cloning_simulation: output.json comparison

comparison output.json @ 6:e1e985913204 draft

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

author	tduigou
date	Wed, 21 May 2025 14:53:05 +0000
parents	254d284a5be9
children	296e5145a862

comparison

equal deleted inserted replaced

-:b0134502203b
+:e1e985913204
 {
 "summary": {
 "num_errors": 0,
-"num_failures": 0,
+"num_failures": 1,
 "num_skips": 0,
-"num_tests": 6
+"num_tests": 7
 },
 "tests": [
 {
 "data": {
 "inputs": {
 "adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "40769e0726e5d2f9",
+"id": "acd1a5e1ec1673bf",
 "src": "hda"
 },
 "assembly_plan_name": "Type2sRestrictionAssembly",
 "genbank_files": {
-"id": "fd8809ceca5b90d8",
+"id": "9f2c11a06c2c8bb2",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/4/b/3/dataset_4b32c6a8-b39d-4f5f-9155-307e142d9193.dat,/tmp/tmpay0tme4v/files/8/e/f/dataset_8ef181dd-5c3a-40eb-9926-3738e1ae4be1.dat,/tmp/tmpay0tme4v/files/b/a/b/dataset_babba200-2afd-434f-8797-9b10cc736ba7.dat,/tmp/tmpay0tme4v/files/b/7/c/dataset_b7c5a88c-05ae-4efd-9887-47a899749178.dat,/tmp/tmpay0tme4v/files/7/f/e/dataset_7fea4ecf-be56-423d-8a11-d6491077e233.dat,/tmp/tmpay0tme4v/files/e/1/f/dataset_e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe.dat,/tmp/tmpay0tme4v/files/f/0/f/dataset_f0fe046c-6132-4bb9-b5dc-521edead32f2.dat,/tmp/tmpay0tme4v/files/e/e/c/dataset_eec197e7-d8fa-4c45-b5cb-89e51ee1db0e.dat,/tmp/tmpay0tme4v/files/3/2/1/dataset_32124f40-ed9b-4d25-b74f-a4ff44581962.dat,/tmp/tmpay0tme4v/files/e/1/2/dataset_e126fe05-d77c-4b33-9782-e5b1e7e6c7ad.dat,/tmp/tmpay0tme4v/files/2/3/4/dataset_234f9855-813e-4297-bbd4-d1327fb0cbad.dat,/tmp/tmpay0tme4v/files/6/b/2/dataset_6b23e127-e4a2-41b6-98f3-4f8f7214b209.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/1/4/6/dataset_14645e90-9105-48af-a071-6ea052fd4aad.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/4/b/3/dataset_4b32c6a8-b39d-4f5f-9155-307e142d9193.dat:part_A.gb,/tmp/tmpay0tme4v/files/8/e/f/dataset_8ef181dd-5c3a-40eb-9926-3738e1ae4be1.dat:part_B.gb,/tmp/tmpay0tme4v/files/b/a/b/dataset_babba200-2afd-434f-8797-9b10cc736ba7.dat:part_C.gb,/tmp/tmpay0tme4v/files/b/7/c/dataset_b7c5a88c-05ae-4efd-9887-47a899749178.dat:part_D.gb,/tmp/tmpay0tme4v/files/7/f/e/dataset_7fea4ecf-be56-423d-8a11-d6491077e233.dat:part_E.gb,/tmp/tmpay0tme4v/files/e/1/f/dataset_e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe.dat:part_F.gb,/tmp/tmpay0tme4v/files/f/0/f/dataset_f0fe046c-6132-4bb9-b5dc-521edead32f2.dat:part_G.gb,/tmp/tmpay0tme4v/files/e/e/c/dataset_eec197e7-d8fa-4c45-b5cb-89e51ee1db0e.dat:part_H.gb,/tmp/tmpay0tme4v/files/3/2/1/dataset_32124f40-ed9b-4d25-b74f-a4ff44581962.dat:part_I.gb,/tmp/tmpay0tme4v/files/e/1/2/dataset_e126fe05-d77c-4b33-9782-e5b1e7e6c7ad.dat:part_J.gb,/tmp/tmpay0tme4v/files/2/3/4/dataset_234f9855-813e-4297-bbd4-d1327fb0cbad.dat:part_K.gb,/tmp/tmpay0tme4v/files/6/b/2/dataset_6b23e127-e4a2-41b6-98f3-4f8f7214b209.dat:part_L.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmpay0tme4v/job_working_directory/000/14/outputs/dataset_f30d906d-2ea4-4cde-b451-b7c6daf25a29.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/a/5/7/dataset_a579429e-eabf-48bf-8baa-4b54e340af46.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/e/8/6/dataset_e86ad306-6960-4dec-80fb-023fa6da5227.dat,/tmp/tmpo3npfzdk/files/d/3/4/dataset_d340b2ee-f061-4028-8e61-c384afc4678a.dat,/tmp/tmpo3npfzdk/files/1/9/5/dataset_19569676-42b8-47f6-bb6d-fd8658cd6a37.dat,/tmp/tmpo3npfzdk/files/0/5/a/dataset_05a63af0-f9a3-42f0-8ba8-74359301395e.dat,/tmp/tmpo3npfzdk/files/c/6/3/dataset_c636704b-8f2a-4cb6-9b8c-17214dadb08d.dat,/tmp/tmpo3npfzdk/files/8/5/5/dataset_855d9062-afe1-48b7-a1e9-a499536155aa.dat,/tmp/tmpo3npfzdk/files/e/3/7/dataset_e37509ff-8016-49ce-a9ca-fb066a5b6be6.dat,/tmp/tmpo3npfzdk/files/e/d/d/dataset_edde499a-6247-4874-8ef6-921fa7d311b6.dat,/tmp/tmpo3npfzdk/files/6/6/c/dataset_66c4decf-8469-4302-8957-320e236c7ee7.dat,/tmp/tmpo3npfzdk/files/0/f/e/dataset_0fe1772a-d8b1-4b91-aee0-1a6d1577590e.dat,/tmp/tmpo3npfzdk/files/c/1/a/dataset_c1aa9b56-f155-44af-8af5-1997f3ae48a7.dat,/tmp/tmpo3npfzdk/files/2/7/1/dataset_27148f5e-d3f0-45b9-a5f6-90d12767b2af.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/e/8/6/dataset_e86ad306-6960-4dec-80fb-023fa6da5227.dat:part_A.gb,/tmp/tmpo3npfzdk/files/d/3/4/dataset_d340b2ee-f061-4028-8e61-c384afc4678a.dat:part_B.gb,/tmp/tmpo3npfzdk/files/1/9/5/dataset_19569676-42b8-47f6-bb6d-fd8658cd6a37.dat:part_C.gb,/tmp/tmpo3npfzdk/files/0/5/a/dataset_05a63af0-f9a3-42f0-8ba8-74359301395e.dat:part_D.gb,/tmp/tmpo3npfzdk/files/c/6/3/dataset_c636704b-8f2a-4cb6-9b8c-17214dadb08d.dat:part_E.gb,/tmp/tmpo3npfzdk/files/8/5/5/dataset_855d9062-afe1-48b7-a1e9-a499536155aa.dat:part_F.gb,/tmp/tmpo3npfzdk/files/e/3/7/dataset_e37509ff-8016-49ce-a9ca-fb066a5b6be6.dat:part_G.gb,/tmp/tmpo3npfzdk/files/e/d/d/dataset_edde499a-6247-4874-8ef6-921fa7d311b6.dat:part_H.gb,/tmp/tmpo3npfzdk/files/6/6/c/dataset_66c4decf-8469-4302-8957-320e236c7ee7.dat:part_I.gb,/tmp/tmpo3npfzdk/files/0/f/e/dataset_0fe1772a-d8b1-4b91-aee0-1a6d1577590e.dat:part_J.gb,/tmp/tmpo3npfzdk/files/c/1/a/dataset_c1aa9b56-f155-44af-8af5-1997f3ae48a7.dat:part_K.gb,/tmp/tmpo3npfzdk/files/2/7/1/dataset_27148f5e-d3f0-45b9-a5f6-90d12767b2af.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/tmpo3npfzdk/job_working_directory/000/14/outputs/dataset_d4a3a824-aae9-4493-811d-77a8abd69905.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-19T13:45:01.696419",
+"create_time": "2025-05-21T14:47:30.360925",
 "dependencies": [],
 "exit_code": 0,
-"external_id": "245391",
+"external_id": "317822",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "fd8809ceca5b90d8",
+"history_id": "9f2c11a06c2c8bb2",
