/dataset_7435335e-896e-47f4-89c7-3a6c2c25f247.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T10:02:02.222212",
+"create_time": "2025-05-26T11:25:23.055332",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "115859",
+"external_id": "153248",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "f1661b71781d8acc",
+"history_id": "038c626e299361e9",
-"id": "80951ee9dc2649e8",
+"id": "56521fbfdcb4ef20",
 "inputs": {
 "assembly_csv": {
-"id": "b07ae8db70ca0b69",
+"id": "2b17a3fa18c23b8a",
 "src": "hda",
-"uuid": "11b19080-d21f-4a3e-a516-77bb7f1eb8ff"
+"uuid": "6be38f7d-b5c4-4308-85d1-3bd6b4dae4fc"
 },
 "genbank_files1": {
-"id": "cd28fb0d133db699",
+"id": "aed8b1a22d89d8c9",
 "src": "hda",
-"uuid": "c13c3bb5-74f3-49b4-979e-08064cbcd96e"
+"uuid": "cba9b297-4dfe-4063-8510-6c48a1b6b7a1"
 },
 "genbank_files2": {
-"id": "204f425176d83e80",
+"id": "eba7a310b55aafdd",
 "src": "hda",
-"uuid": "220d8ce3-65a2-4880-9924-e41f685e1386"
+"uuid": "3e8dfce1-7a05-4665-9277-388e3aa42581"
 },
 "genbank_files3": {
-"id": "a412e91f962611fc",
+"id": "eca1089322e0a5fc",
 "src": "hda",
-"uuid": "264d7e95-807d-45aa-ada7-244e7896dd95"
+"uuid": "a5d093c2-0087-453e-b7d1-d94a7cb664e0"
 },
 "genbank_files4": {
-"id": "80951ee9dc2649e8",
+"id": "0b586e83183b9891",
 "src": "hda",
-"uuid": "7eede81c-a796-4189-94df-82245763e19f"
+"uuid": "0ec72cc0-2a95-474b-aa77-7a436dad6a9b"
 },
 "genbank_files5": {
-"id": "02cc6fb051fdc602",
+"id": "18d15f79e0c5cee5",
 "src": "hda",
-"uuid": "c9537938-db0d-4d07-9eee-2cfeec50a90d"
+"uuid": "d272199f-2e1b-49e1-a597-5ffa11507e83"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "82689942017f4326",
+"id": "cf00b67a5455eb5a",
 "src": "hdca"
 }
 },
 "outputs": {
 "output_zip": {
-"id": "68883cc453ec32a5",
+"id": "684e8d7e5eb8731e",
 "src": "hda",
-"uuid": "b055edc9-ea72-46ca-8971-352c46db387e"
+"uuid": "7435335e-896e-47f4-89c7-3a6c2c25f247"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"BASICAssembly\"",
-"chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"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",
+"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, 50.04it/s, now=None]\r                                                                 \r",
-"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",
+"stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"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",
+"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, 50.04it/s, now=None]\r                                                                 \r",
-"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",
+"tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T10:02:12.965513",
+"update_time": "2025-05-26T11:25:33.071688",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "66f8380583c086e1"
+"user_id": "fcc5b7d13a1328f6"
 },
 "status": "success",
 "test_index": 3,
-"time_seconds": 32.275617599487305,
+"time_seconds": 30.88078260421753,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-3"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "ab2d796f030478a4",
+"id": "8484dc7b019fd65a",
 "src": "hda"
 },
 "assembly_plan_name": "BioBrickStandardAssembly",
 "genbank_files": {
-"id": "ecc2b8a59c690090",