-"id": "d25964a649f0fc81",
+"id": "18479e206f3c823f",
 "inputs": {
 "assembly_csv": {
-"id": "40769e0726e5d2f9",
+"id": "acd1a5e1ec1673bf",
 "src": "hda",
-"uuid": "14645e90-9105-48af-a071-6ea052fd4aad"
+"uuid": "a579429e-eabf-48bf-8baa-4b54e340af46"
 },
 "genbank_files1": {
-"id": "fd8809ceca5b90d8",
+"id": "9f2c11a06c2c8bb2",
 "src": "hda",
-"uuid": "4b32c6a8-b39d-4f5f-9155-307e142d9193"
+"uuid": "e86ad306-6960-4dec-80fb-023fa6da5227"
 },
 "genbank_files10": {
-"id": "171b3bd3b2ffa75e",
+"id": "d905212b22d14b29",
 "src": "hda",
-"uuid": "e126fe05-d77c-4b33-9782-e5b1e7e6c7ad"
+"uuid": "0fe1772a-d8b1-4b91-aee0-1a6d1577590e"
 },
 "genbank_files11": {
-"id": "ec7f951857c74506",
+"id": "64a027171405da09",
 "src": "hda",
-"uuid": "234f9855-813e-4297-bbd4-d1327fb0cbad"
+"uuid": "c1aa9b56-f155-44af-8af5-1997f3ae48a7"
 },
 "genbank_files12": {
-"id": "8c74660869d2dd19",
+"id": "f3ab5b94869b932e",
 "src": "hda",
-"uuid": "6b23e127-e4a2-41b6-98f3-4f8f7214b209"
+"uuid": "27148f5e-d3f0-45b9-a5f6-90d12767b2af"
 },
 "genbank_files2": {
-"id": "132b871e5e3014ee",
+"id": "edba41b605a9f854",
 "src": "hda",
-"uuid": "8ef181dd-5c3a-40eb-9926-3738e1ae4be1"
+"uuid": "d340b2ee-f061-4028-8e61-c384afc4678a"
 },
 "genbank_files3": {
-"id": "65f48584dd2a1828",
+"id": "b1906c2e1f5de664",
 "src": "hda",
-"uuid": "babba200-2afd-434f-8797-9b10cc736ba7"
+"uuid": "19569676-42b8-47f6-bb6d-fd8658cd6a37"
 },
 "genbank_files4": {
-"id": "543bb64c618cca80",
+"id": "d28b58e6679c5691",
 "src": "hda",
-"uuid": "b7c5a88c-05ae-4efd-9887-47a899749178"
+"uuid": "05a63af0-f9a3-42f0-8ba8-74359301395e"
 },
 "genbank_files5": {
-"id": "e550d863bf084702",
+"id": "39de46ba349dfcbe",
 "src": "hda",
-"uuid": "7fea4ecf-be56-423d-8a11-d6491077e233"
+"uuid": "c636704b-8f2a-4cb6-9b8c-17214dadb08d"
 },
 "genbank_files6": {
-"id": "6a73e15df176b356",
+"id": "d10d7a9bf6c42600",
 "src": "hda",
-"uuid": "e1f9ab9e-c9e0-4acd-ac63-e4299c3792fe"
+"uuid": "855d9062-afe1-48b7-a1e9-a499536155aa"
 },
 "genbank_files7": {
-"id": "7faba24a30f85c9d",
+"id": "6f2e93d50b248cee",
 "src": "hda",
-"uuid": "f0fe046c-6132-4bb9-b5dc-521edead32f2"
+"uuid": "e37509ff-8016-49ce-a9ca-fb066a5b6be6"
 },
 "genbank_files8": {
-"id": "f121a1ae40e58e96",
+"id": "00a7ec1d542ff3f2",
 "src": "hda",
-"uuid": "eec197e7-d8fa-4c45-b5cb-89e51ee1db0e"
+"uuid": "edde499a-6247-4874-8ef6-921fa7d311b6"
 },
 "genbank_files9": {
-"id": "fc2d53421d7989de",
+"id": "39eaa2809c3cd4cb",
 "src": "hda",
-"uuid": "32124f40-ed9b-4d25-b74f-a4ff44581962"
+"uuid": "66c4decf-8469-4302-8957-320e236c7ee7"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "132b871e5e3014ee",
+"id": "edba41b605a9f854",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "6d4f2c14c91fd6e1",
+"id": "fae073f924dc0737",
 "src": "hda",
-"uuid": "32687278-a139-4ee2-bfc0-86735e813b3e"
+"uuid": "41fc11c8-e2d3-4dad-9886-b8b318d263b0"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "ce0686b9d731295a",
+"id": "a0099218a00b3fc6",
 "src": "hda",
-"uuid": "a78e87bc-7aa1-4e9e-8625-78450d68b18d"
+"uuid": "7bc46185-b70d-4e82-b1fe-e0bc1710c1c7"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "9fb491af1d40ed73",
+"id": "87b4cc5bde3d0d60",
 "src": "hda",
-"uuid": "6ce970af-f5f4-4193-9d0a-d1fc701d17d5"
+"uuid": "79f1a377-2d26-4e23-aa72-01151870f643"
 },
 "__new_primary_file_construct_gb|construct_4__": {
-"id": "0a54ce1a82948d59",
+"id": "b1ff512a2804398b",
 "src": "hda",
-"uuid": "b76d3345-d556-4f55-9285-6a7ce76d9150"
+"uuid": "63ad38c1-369e-4ef2-b296-6c80774439a1"
 },
 "output_zip": {
-"id": "d25964a649f0fc81",
+"id": "18479e206f3c823f",
 "src": "hda",
-"uuid": "f30d906d-2ea4-4cde-b451-b7c6daf25a29"
+"uuid": "d4a3a824-aae9-4493-811d-77a8abd69905"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 1, \"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,  2.14it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.77it/s, now=None]\r                                                                 \r",
+"stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.42it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.20it/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",
 "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,  2.14it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.15it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.77it/s, now=None]\r                                                                 \r",
+"tool_stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.42it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.20it/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_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-19T13:45:15.319665",
+"update_time": "2025-05-21T14:47:43.254778",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fd8809ceca5b90d8"
+"user_id": "9f2c11a06c2c8bb2"
 },
 "status": "success",
 "test_index": 0,
-"time_seconds": 54.20177435874939,
+"time_seconds": 52.45778512954712,
 "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": "e820aa9b959ea863",
+"id": "289d42720aa731f0",
 "src": "hda"
 },
 "assembly_plan_name": "GibsonAssembly",
 "genbank_files": {
-"id": "65f48584dd2a1828",
+"id": "b1906c2e1f5de664",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/0/6/9/dataset_069f9137-705b-4e17-b931-1ebd547a7fe4.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/3/d/1/dataset_3d1a91ee-d9ba-41fc-bd79-f012ae654250.dat' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/0/6/9/dataset_069f9137-705b-4e17-b931-1ebd547a7fe4.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmpay0tme4v/job_working_directory/000/17/outputs/dataset_3327e282-d219-43e3-94d7-88fd08aa6867.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/e/c/2/dataset_ec2445f2-3c65-4da8-8eff-b766983bfc67.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/6/7/f/dataset_67f88938-ad76-4760-9f37-0ad6563677d2.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/6/7/f/dataset_67f88938-ad76-4760-9f37-0ad6563677d2.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/tmpo3npfzdk/job_working_directory/000/17/outputs/dataset_989e415d-7117-4c6a-9721-a471d4848b28.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-19T13:45:26.929597",
+"create_time": "2025-05-21T14:47:54.065116",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "245766",
+"external_id": "318162",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "132b871e5e3014ee",
+"history_id": "edba41b605a9f854",
-"id": "9fb491af1d40ed73",
+"id": "87b4cc5bde3d0d60",
 "inputs": {
 "assembly_csv": {
-"id": "e820aa9b959ea863",
+"id": "289d42720aa731f0",
 "src": "hda",
-"uuid": "3d1a91ee-d9ba-41fc-bd79-f012ae654250"
+"uuid": "ec2445f2-3c65-4da8-8eff-b766983bfc67"
 },
 "genbank_files1": {
-"id": "82720a2239e02ea4",
+"id": "761015980e0fa5bb",
 "src": "hda",
-"uuid": "069f9137-705b-4e17-b931-1ebd547a7fe4"
+"uuid": "67f88938-ad76-4760-9f37-0ad6563677d2"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "543bb64c618cca80",
+"id": "d28b58e6679c5691",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "4aace7d444c68122",
+"id": "250fdbecb1e4e593",
 "src": "hda",
-"uuid": "24381c81-ce88-4584-94dd-e84c078419f8"
+"uuid": "20319120-7aa4-4a7b-8e21-e283565ebc51"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "894db8882e848d71",
+"id": "b6d4ee56c656e869",
 "src": "hda",
-"uuid": "9f704297-19e6-4faf-a500-b6b64578b376"
+"uuid": "ba35f878-8819-459e-acff-364b6393cd75"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "4d49f848d91861cd",
+"id": "d670a65869e0ee8d",
 "src": "hda",
-"uuid": "ac0d0bab-faee-48eb-bdcf-f71f1ae7dff9"
+"uuid": "646cac10-dab3-4b60-bb38-1a21ce52a0af"
 },
 "output_zip": {
-"id": "314f9466454a965d",
+"id": "3cd20c46fb8f3785",
 "src": "hda",
-"uuid": "3327e282-d219-43e3-94d7-88fd08aa6867"
+"uuid": "989e415d-7117-4c6a-9721-a471d4848b28"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"GibsonAssembly\"",
-"chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpo3npfzdk/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,  4.20it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.12it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.34it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.62it/s, now=None]\r                                                                 \r",
+"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,  4.41it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.23it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.23it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.54it/s, now=None]\r                                                                 \r",
 "stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\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,  4.20it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.12it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.34it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.62it/s, now=None]\r                                                                 \r",
+"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,  4.41it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.23it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.23it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.54it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-19T13:45:38.810356",
+"update_time": "2025-05-21T14:48:06.111506",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fd8809ceca5b90d8"
+"user_id": "9f2c11a06c2c8bb2"
 },
 "status": "success",
 "test_index": 1,
-"time_seconds": 23.490375518798828,
+"time_seconds": 22.7187819480896,
 "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": "675dca381201b1fe",
+"id": "85c339cda4aedd7c",
 "src": "hda"
 },
 "assembly_plan_name": "LigaseCyclingReactionAssembly",
 "genbank_files": {
-"id": "e550d863bf084702",
+"id": "39de46ba349dfcbe",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/e/0/f/dataset_e0f8296e-094d-4971-976b-6e534148d1d5.dat,/tmp/tmpay0tme4v/files/6/0/8/dataset_608722d5-ead5-49fb-8736-04fa7ab027f3.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/1/d/9/dataset_1d9ed268-bc25-40c0-a67f-439accae7e40.dat' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/e/0/f/dataset_e0f8296e-094d-4971-976b-6e534148d1d5.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpay0tme4v/files/6/0/8/dataset_608722d5-ead5-49fb-8736-04fa7ab027f3.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmpay0tme4v/job_working_directory/000/21/outputs/dataset_b1af7192-a26f-4e6a-ba22-9aeffac2ea46.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/f/8/e/dataset_f8e8f190-6448-4143-9c9d-318983554f6e.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/f/0/d/dataset_f0d601f5-aeb5-4dde-88f2-1ef90f2cee9d.dat,/tmp/tmpo3npfzdk/files/0/1/e/dataset_01ef92eb-7297-49ed-b933-21e2fd13abde.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/f/0/d/dataset_f0d601f5-aeb5-4dde-88f2-1ef90f2cee9d.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpo3npfzdk/files/0/1/e/dataset_01ef92eb-7297-49ed-b933-21e2fd13abde.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/tmpo3npfzdk/job_working_directory/000/21/outputs/dataset_27a350cf-f7f3-41f3-8b7d-a7f5a3857cda.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-19T13:45:50.704320",
+"create_time": "2025-05-21T14:48:17.296961",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "246155",
+"external_id": "318555",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "65f48584dd2a1828",
+"history_id": "b1906c2e1f5de664",
-"id": "314f9466454a965d",