+"id": "a3780ecc1a00a0d8",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"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'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/8/e/2/dataset_8e2dcaab-3dd7-48c4-920e-bdffaad39793.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/d/4/2/dataset_d4271a43-8722-4344-9562-00e9a36d07e5.dat,/tmp/tmpc6lic4p9/files/2/4/8/dataset_2484bbfb-d4b0-4c8b-a57f-675625f98753.dat,/tmp/tmpc6lic4p9/files/8/3/f/dataset_83f035f7-25fc-4a59-83b2-d377e3cd59ad.dat,/tmp/tmpc6lic4p9/files/5/a/a/dataset_5aa7b19e-0ad1-43b1-9083-954067ff2010.dat,/tmp/tmpc6lic4p9/files/d/6/4/dataset_d646b71c-5393-4291-bcc5-7d6cbe22f055.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/d/4/2/dataset_d4271a43-8722-4344-9562-00e9a36d07e5.dat:BBa_E0040_GFP.gb,/tmp/tmpc6lic4p9/files/2/4/8/dataset_2484bbfb-d4b0-4c8b-a57f-675625f98753.dat:BBa_J23119_prom.gb,/tmp/tmpc6lic4p9/files/8/3/f/dataset_83f035f7-25fc-4a59-83b2-d377e3cd59ad.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpc6lic4p9/files/5/a/a/dataset_5aa7b19e-0ad1-43b1-9083-954067ff2010.dat:BBa_J61048_term.gb,/tmp/tmpc6lic4p9/files/d/6/4/dataset_d646b71c-5393-4291-bcc5-7d6cbe22f055.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/tmpc6lic4p9/job_working_directory/000/35/outputs/dataset_8086c8c0-24b8-4a51-84db-6b4c9b0e76d0.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T10:02:34.725504",
+"create_time": "2025-05-26T11:25:53.885012",
-"dependencies": [],
+"dependencies": [
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "flametree",
+"version": "0.1.11"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "biopython",
+"version": "1.85"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "proglog",
+"version": "0.1.10"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "pandas",
+"version": "2.2.3"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "dnacauldron",
+"version": "2.0.12"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "pdf-reports",
+"version": "0.3.9"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "sequenticon",
+"version": "0.1.8"
+},
+{
+"cacheable": false,
+"dependency_resolver": {
+"auto_init": true,
+"auto_install": true,
+"can_uninstall_dependencies": true,
+"ensure_channels": "conda-forge,bioconda",
+"model_class": "CondaDependencyResolver",
+"prefix": "/home/rkhaled/miniconda3",
+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
+"versionless": false
+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
+"name": "dna_features_viewer",
+"version": "3.1.5"
+}
+],
 "exit_code": 0,
-"external_id": "116476",
+"external_id": "153816",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "e1129f30c30438be",
+"history_id": "c7c3cd49f3337c1a",
-"id": "2edb1d8c4fcdfa57",
+"id": "684e8d7e5eb8731e",
 "inputs": {
 "assembly_csv": {
-"id": "ab2d796f030478a4",
+"id": "8484dc7b019fd65a",
 "src": "hda",
-"uuid": "56e880bc-1f93-495f-bfa8-0873cb8182a9"
+"uuid": "8e2dcaab-3dd7-48c4-920e-bdffaad39793"
 },
 "genbank_files1": {
-"id": "70033f808724210d",
+"id": "f007b0e97c7852a9",
 "src": "hda",
-"uuid": "dded78e6-5d3a-466d-a378-5793c801f32c"
+"uuid": "d4271a43-8722-4344-9562-00e9a36d07e5"
 },
 "genbank_files2": {
-"id": "e4c403c1aada23ec",
+"id": "0776247cf19fcdeb",
 "src": "hda",