+"id": "3cd20c46fb8f3785",
 "inputs": {
 "assembly_csv": {
-"id": "675dca381201b1fe",
+"id": "85c339cda4aedd7c",
 "src": "hda",
-"uuid": "1d9ed268-bc25-40c0-a67f-439accae7e40"
+"uuid": "f8e8f190-6448-4143-9c9d-318983554f6e"
 },
 "genbank_files1": {
-"id": "1b1aadbedc3f334a",
+"id": "65b6153cb018bc73",
 "src": "hda",
-"uuid": "e0f8296e-094d-4971-976b-6e534148d1d5"
+"uuid": "f0d601f5-aeb5-4dde-88f2-1ef90f2cee9d"
 },
 "genbank_files2": {
-"id": "05b5deb4bb488223",
+"id": "bad7991cd53808a2",
 "src": "hda",
-"uuid": "608722d5-ead5-49fb-8736-04fa7ab027f3"
+"uuid": "01ef92eb-7297-49ed-b933-21e2fd13abde"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "6a73e15df176b356",
+"id": "d10d7a9bf6c42600",
 "src": "hdca"
 }
 },
 "outputs": {
 "output_zip": {
-"id": "499c1d005d68ae46",
+"id": "a6615d25b678d53d",
 "src": "hda",
-"uuid": "b1af7192-a26f-4e6a-ba22-9aeffac2ea46"
+"uuid": "27a350cf-f7f3-41f3-8b7d-a7f5a3857cda"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"LigaseCyclingReactionAssembly\"",
-"chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpo3npfzdk/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,  2.05it/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,  2.35it/s, now=None]\r                                                                 \r",
 "stdout": "Simulating 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,  2.05it/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,  2.35it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-19T13:46:02.749327",
+"update_time": "2025-05-21T14:48:29.682156",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fd8809ceca5b90d8"
+"user_id": "9f2c11a06c2c8bb2"
 },
 "status": "success",
 "test_index": 2,
-"time_seconds": 23.55416440963745,
+"time_seconds": 23.41460394859314,
 "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": "c06583b31ad25e9f",
+"id": "5685dbd0270421a3",
 "src": "hda"
 },
 "assembly_plan_name": "BASICAssembly",
 "genbank_files": {
-"id": "7faba24a30f85c9d",
+"id": "6f2e93d50b248cee",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/5/0/9/dataset_509fa87d-4af9-46f7-b323-48f8128675c8.dat,/tmp/tmpay0tme4v/files/0/2/b/dataset_02b8b6f2-43ab-4885-a9de-336d903edc55.dat,/tmp/tmpay0tme4v/files/9/5/a/dataset_95aa5a16-9b61-45be-94e6-35284531fcd7.dat,/tmp/tmpay0tme4v/files/1/7/c/dataset_17c94fe6-e0ce-4c72-9adc-5f8132a6df81.dat,/tmp/tmpay0tme4v/files/d/b/6/dataset_db6bb8ba-4682-476e-a688-be9e5cfb0afd.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/3/4/4/dataset_344ef380-e9d3-4729-bc6e-45a003000613.dat' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/5/0/9/dataset_509fa87d-4af9-46f7-b323-48f8128675c8.dat:GFP.gb,/tmp/tmpay0tme4v/files/0/2/b/dataset_02b8b6f2-43ab-4885-a9de-336d903edc55.dat:p15A_kan.gb,/tmp/tmpay0tme4v/files/9/5/a/dataset_95aa5a16-9b61-45be-94e6-35284531fcd7.dat:promoter.gb,/tmp/tmpay0tme4v/files/1/7/c/dataset_17c94fe6-e0ce-4c72-9adc-5f8132a6df81.dat:RFP.gb,/tmp/tmpay0tme4v/files/d/b/6/dataset_db6bb8ba-4682-476e-a688-be9e5cfb0afd.dat:oligos.fa' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmpay0tme4v/job_working_directory/000/28/outputs/dataset_cdb61cbc-c9c5-45fc-9fc8-e00c1f3d4f0f.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/2/e/b/dataset_2ebce83f-23bd-4ed9-bf81-84719ce47f36.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/b/a/9/dataset_ba9f3fda-e65a-4367-9883-988cf2a55bc7.dat,/tmp/tmpo3npfzdk/files/5/6/4/dataset_56477dbf-4a9f-4d85-8639-49bc05bff7b7.dat,/tmp/tmpo3npfzdk/files/7/5/d/dataset_75d82485-e3c8-4311-8952-658d8522f8a5.dat,/tmp/tmpo3npfzdk/files/f/a/f/dataset_faff73fe-2ef9-4c25-913c-df5e8b93306a.dat,/tmp/tmpo3npfzdk/files/8/5/9/dataset_859dcf3d-e0f7-4667-9c8d-9a9587d934fb.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/b/a/9/dataset_ba9f3fda-e65a-4367-9883-988cf2a55bc7.dat:GFP.gb,/tmp/tmpo3npfzdk/files/5/6/4/dataset_56477dbf-4a9f-4d85-8639-49bc05bff7b7.dat:p15A_kan.gb,/tmp/tmpo3npfzdk/files/7/5/d/dataset_75d82485-e3c8-4311-8952-658d8522f8a5.dat:promoter.gb,/tmp/tmpo3npfzdk/files/f/a/f/dataset_faff73fe-2ef9-4c25-913c-df5e8b93306a.dat:RFP.gb,/tmp/tmpo3npfzdk/files/8/5/9/dataset_859dcf3d-e0f7-4667-9c8d-9a9587d934fb.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/tmpo3npfzdk/job_working_directory/000/28/outputs/dataset_9a1970ad-354f-4dab-8065-2e37cd1d196b.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-19T13:46:24.141767",
+"create_time": "2025-05-21T14:48:51.044629",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "246833",
+"external_id": "319145",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "543bb64c618cca80",
+"history_id": "d28b58e6679c5691",
-"id": "499c1d005d68ae46",
+"id": "a6615d25b678d53d",
 "inputs": {
 "assembly_csv": {
-"id": "c06583b31ad25e9f",
+"id": "5685dbd0270421a3",
 "src": "hda",
-"uuid": "344ef380-e9d3-4729-bc6e-45a003000613"
+"uuid": "2ebce83f-23bd-4ed9-bf81-84719ce47f36"
 },
 "genbank_files1": {
-"id": "dcd17297edd6443c",
+"id": "78532c2c58a6724d",
 "src": "hda",
-"uuid": "509fa87d-4af9-46f7-b323-48f8128675c8"
+"uuid": "ba9f3fda-e65a-4367-9883-988cf2a55bc7"
 },
 "genbank_files2": {
-"id": "5255abeff5637f7e",
+"id": "6068244592d47240",
 "src": "hda",
-"uuid": "02b8b6f2-43ab-4885-a9de-336d903edc55"
+"uuid": "56477dbf-4a9f-4d85-8639-49bc05bff7b7"
 },
 "genbank_files3": {
-"id": "a30c1b2be38d49df",
+"id": "f632d706e94b2046",
 "src": "hda",
-"uuid": "95aa5a16-9b61-45be-94e6-35284531fcd7"
+"uuid": "75d82485-e3c8-4311-8952-658d8522f8a5"
 },
 "genbank_files4": {
-"id": "70728511d187b46b",
+"id": "3089f20183c33fb7",
 "src": "hda",
-"uuid": "17c94fe6-e0ce-4c72-9adc-5f8132a6df81"
+"uuid": "faff73fe-2ef9-4c25-913c-df5e8b93306a"
 },
 "genbank_files5": {
-"id": "db356309fe5e8361",
+"id": "b20d2aa5f122518a",