-"uuid": "2a07a992-6527-4ac7-9c49-7fd9acbdea57"
+"uuid": "2484bbfb-d4b0-4c8b-a57f-675625f98753"
 },
 "genbank_files3": {
-"id": "afa1993aa783dac3",
+"id": "428c69cf899eb78e",
 "src": "hda",
-"uuid": "12faa3d9-c95d-4c34-9df7-6c53174d4276"
+"uuid": "83f035f7-25fc-4a59-83b2-d377e3cd59ad"
 },
 "genbank_files4": {
-"id": "2edb1d8c4fcdfa57",
+"id": "6576e427b69a444e",
 "src": "hda",
-"uuid": "581a4c55-0ce2-4c3b-a380-756448871f32"
+"uuid": "5aa7b19e-0ad1-43b1-9083-954067ff2010"
 },
 "genbank_files5": {
-"id": "cc59f77d482719ba",
+"id": "bd5ff021b11f5160",
 "src": "hda",
-"uuid": "abf255f7-9841-4991-9b65-598df368ff85"
+"uuid": "d646b71c-5393-4291-bcc5-7d6cbe22f055"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "d3a48cfe9e5a1f02",
+"id": "cf75f655bb15877b",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|C1_prom_barcode__": {
-"id": "b5e4bb927c5912de",
+"id": "db302e29238adc09",
 "src": "hda",
-"uuid": "1689e287-c7c5-488c-b397-a0d14018a93a"
+"uuid": "d9b71247-a39f-49ea-b279-18a95173730d"
 },
 "__new_primary_file_construct_gb|C2_gfp_term__": {
-"id": "924199a1dc6199a2",
+"id": "a0c89ee18eccf84a",
 "src": "hda",
-"uuid": "82e60c5f-9305-4962-984c-4e667dc08972"
+"uuid": "cf4710c7-cf67-4f0e-a486-606e525f5689"
 },
 "__new_primary_file_construct_gb|C3_final__": {
-"id": "f95eef361447e9a0",
+"id": "b326684e3f9ff9a4",
 "src": "hda",
-"uuid": "50703365-ca24-444a-8cc2-ac9467884479"
+"uuid": "a4ed1a6f-9385-45da-9eda-3fae86d46b5b"
 },
 "output_zip": {
-"id": "5165064d73efc2e3",
+"id": "e3a5c74dec901fc5",
 "src": "hda",
-"uuid": "d5e2affd-9228-4b21-8e89-36a43c59ab37"
+"uuid": "8086c8c0-24b8-4a51-84db-6b4c9b0e76d0"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"BioBrickStandardAssembly\"",
-"chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"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",
+"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 [00:00<00:00,  2.10it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.72it/s, now=None]\r                                                                 \r",
-"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",
+"stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"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",
+"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 [00:00<00:00,  2.10it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.72it/s, now=None]\r                                                                 \r",
-"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",
+"tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T10:02:47.655383",
+"update_time": "2025-05-26T11:26:06.650033",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "66f8380583c086e1"
+"user_id": "fcc5b7d13a1328f6"
 },
 "status": "success",
 "test_index": 4,
-"time_seconds": 34.81275129318237,
+"time_seconds": 33.60218787193298,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-4"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "3494efe97c2aacb8",
+"id": "ffdd8176dffd877d",
 "src": "hda"
 },
 "assembly_plan_name": "Type2sRestrictionAssembly",
 "domesticated_input": {
-"id": "4fffd7776804f395",
+"id": "744832bdd7ccd728",
 "src": "hdca"
 },
 "genbank_files": {
-"id": "193b12b5837c3789",
+"id": "855b83dd0dec8eab",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"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'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/9/8/e/dataset_98e1b862-2d3e-4164-aecf-56bd464d0f11.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/b/6/6/dataset_b66afa5b-682d-49f8-9753-c78c356ff228.dat,/tmp/tmpc6lic4p9/files/4/6/e/dataset_46ea3fb9-8e60-42f3-b7d3-c1a6edc1837c.dat,/tmp/tmpc6lic4p9/files/8/3/5/dataset_8358e657-0e61-486b-adb4-e886f0f354ba.dat,/tmp/tmpc6lic4p9/files/4/c/f/dataset_4cfbb2dd-c5a5-42fe-889b-da6510422b72.dat,/tmp/tmpc6lic4p9/files/2/8/c/dataset_28c96444-abfb-4173-970e-e895146aef97.dat,/tmp/tmpc6lic4p9/files/f/5/4/dataset_f54c7a16-ac6f-42c2-9b6c-345af3050d83.dat,/tmp/tmpc6lic4p9/files/2/a/3/dataset_2a330eb7-d033-4e75-be7a-4473748a6f2d.dat' --domesticated_seq '/tmp/tmpc6lic4p9/files/6/8/7/dataset_6877c227-2c70-4080-962e-ee1855dd797f.dat,/tmp/tmpc6lic4p9/files/e/2/1/dataset_e212262c-a336-4263-a076-2cd300590ba4.dat,/tmp/tmpc6lic4p9/files/4/1/1/dataset_4112d545-7e37-4a6e-8ca8-7c1b8f90a71e.dat,/tmp/tmpc6lic4p9/files/b/3/1/dataset_b31955ce-ea44-4e3a-86a1-6aebc47be841.dat,/tmp/tmpc6lic4p9/files/d/4/d/dataset_d4d14388-55d3-4aec-810d-aa902028f29f.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/b/6/6/dataset_b66afa5b-682d-49f8-9753-c78c356ff228.dat:part_A.gb,/tmp/tmpc6lic4p9/files/4/6/e/dataset_46ea3fb9-8e60-42f3-b7d3-c1a6edc1837c.dat:part_B.gb,/tmp/tmpc6lic4p9/files/8/3/5/dataset_8358e657-0e61-486b-adb4-e886f0f354ba.dat:part_C.gb,/tmp/tmpc6lic4p9/files/4/c/f/dataset_4cfbb2dd-c5a5-42fe-889b-da6510422b72.dat:part_D.gb,/tmp/tmpc6lic4p9/files/2/8/c/dataset_28c96444-abfb-4173-970e-e895146aef97.dat:part_E.gb,/tmp/tmpc6lic4p9/files/f/5/4/dataset_f54c7a16-ac6f-42c2-9b6c-345af3050d83.dat:part_F.gb,/tmp/tmpc6lic4p9/files/2/a/3/dataset_2a330eb7-d033-4e75-be7a-4473748a6f2d.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpc6lic4p9/files/6/8/7/dataset_6877c227-2c70-4080-962e-ee1855dd797f.dat:part_H.gb,/tmp/tmpc6lic4p9/files/e/2/1/dataset_e212262c-a336-4263-a076-2cd300590ba4.dat:part_I.gb,/tmp/tmpc6lic4p9/files/4/1/1/dataset_4112d545-7e37-4a6e-8ca8-7c1b8f90a71e.dat:part_J.gb,/tmp/tmpc6lic4p9/files/b/3/1/dataset_b31955ce-ea44-4e3a-86a1-6aebc47be841.dat:part_K.gb,/tmp/tmpc6lic4p9/files/d/4/d/dataset_d4d14388-55d3-4aec-810d-aa902028f29f.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/tmpc6lic4p9/job_working_directory/000/49/outputs/dataset_77f39d12-532c-468b-bcf7-fcc1fdedd34c.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T10:03:29.120983",
+"create_time": "2025-05-26T11:26:47.030790",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "117561",
+"external_id": "154908",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "abbaf1e2c3c282ad",
+"history_id": "51c35891e43131e2",
-"id": "3494efe97c2aacb8",
+"id": "0b19a103e85bbfbf",
 "inputs": {
 "assembly_csv": {
-"id": "3494efe97c2aacb8",
+"id": "ffdd8176dffd877d",
 "src": "hda",
-"uuid": "6c2089de-5285-4ae6-8e08-afa38810c0ee"
+"uuid": "98e1b862-2d3e-4164-aecf-56bd464d0f11"
 },
 "domesticated_input1": {
-"id": "a4800f28d8ead13a",
+"id": "96e47893a0f61173",
 "src": "hda",
-"uuid": "0f38d420-af2a-42ba-a6d3-f16807653402"
+"uuid": "6877c227-2c70-4080-962e-ee1855dd797f"
 },