 "src": "hda",
-"uuid": "db6bb8ba-4682-476e-a688-be9e5cfb0afd"
+"uuid": "859dcf3d-e0f7-4667-9c8d-9a9587d934fb"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "f121a1ae40e58e96",
+"id": "00a7ec1d542ff3f2",
 "src": "hdca"
 }
 },
 "outputs": {
 "output_zip": {
-"id": "15b1f0554a03958d",
+"id": "2accc8a350a16be5",
 "src": "hda",
-"uuid": "cdb61cbc-c9c5-45fc-9fc8-e00c1f3d4f0f"
+"uuid": "9a1970ad-354f-4dab-8065-2e37cd1d196b"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"BASICAssembly\"",
-"chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpo3npfzdk/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, 44.90it/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, 48.44it/s, now=None]\r                                                                 \r",
 "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, 44.90it/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, 48.44it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 2, 'errored_assemblies': 8, 'valid_assemblies': 0}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-19T13:46:34.776797",
+"update_time": "2025-05-21T14:49:01.657843",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fd8809ceca5b90d8"
+"user_id": "9f2c11a06c2c8bb2"
 },
 "status": "success",
 "test_index": 3,
-"time_seconds": 32.1408953666687,
+"time_seconds": 32.04251265525818,
 "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": "e7b347ef21d63fab",
+"id": "19069e20577e5aff",
 "src": "hda"
 },
 "assembly_plan_name": "BioBrickStandardAssembly",
 "genbank_files": {
-"id": "fc2d53421d7989de",
+"id": "39eaa2809c3cd4cb",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/6/e/0/dataset_6e0453c4-6edd-4d76-9504-4cc4941610f6.dat,/tmp/tmpay0tme4v/files/6/d/3/dataset_6d3c24e5-73cd-4bed-95aa-d1c361c74180.dat,/tmp/tmpay0tme4v/files/7/7/9/dataset_7793541b-18cc-4f7d-a9df-12396807c368.dat,/tmp/tmpay0tme4v/files/a/e/1/dataset_ae1611ed-a5e2-46e8-b975-613ada1bb8db.dat,/tmp/tmpay0tme4v/files/9/a/d/dataset_9adfafe3-b0ad-449b-8555-286ca83e65a4.dat' --domesticated_seq '' --assembly_csv '/tmp/tmpay0tme4v/files/9/7/6/dataset_976f7d99-07e5-4d5c-ab79-a96ae42760d4.dat' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/6/e/0/dataset_6e0453c4-6edd-4d76-9504-4cc4941610f6.dat:BBa_E0040_GFP.gb,/tmp/tmpay0tme4v/files/6/d/3/dataset_6d3c24e5-73cd-4bed-95aa-d1c361c74180.dat:BBa_J23119_prom.gb,/tmp/tmpay0tme4v/files/7/7/9/dataset_7793541b-18cc-4f7d-a9df-12396807c368.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpay0tme4v/files/a/e/1/dataset_ae1611ed-a5e2-46e8-b975-613ada1bb8db.dat:BBa_J61048_term.gb,/tmp/tmpay0tme4v/files/9/a/d/dataset_9adfafe3-b0ad-449b-8555-286ca83e65a4.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmpay0tme4v/job_working_directory/000/35/outputs/dataset_deeb975f-4ae8-44d3-9c3c-51dc05e74f05.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/1/d/4/dataset_1d489746-618d-43f9-ac80-377b4dd34b24.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/8/9/7/dataset_897a659b-ded6-4f1d-ae66-2a1cef19fe20.dat,/tmp/tmpo3npfzdk/files/7/4/c/dataset_74cd9512-f6fd-41db-8b25-6d9edd13fb35.dat,/tmp/tmpo3npfzdk/files/2/6/4/dataset_264baf3b-d201-449d-93bf-1408b04e3cc8.dat,/tmp/tmpo3npfzdk/files/b/8/7/dataset_b877c492-f532-4f4f-a95d-8dea0497c7ff.dat,/tmp/tmpo3npfzdk/files/f/a/1/dataset_fa14d755-6f98-4e94-9f24-cfbca2726e31.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/8/9/7/dataset_897a659b-ded6-4f1d-ae66-2a1cef19fe20.dat:BBa_E0040_GFP.gb,/tmp/tmpo3npfzdk/files/7/4/c/dataset_74cd9512-f6fd-41db-8b25-6d9edd13fb35.dat:BBa_J23119_prom.gb,/tmp/tmpo3npfzdk/files/2/6/4/dataset_264baf3b-d201-449d-93bf-1408b04e3cc8.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpo3npfzdk/files/b/8/7/dataset_b877c492-f532-4f4f-a95d-8dea0497c7ff.dat:BBa_J61048_term.gb,/tmp/tmpo3npfzdk/files/f/a/1/dataset_fa14d755-6f98-4e94-9f24-cfbca2726e31.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/tmpo3npfzdk/job_working_directory/000/35/outputs/dataset_ef294752-b154-44c3-828c-7165200df44d.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-19T13:46:57.146002",
+"create_time": "2025-05-21T14:49:23.080076",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "247581",
+"external_id": "319763",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "e550d863bf084702",
+"history_id": "39de46ba349dfcbe",
-"id": "15b1f0554a03958d",
+"id": "2accc8a350a16be5",
 "inputs": {
 "assembly_csv": {
-"id": "e7b347ef21d63fab",
+"id": "19069e20577e5aff",
 "src": "hda",
-"uuid": "976f7d99-07e5-4d5c-ab79-a96ae42760d4"
+"uuid": "1d489746-618d-43f9-ac80-377b4dd34b24"
 },
 "genbank_files1": {
-"id": "0d1c6bc715df133f",
+"id": "d016498c10e59856",
 "src": "hda",
-"uuid": "6e0453c4-6edd-4d76-9504-4cc4941610f6"
+"uuid": "897a659b-ded6-4f1d-ae66-2a1cef19fe20"
 },
 "genbank_files2": {
-"id": "7d9d065fa6859d88",
+"id": "8ce5f5c286574bf4",
 "src": "hda",
-"uuid": "6d3c24e5-73cd-4bed-95aa-d1c361c74180"
+"uuid": "74cd9512-f6fd-41db-8b25-6d9edd13fb35"
 },
 "genbank_files3": {
-"id": "28aa4b1f3fb7d62b",
+"id": "b8e0a36ad3584e57",
 "src": "hda",
-"uuid": "7793541b-18cc-4f7d-a9df-12396807c368"
+"uuid": "264baf3b-d201-449d-93bf-1408b04e3cc8"
 },
 "genbank_files4": {
-"id": "7423dfb808ef4761",
+"id": "14b4e4f7b248fbc1",
 "src": "hda",
-"uuid": "ae1611ed-a5e2-46e8-b975-613ada1bb8db"
+"uuid": "b877c492-f532-4f4f-a95d-8dea0497c7ff"
 },
 "genbank_files5": {
-"id": "175236d72b015bf8",
+"id": "773bba263401ee3f",
 "src": "hda",
-"uuid": "9adfafe3-b0ad-449b-8555-286ca83e65a4"
+"uuid": "fa14d755-6f98-4e94-9f24-cfbca2726e31"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "171b3bd3b2ffa75e",
+"id": "d905212b22d14b29",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|C1_prom_barcode__": {