 "domesticated_input2": {
-"id": "73a220014461252c",
+"id": "07b1a06cea2f6611",
 "src": "hda",
-"uuid": "0b653ed4-f458-4567-b9b7-074257934433"
+"uuid": "e212262c-a336-4263-a076-2cd300590ba4"
 },
 "domesticated_input3": {
-"id": "7d1b502fc1fb844a",
+"id": "7c42ebb9622f8a60",
 "src": "hda",
-"uuid": "70d7c859-83f1-4aa7-b1db-fee1b4d384c0"
+"uuid": "4112d545-7e37-4a6e-8ca8-7c1b8f90a71e"
 },
 "domesticated_input4": {
-"id": "6a344bf502116f62",
+"id": "33456f383510d381",
 "src": "hda",
-"uuid": "ce2505e6-35c7-4858-a27e-6c5761a35be3"
+"uuid": "b31955ce-ea44-4e3a-86a1-6aebc47be841"
 },
 "domesticated_input5": {
-"id": "a28d730bd7e6d71e",
+"id": "3c2a17e7ec6c065d",
 "src": "hda",
-"uuid": "68b8d30e-6c0c-466f-a70c-0e58bcc27e0d"
+"uuid": "d4d14388-55d3-4aec-810d-aa902028f29f"
 },
 "genbank_files1": {
-"id": "b4c6f22fd42e2fbc",
+"id": "c2ddc784389f17d2",
 "src": "hda",
-"uuid": "b68d8dba-f098-4f14-ac9f-b69541a834c8"
+"uuid": "b66afa5b-682d-49f8-9753-c78c356ff228"
 },
 "genbank_files2": {
-"id": "60c65d41f8ff0e9b",
+"id": "79b5ff6df7bc6716",
 "src": "hda",
-"uuid": "a94042d7-2d70-4257-bbc5-ac3f2be93aff"
+"uuid": "46ea3fb9-8e60-42f3-b7d3-c1a6edc1837c"
 },
 "genbank_files3": {
-"id": "554995f2d7672bb2",
+"id": "6f172ec7c3220722",
 "src": "hda",
-"uuid": "1de72341-f4c1-48df-9466-a1c80e23fdfb"
+"uuid": "8358e657-0e61-486b-adb4-e886f0f354ba"
 },
 "genbank_files4": {
-"id": "9450471e42664058",
+"id": "0b19a103e85bbfbf",
 "src": "hda",
-"uuid": "c1128abd-86a1-48b9-b66c-0152d76c85c9"
+"uuid": "4cfbb2dd-c5a5-42fe-889b-da6510422b72"
 },
 "genbank_files5": {
-"id": "9a370553f77d6a31",
+"id": "00fa99289b8a441d",
 "src": "hda",
-"uuid": "2f2ab7b7-d6ef-4a2e-90b8-f15cddf56eea"
+"uuid": "28c96444-abfb-4173-970e-e895146aef97"
 },
 "genbank_files6": {
-"id": "cecfeefdcb127887",
+"id": "95a08e54dcf8e4b4",
 "src": "hda",
-"uuid": "90485827-d839-4e32-b546-9c32f77fd264"
+"uuid": "f54c7a16-ac6f-42c2-9b6c-345af3050d83"
 },
 "genbank_files7": {
-"id": "88bfe38878128ef9",
+"id": "46fceb9ab6cb9139",
 "src": "hda",
-"uuid": "7c56a071-e9fe-4133-8a99-8a7d58e7b1fd"
+"uuid": "2a330eb7-d033-4e75-be7a-4473748a6f2d"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "41ca6db0600d7999",
+"id": "c173cff58a987f8f",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "1750f123cc89cd74",
+"id": "887639ccacb877d4",
 "src": "hda",
-"uuid": "2402ee1c-8048-48aa-9180-d84ffbac4c0d"
+"uuid": "ac0f5082-55fc-4fb6-b3ef-f2587cdd2662"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "0a1a12a9af9d8d2a",
+"id": "97c509c62c06ea77",
 "src": "hda",
-"uuid": "4f5260cc-c112-4966-83c6-f3cd6f9cdd09"
+"uuid": "9e439105-9563-450d-96a3-bec58242389e"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "a7850a538357f009",
+"id": "05372c5ab71bbd4d",
 "src": "hda",
-"uuid": "d2eb027d-9f28-4cf0-bd60-f8856220a681"
+"uuid": "13079e9f-8185-4b43-898a-83348a3fe55b"
 },
 "__new_primary_file_construct_gb|construct_4__": {
-"id": "eeb0994ae957c814",
+"id": "14e667eccbf3c9ac",
 "src": "hda",
-"uuid": "df9e0b45-10c1-46a2-a1bf-fccc2817a77e"
+"uuid": "4aec2395-19a8-49b5-a927-39b5b06dabe7"
 },
 "output_zip": {
-"id": "4d7f94dc70c8b750",
+"id": "edb47c5501e52d48",
 "src": "hda",
-"uuid": "445bab41-baa4-4de1-adfc-d4fd56892c5f"
+"uuid": "77f39d12-532c-468b-bcf7-fcc1fdedd34c"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": "{\"values\": [{\"id\": 11, \"src\": \"hdca\"}]}",
 "genbank_files": "{\"values\": [{\"id\": 12, \"src\": \"hdca\"}]}",
 "topology": "\"circular\""
 },
 "state": "ok",
-"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",
+"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,  2.14it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.74it/s, now=None]\r                                                                 \r",
-"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",
+"stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"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",
+"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,  2.14it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.74it/s, now=None]\r                                                                 \r",
-"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",
+"tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T10:03:41.864270",
+"update_time": "2025-05-26T11:27:00.365017",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "66f8380583c086e1"
+"user_id": "fcc5b7d13a1328f6"
 },
 "status": "success",
 "test_index": 5,
-"time_seconds": 53.94194722175598,
+"time_seconds": 53.75153422355652,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-5"
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "6fb8fb3f063f475d",
+"id": "59a0a00f5fa501d5",
 "src": "hda"
 },
 "assembly_plan_name": "Type2sRestrictionAssembly",
 "domesticated_input": {
-"id": "7f406d9538852eeb",
+"id": "c9445e550eef23d0",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"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'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpc6lic4p9/files/9/5/0/dataset_9504897d-0d99-44a4-9033-7d14e3943ec9.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpc6lic4p9/files/a/c/d/dataset_acd9e546-bb31-4391-b867-1d81cab10920.dat,/tmp/tmpc6lic4p9/files/c/f/e/dataset_cfe852f6-5b32-46fd-a9d8-2b777016d403.dat,/tmp/tmpc6lic4p9/files/2/5/b/dataset_25be2770-f768-4b0e-be96-459e47e6ae8d.dat,/tmp/tmpc6lic4p9/files/e/5/8/dataset_e580f806-e8ba-4dac-b8d5-6b76b4a7421b.dat,/tmp/tmpc6lic4p9/files/0/d/6/dataset_0d6de31a-aab1-427f-a2a1-7c8bc988208e.dat,/tmp/tmpc6lic4p9/files/1/2/7/dataset_1272b23f-7cef-4deb-bf92-fbad973bf2c6.dat,/tmp/tmpc6lic4p9/files/7/4/7/dataset_7476b10d-c143-4be7-adb5-118dcf372287.dat,/tmp/tmpc6lic4p9/files/e/2/e/dataset_e2ed0e46-b159-4bca-aeaa-9bef9a5b9c9a.dat,/tmp/tmpc6lic4p9/files/c/a/1/dataset_ca18b50c-3b4c-4201-88b0-dffd049718f8.dat,/tmp/tmpc6lic4p9/files/1/b/4/dataset_1b480e84-03cf-4483-9e9e-ccf79bf654a1.dat,/tmp/tmpc6lic4p9/files/b/e/8/dataset_be83b8f4-73de-4775-abb8-75483d4e8ab2.dat,/tmp/tmpc6lic4p9/files/5/d/d/dataset_5ddde548-4828-4067-93b7-1377a71221d7.