-"id": "2607809b86839f90",
+"id": "663fbeeba9821aac",
 "src": "hda",
-"uuid": "4e873fda-e181-4d71-b03b-61441dad6432"
+"uuid": "17dc07bc-ee88-4d0a-914a-bd5e219c3c02"
 },
 "__new_primary_file_construct_gb|C2_gfp_term__": {
-"id": "d61271ad2bd59452",
+"id": "522d7c5bcadc14e8",
 "src": "hda",
-"uuid": "1c217e77-9cfa-48b2-aabb-ccdcd23275ca"
+"uuid": "9e3bf994-7926-4d59-8cba-2ea85e34d4c1"
 },
 "__new_primary_file_construct_gb|C3_final__": {
-"id": "cdfae6a044106877",
+"id": "092101d28c5662b8",
 "src": "hda",
-"uuid": "54b8bb86-f05d-4ec1-b551-7ed8ca22aedd"
+"uuid": "080209e3-58a5-4181-b460-bf02871b2f82"
 },
 "output_zip": {
-"id": "451b6ce8fd13ed5c",
+"id": "aa2a9c27c57d7b71",
 "src": "hda",
-"uuid": "deeb975f-4ae8-44d3-9c3c-51dc05e74f05"
+"uuid": "ef294752-b154-44c3-828c-7165200df44d"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"BioBrickStandardAssembly\"",
-"chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpo3npfzdk/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,  1.74it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:02<00:00,  1.43it/s, now=None]\r                                                                 \r",
+"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,  1.92it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.56it/s, now=None]\r                                                                 \r",
 "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,  1.74it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:02<00:00,  1.43it/s, now=None]\r                                                                 \r",
+"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,  1.92it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.56it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-19T13:47:10.784667",
+"update_time": "2025-05-21T14:49:36.465998",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fd8809ceca5b90d8"
+"user_id": "9f2c11a06c2c8bb2"
 },
 "status": "success",
 "test_index": 4,
-"time_seconds": 35.92383527755737,
+"time_seconds": 34.58101224899292,
 "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": "8970dbe72f491b25",
+"id": "79581be26281c6bb",
 "src": "hda"
 },
 "assembly_plan_name": "Type2sRestrictionAssembly",
 "domesticated_input": {
-"id": "ec7f951857c74506",
+"id": "64a027171405da09",
 "src": "hdca"
 },
 "genbank_files": {
-"id": "8c74660869d2dd19",
+"id": "f3ab5b94869b932e",
 "src": "hdca"
 },
 "topology": "circular"
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpay0tme4v/files/1/9/3/dataset_193cbd10-4b76-46d9-b377-a7f06471d4d4.dat,/tmp/tmpay0tme4v/files/f/a/3/dataset_fa31c5f5-e678-471e-b1a3-4f8a168bbee1.dat,/tmp/tmpay0tme4v/files/6/9/7/dataset_697c83fe-168b-4319-a6e5-3db90c504c8b.dat,/tmp/tmpay0tme4v/files/0/6/d/dataset_06d4dd94-5f33-4ce0-ab0a-e6efe96ca222.dat,/tmp/tmpay0tme4v/files/7/0/1/dataset_701b72c6-ec2e-4435-b0d5-8f419811a4dd.dat,/tmp/tmpay0tme4v/files/5/a/0/dataset_5a07f059-f6f9-49de-b0fc-3cded157f44b.dat,/tmp/tmpay0tme4v/files/7/5/3/dataset_753f0297-4bff-49c8-b22a-1377e43a81f6.dat' --domesticated_seq '/tmp/tmpay0tme4v/files/f/6/d/dataset_f6d602b9-7772-4a93-969d-f0dcdad98c6a.dat,/tmp/tmpay0tme4v/files/d/4/d/dataset_d4dc3ecb-77ff-4b28-a55a-7b263416c6c7.dat,/tmp/tmpay0tme4v/files/7/d/4/dataset_7d489dbd-161e-4f04-a3df-ef5b989ad1e0.dat,/tmp/tmpay0tme4v/files/4/c/a/dataset_4ca3c222-672a-4806-b60c-081f1b7b64cb.dat,/tmp/tmpay0tme4v/files/9/0/6/dataset_906707db-b3cf-40f9-af0b-1ffc143f91e8.dat' --assembly_csv '/tmp/tmpay0tme4v/files/9/c/8/dataset_9c8ec693-02f9-4cc7-b7e3-8bfb0a4dd1dc.dat' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpay0tme4v/files/1/9/3/dataset_193cbd10-4b76-46d9-b377-a7f06471d4d4.dat:part_A.gb,/tmp/tmpay0tme4v/files/f/a/3/dataset_fa31c5f5-e678-471e-b1a3-4f8a168bbee1.dat:part_B.gb,/tmp/tmpay0tme4v/files/6/9/7/dataset_697c83fe-168b-4319-a6e5-3db90c504c8b.dat:part_C.gb,/tmp/tmpay0tme4v/files/0/6/d/dataset_06d4dd94-5f33-4ce0-ab0a-e6efe96ca222.dat:part_D.gb,/tmp/tmpay0tme4v/files/7/0/1/dataset_701b72c6-ec2e-4435-b0d5-8f419811a4dd.dat:part_E.gb,/tmp/tmpay0tme4v/files/5/a/0/dataset_5a07f059-f6f9-49de-b0fc-3cded157f44b.dat:part_F.gb,/tmp/tmpay0tme4v/files/7/5/3/dataset_753f0297-4bff-49c8-b22a-1377e43a81f6.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpay0tme4v/files/f/6/d/dataset_f6d602b9-7772-4a93-969d-f0dcdad98c6a.dat:part_H.gb,/tmp/tmpay0tme4v/files/d/4/d/dataset_d4dc3ecb-77ff-4b28-a55a-7b263416c6c7.dat:part_I.gb,/tmp/tmpay0tme4v/files/7/d/4/dataset_7d489dbd-161e-4f04-a3df-ef5b989ad1e0.dat:part_J.gb,/tmp/tmpay0tme4v/files/4/c/a/dataset_4ca3c222-672a-4806-b60c-081f1b7b64cb.dat:part_K.gb,/tmp/tmpay0tme4v/files/9/0/6/dataset_906707db-b3cf-40f9-af0b-1ffc143f91e8.dat:part_L.gb' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' --enzyme 'auto' --topology 'circular'&& cp 'output_zip.zip' '/tmp/tmpay0tme4v/job_working_directory/000/49/outputs/dataset_800320dc-d181-40bf-b1cb-541f43a838c3.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/8/c/c/dataset_8ccb55a4-733f-4671-a12c-c89cee5a694b.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/5/8/6/dataset_586fc714-17c7-4356-a812-a25593d0b941.dat,/tmp/tmpo3npfzdk/files/f/7/5/dataset_f75d3cb4-8d11-4da3-99ae-56a96adeb45c.dat,/tmp/tmpo3npfzdk/files/0/f/2/dataset_0f2c03d7-84e9-4908-8cc2-ce94b456ad1d.dat,/tmp/tmpo3npfzdk/files/6/1/6/dataset_616f4db3-1967-47c9-b869-b02bcebad7c0.dat,/tmp/tmpo3npfzdk/files/5/b/4/dataset_5b4d9931-2f94-469f-8fbb-dddd1b4f23fe.dat,/tmp/tmpo3npfzdk/files/1/c/9/dataset_1c9febe8-b1ff-4f7e-a395-fbd671fdbf0a.dat,/tmp/tmpo3npfzdk/files/1/5/6/dataset_156ffebe-1d63-442a-822e-94c26612aebb.dat' --domesticated_seq '/tmp/tmpo3npfzdk/files/a/3/2/dataset_a32d019a-ef10-42b8-92d3-b1a89149114e.dat,/tmp/tmpo3npfzdk/files/3/4/c/dataset_34ca3b9a-6d8e-4790-8e04-946f777aaa2f.dat,/tmp/tmpo3npfzdk/files/7/d/4/dataset_7d434fd6-3da6-4a35-a935-6262c2be3b95.dat,/tmp/tmpo3npfzdk/files/5/0/a/dataset_50a304a8-ff94-4efc-8d3c-9dd5714d0ab9.dat,/tmp/tmpo3npfzdk/files/d/4/7/dataset_d476b171-9eb3-4fcb-9e16-1d4631b211ae.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/5/8/6/dataset_586fc714-17c7-4356-a812-a25593d0b941.dat:part_A.gb,/tmp/tmpo3npfzdk/files/f/7/5/dataset_f75d3cb4-8d11-4da3-99ae-56a96adeb45c.dat:part_B.gb,/tmp/tmpo3npfzdk/files/0/f/2/dataset_0f2c03d7-84e9-4908-8cc2-ce94b456ad1d.dat:part_C.gb,/tmp/tmpo3npfzdk/files/6/1/6/dataset_616f4db3-1967-47c9-b869-b02bcebad7c0.dat:part_D.gb,/tmp/tmpo3npfzdk/files/5/b/4/dataset_5b4d9931-2f94-469f-8fbb-dddd1b4f23fe.dat:part_E.gb,/tmp/tmpo3npfzdk/files/1/c/9/dataset_1c9febe8-b1ff-4f7e-a395-fbd671fdbf0a.dat:part_F.gb,/tmp/tmpo3npfzdk/files/1/5/6/dataset_156ffebe-1d63-442a-822e-94c26612aebb.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpo3npfzdk/files/a/3/2/dataset_a32d019a-ef10-42b8-92d3-b1a89149114e.dat:part_H.gb,/tmp/tmpo3npfzdk/files/3/4/c/dataset_34ca3b9a-6d8e-4790-8e04-946f777aaa2f.dat:part_I.gb,/tmp/tmpo3npfzdk/files/7/d/4/dataset_7d434fd6-3da6-4a35-a935-6262c2be3b95.dat:part_J.gb,/tmp/tmpo3npfzdk/files/5/0/a/dataset_50a304a8-ff94-4efc-8d3c-9dd5714d0ab9.dat:part_K.gb,/tmp/tmpo3npfzdk/files/d/4/7/dataset_d476b171-9eb3-4fcb-9e16-1d4631b211ae.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/tmpo3npfzdk/job_working_directory/000/49/outputs/dataset_26f09d54-6733-4b4f-9110-58b7422f6584.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-19T13:47:53.361341",
+"create_time": "2025-05-21T14:50:16.787614",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "248775",
+"external_id": "320811",
 "galaxy_version": "24.2",
 "handler": null,
-"history_id": "6a73e15df176b356",
+"history_id": "d10d7a9bf6c42600",
-"id": "95f3db52d6362602",
+"id": "056fda651c637916",
 "inputs": {
 "assembly_csv": {
-"id": "8970dbe72f491b25",
+"id": "79581be26281c6bb",
 "src": "hda",
-"uuid": "9c8ec693-02f9-4cc7-b7e3-8bfb0a4dd1dc"
+"uuid": "8ccb55a4-733f-4671-a12c-c89cee5a694b"
 },
 "domesticated_input1": {
-"id": "e666d72d584b2f08",
+"id": "85db74d9c0951b21",
 "src": "hda",
-"uuid": "f6d602b9-7772-4a93-969d-f0dcdad98c6a"
+"uuid": "a32d019a-ef10-42b8-92d3-b1a89149114e"
 },
 "domesticated_input2": {
-"id": "55c4a2e28d82e47c",
+"id": "1088aa990b0f6a3e",
 "src": "hda",
-"uuid": "d4dc3ecb-77ff-4b28-a55a-7b263416c6c7"
+"uuid": "34ca3b9a-6d8e-4790-8e04-946f777aaa2f"
 },
 "domesticated_input3": {
-"id": "b7e1b2e4287fecf1",
+"id": "0adf69845d3170b2",
 "src": "hda",
-"uuid": "7d489dbd-161e-4f04-a3df-ef5b989ad1e0"
+"uuid": "7d434fd6-3da6-4a35-a935-6262c2be3b95"
 },
 "domesticated_input4": {
-"id": "fc5d10a4986179ce",
+"id": "f38cba32d894e055",
 "src": "hda",
-"uuid": "4ca3c222-672a-4806-b60c-081f1b7b64cb"
+"uuid": "50a304a8-ff94-4efc-8d3c-9dd5714d0ab9"
 },
 "domesticated_input5": {
-"id": "34217302c7a82039",
+"id": "d03e2be198c26beb",
 "src": "hda",
-"uuid": "906707db-b3cf-40f9-af0b-1ffc143f91e8"
+"uuid": "d476b171-9eb3-4fcb-9e16-1d4631b211ae"
 },
 "genbank_files1": {
-"id": "bb3a8c61045de2bc",
+"id": "7f005c8d8137335e",
 "src": "hda",
-"uuid": "193cbd10-4b76-46d9-b377-a7f06471d4d4"
+"uuid": "586fc714-17c7-4356-a812-a25593d0b941"
 },
 "genbank_files2": {
-"id": "ca37518126b9f794",
+"id": "2893678ebcfeac31",
 "src": "hda",
-"uuid": "fa31c5f5-e678-471e-b1a3-4f8a168bbee1"
+"uuid": "f75d3cb4-8d11-4da3-99ae-56a96adeb45c"
 },
 "genbank_files3": {
-"id": "f5318c255dfd98f3",
+"id": "eebf6b53a0733527",
 "src": "hda",
-"uuid": "697c83fe-168b-4319-a6e5-3db90c504c8b"
+"uuid": "0f2c03d7-84e9-4908-8cc2-ce94b456ad1d"
 },
 "genbank_files4": {
-"id": "95f3db52d6362602",
+"id": "056fda651c637916",
 "src": "hda",
-"uuid": "06d4dd94-5f33-4ce0-ab0a-e6efe96ca222"
+"uuid": "616f4db3-1967-47c9-b869-b02bcebad7c0"
 },
 "genbank_files5": {
-"id": "22334014eeb47b8b",
+"id": "554aac66b6b91c95",
 "src": "hda",
-"uuid": "701b72c6-ec2e-4435-b0d5-8f419811a4dd"
+"uuid": "5b4d9931-2f94-469f-8fbb-dddd1b4f23fe"
 },
 "genbank_files6": {
-"id": "aebcfa6b078c848c",
+"id": "e0b55cd244232b92",
 "src": "hda",
-"uuid": "5a07f059-f6f9-49de-b0fc-3cded157f44b"
+"uuid": "1c9febe8-b1ff-4f7e-a395-fbd671fdbf0a"
 },
 "genbank_files7": {
-"id": "63b7227f824d465f",
+"id": "5de07666a9f74c14",
 "src": "hda",
-"uuid": "753f0297-4bff-49c8-b22a-1377e43a81f6"
+"uuid": "156ffebe-1d63-442a-822e-94c26612aebb"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "40769e0726e5d2f9",
+"id": "acd1a5e1ec1673bf",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "00e4fea3ca53d1d5",
+"id": "bee5eb96186aeef0",
 "src": "hda",
-"uuid": "5cef395a-54ba-474b-b40b-1e5b3b2c4269"
+"uuid": "e0540e16-fb06-474f-9574-a0f8c8f44fae"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "684375afe9650993",
+"id": "19dda9511f29e82d",
 "src": "hda",
-"uuid": "77cca133-2fb3-4cf3-b4b1-a802a1f09ea3"
+"uuid": "3de1208e-5fa3-4899-b496-f1e4b8a69e8e"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "45afc15ea654e191",
+"id": "75d4ef21ebceb84b",
 "src": "hda",
-"uuid": "dbd53cde-61b2-4db8-b6bf-f0caaec76ace"
+"uuid": "39adc107-3c51-4ceb-a401-d1e85b10d36c"
 },
 "__new_primary_file_construct_gb|construct_4__": {
-"id": "8aa0c494b99ce49f",
+"id": "7d27617ebf2a7ca2",
 "src": "hda",
-"uuid": "8ea5339c-3186-4886-8af7-2a2d8134e161"
+"uuid": "5ff68ddd-6e45-47d3-877e-f0874370d1d7"
 },
 "output_zip": {
-"id": "4d559b2811c6a30e",
+"id": "aff3a7c3a5e84c2e",
 "src": "hda",
-"uuid": "800320dc-d181-40bf-b1cb-541f43a838c3"
+"uuid": "26f09d54-6733-4b4f-9110-58b7422f6584"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