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpc6lic4p9/files/a/c/d/dataset_acd9e546-bb31-4391-b867-1d81cab10920.dat:part_A.gb,/tmp/tmpc6lic4p9/files/c/f/e/dataset_cfe852f6-5b32-46fd-a9d8-2b777016d403.dat:part_B.gb,/tmp/tmpc6lic4p9/files/2/5/b/dataset_25be2770-f768-4b0e-be96-459e47e6ae8d.dat:part_C.gb,/tmp/tmpc6lic4p9/files/e/5/8/dataset_e580f806-e8ba-4dac-b8d5-6b76b4a7421b.dat:part_D.gb,/tmp/tmpc6lic4p9/files/0/d/6/dataset_0d6de31a-aab1-427f-a2a1-7c8bc988208e.dat:part_E.gb,/tmp/tmpc6lic4p9/files/1/2/7/dataset_1272b23f-7cef-4deb-bf92-fbad973bf2c6.dat:part_F.gb,/tmp/tmpc6lic4p9/files/7/4/7/dataset_7476b10d-c143-4be7-adb5-118dcf372287.dat:part_G.gb,/tmp/tmpc6lic4p9/files/e/2/e/dataset_e2ed0e46-b159-4bca-aeaa-9bef9a5b9c9a.dat:part_H.gb,/tmp/tmpc6lic4p9/files/c/a/1/dataset_ca18b50c-3b4c-4201-88b0-dffd049718f8.dat:part_I.gb,/tmp/tmpc6lic4p9/files/1/b/4/dataset_1b480e84-03cf-4483-9e9e-ccf79bf654a1.dat:part_J.gb,/tmp/tmpc6lic4p9/files/b/e/8/dataset_be83b8f4-73de-4775-abb8-75483d4e8ab2.dat:part_K.gb,/tmp/tmpc6lic4p9/files/5/d/d/dataset_5ddde548-4828-4067-93b7-1377a71221d7.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/tmpc6lic4p9/job_working_directory/000/63/outputs/dataset_e10784a6-3050-4131-a684-3847397c4c4d.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T10:04:22.340769",
+"create_time": "2025-05-26T11:27:41.184534",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "118646",
+"external_id": "155964",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "18bb6cd07b986e37",
+"history_id": "84db48b219855f4d",
-"id": "3b86e96397860676",
+"id": "14e667eccbf3c9ac",
 "inputs": {
 "assembly_csv": {
-"id": "6fb8fb3f063f475d",
+"id": "59a0a00f5fa501d5",
 "src": "hda",
-"uuid": "aadc2ac5-b92d-4489-ba9c-9e30c79da207"
+"uuid": "9504897d-0d99-44a4-9033-7d14e3943ec9"
 },
 "domesticated_input1": {
-"id": "3eddddb1a3bb1719",
+"id": "2252f6534dc04be9",
 "src": "hda",
-"uuid": "388674d2-24fe-4e76-b0b8-2db6463e788f"
+"uuid": "acd9e546-bb31-4391-b867-1d81cab10920"
 },
 "domesticated_input10": {
-"id": "6baf136e951fa3e9",
+"id": "b26f1eae65161bae",
 "src": "hda",
-"uuid": "b0e2ce07-ccf0-4805-958c-8de174c3d4c1"
+"uuid": "1b480e84-03cf-4483-9e9e-ccf79bf654a1"
 },
 "domesticated_input11": {
-"id": "11a588ee1ee4e36e",
+"id": "748ef145f2d110fe",
 "src": "hda",
-"uuid": "33ad2072-fb76-47c4-b3f7-60a2a097ab87"
+"uuid": "be83b8f4-73de-4775-abb8-75483d4e8ab2"
 },
 "domesticated_input12": {
-"id": "8f43de78738fc703",
+"id": "37a05bd56b325e88",
 "src": "hda",
-"uuid": "9d13c418-bbb1-457e-bdaf-0f2bf5232f78"
+"uuid": "5ddde548-4828-4067-93b7-1377a71221d7"
 },
 "domesticated_input2": {
-"id": "df551757dda63084",
+"id": "2441550d408330ea",
 "src": "hda",
-"uuid": "75c27ee5-fd9b-46a1-be07-f0cdc4e16bc1"
+"uuid": "cfe852f6-5b32-46fd-a9d8-2b777016d403"
 },
 "domesticated_input3": {
-"id": "3b86e96397860676",
+"id": "7982f5ab86225272",
 "src": "hda",
-"uuid": "bbba5ff9-69e7-4d41-af82-992df5f065fb"
+"uuid": "25be2770-f768-4b0e-be96-459e47e6ae8d"
 },
 "domesticated_input4": {
-"id": "125f9d0e88ccc764",
+"id": "1d0be35bf9fc6600",
 "src": "hda",
-"uuid": "dc982e9d-6d93-4638-b4fc-67fc8238b295"
+"uuid": "e580f806-e8ba-4dac-b8d5-6b76b4a7421b"
 },
 "domesticated_input5": {
-"id": "68e8d3b1610203e4",
+"id": "40fe86a604adcf6d",
 "src": "hda",
-"uuid": "ed2d7b35-625f-429e-ae50-ce1098a20b85"
+"uuid": "0d6de31a-aab1-427f-a2a1-7c8bc988208e"
 },
 "domesticated_input6": {
-"id": "f9ce2b01423639ed",
+"id": "7355915c318fd136",
 "src": "hda",
-"uuid": "5a2010cb-64cf-4ff9-8852-f883f7ab0269"
+"uuid": "1272b23f-7cef-4deb-bf92-fbad973bf2c6"
 },
 "domesticated_input7": {
-"id": "af7dc246cf57ca17",
+"id": "bacbde4487432826",
 "src": "hda",
-"uuid": "0fa8ed6a-b848-4b0d-9474-13cd22d4a47e"
+"uuid": "7476b10d-c143-4be7-adb5-118dcf372287"
 },
 "domesticated_input8": {
-"id": "73904d43e96b8397",
+"id": "3b9b440d32d1c6f3",
 "src": "hda",
-"uuid": "abead413-c3d4-42d3-bd97-c02a6bd69779"
+"uuid": "e2ed0e46-b159-4bca-aeaa-9bef9a5b9c9a"
 },
 "domesticated_input9": {
-"id": "5dd99ba27cc0c63e",
+"id": "a19ae27f3bb8e8c1",
 "src": "hda",
-"uuid": "6ab6c472-c672-4bdf-9814-8e069a8a07e1"
+"uuid": "ca18b50c-3b4c-4201-88b0-dffd049718f8"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "9677ca5db33658a1",
+"id": "fedb85639c7c80b9",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "df1d56fe5378c54b",
+"id": "94b6b8378debd859",
 "src": "hda",
-"uuid": "c3d590de-2171-4d9a-a1c0-01110787a4ea"
+"uuid": "5145585f-443e-4934-af0b-60e1552a08a9"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "a443c6a3159c515a",
+"id": "dfa4bbdeadf76cd3",
 "src": "hda",
-"uuid": "14cde463-8656-4342-be37-c28798003a81"
+"uuid": "6f0dcaec-2131-4c0c-820b-bb5c895103e2"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "4048e6cd68dc21c7",
+"id": "e48032fd92b02fbb",
 "src": "hda",
-"uuid": "87c175e5-05d6-48e7-b617-e15d49a7027d"
+"uuid": "8c4da7fd-9c6b-4430-9444-c6e89b41c5df"
 },
 "__new_primary_file_construct_gb|construct_4__": {
-"id": "f601f1baaea8c27e",
+"id": "68bf450f38f03a28",
 "src": "hda",
-"uuid": "8e8367d5-caae-467d-a9d7-c681fd5497c7"
+"uuid": "a878e0a8-6f34-4cdf-8990-e178d0f15d52"
 },
 "output_zip": {
-"id": "8c0bd3fd394dbc64",
+"id": "1062de4bcda0d565",
 "src": "hda",
-"uuid": "fbeb57ed-1718-4d2b-a22b-5c4a5779d9ab"
+"uuid": "e10784a6-3050-4131-a684-3847397c4c4d"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpy2ysv6tn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpc6lic4p9/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}",
 "genbank_files": null,
 "topology": "\"circular\""
 },
 "state": "ok",
-"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",
+"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,  2.45it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.24it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.84it/s, now=None]\r                                                                 \r",
-"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",
+"stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
 "tool_id": "cloning_simulation",
-"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",
+"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,  2.45it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.24it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.84it/s, now=None]\r                                                                 \r",
-"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",
+"tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T10:04:35.116441",
+"update_time": "2025-05-26T11:27:53.929264",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "66f8380583c086e1"
+"user_id": "fcc5b7d13a1328f6"
 },
 "status": "success",
 "test_index": 6,
-"time_seconds": 53.07335948944092,
+"time_seconds": 53.42731332778931,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-6"

Mercurial > repos > tduigou > cloning_simulation

comparison output.json @ 14:16ccb36aa8e3 draft