 "adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpay0tme4v/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"chromInfo": "\"/tmp/tmpo3npfzdk/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,  2.35it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.13it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.77it/s, now=None]\r                                                                 \r",
+"stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.41it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.20it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.80it/s, now=None]\r                                                                 \r",
 "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,  2.35it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.13it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.77it/s, now=None]\r                                                                 \r",
+"tool_stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.41it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.20it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.80it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-19T13:48:06.412363",
+"update_time": "2025-05-21T14:50:29.418254",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "fd8809ceca5b90d8"
+"user_id": "9f2c11a06c2c8bb2"
 },
 "status": "success",
 "test_index": 5,
-"time_seconds": 55.54361414909363,
+"time_seconds": 52.95538687705994,
 "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": "1cfd8c9510cd79b8",
+"src": "hda"
+},
+"assembly_plan_name": "Type2sRestrictionAssembly",
+"domesticated_input": {
+"id": "18479e206f3c823f",
+"src": "hdca"
+},
+"topology": "circular"
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+"job": {
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpo3npfzdk/files/8/6/8/dataset_868edfc6-e59e-4522-bd0c-287140d27bcf.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.dat' --domesticated_seq '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat:part_A.gb,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat:part_B.gb,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat:part_C.gb,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat:part_D.gb,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat:part_E.gb,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat:part_F.gb,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat:part_G.gb,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat:part_H.gb,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat:part_I.gb,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat:part_J.gb,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat:part_K.gb,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.dat:part_L.gb' --file_name_mapping_dom '/tmp/tmpo3npfzdk/files/4/c/7/dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d.dat:part_A.gb,/tmp/tmpo3npfzdk/files/4/c/6/dataset_4c6b4c02-8f84-4314-8a13-682a855005e0.dat:part_B.gb,/tmp/tmpo3npfzdk/files/2/9/c/dataset_29c207fc-3958-40b7-8d3a-29486ebe729e.dat:part_C.gb,/tmp/tmpo3npfzdk/files/c/6/e/dataset_c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c.dat:part_D.gb,/tmp/tmpo3npfzdk/files/c/b/9/dataset_cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd.dat:part_E.gb,/tmp/tmpo3npfzdk/files/e/b/6/dataset_eb6733f2-ea91-4ce2-878c-0bca789bfe95.dat:part_F.gb,/tmp/tmpo3npfzdk/files/d/e/a/dataset_dea7a300-b098-41a1-863d-ec55e3b78bda.dat:part_G.gb,/tmp/tmpo3npfzdk/files/1/3/3/dataset_13300353-8b8d-4bd4-9d25-88dceda7594b.dat:part_H.gb,/tmp/tmpo3npfzdk/files/6/1/f/dataset_61ffb7d6-856a-4e4a-9da3-48a419455e92.dat:part_I.gb,/tmp/tmpo3npfzdk/files/e/6/4/dataset_e6431634-077e-451e-afa3-b12c08fc5c7c.dat:part_J.gb,/tmp/tmpo3npfzdk/files/7/5/8/dataset_758b4a45-c17d-4d1a-a289-79d3b2dfe524.dat:part_K.gb,/tmp/tmpo3npfzdk/files/2/2/6/dataset_226889a1-0543-4052-9d94-3276acdbd8ad.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/tmpo3npfzdk/job_working_directory/000/63/outputs/dataset_7ec4ccea-6d53-4d2c-b343-476013e8c0d9.dat'",
+"command_version": "",
+"copied_from_job_id": null,
+"create_time": "2025-05-21T14:51:10.356913",
+"dependencies": [
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+"model_class": "CondaDependencyResolver",
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+"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,
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+"exact": true,
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+},
+"dependency_type": "conda",
+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
+"exact": true,
+"model_class": "MergedCondaDependency",
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+"read_only": false,
+"resolver_type": "conda",
+"resolves_simple_dependencies": true,
+"use_local": false,
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+"environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf",
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+}
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+"exit_code": 1,
+"external_id": "321954",
+"galaxy_version": "24.2",
+"handler": null,
+"history_id": "6f2e93d50b248cee",
+"id": "7d27617ebf2a7ca2",
+"inputs": {
+"assembly_csv": {
+"id": "1cfd8c9510cd79b8",
+"src": "hda",
+"uuid": "868edfc6-e59e-4522-bd0c-287140d27bcf"
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+"domesticated_input1": {
+"id": "515ae798a3a66959",
+"src": "hda",
+"uuid": "4c7c671b-5fc3-4e96-b7f2-7e309d53588d"
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+"domesticated_input10": {
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+"src": "hda",
+"uuid": "e6431634-077e-451e-afa3-b12c08fc5c7c"
+},
+"domesticated_input11": {
+"id": "6d393a4d656a3907",
+"src": "hda",
+"uuid": "758b4a45-c17d-4d1a-a289-79d3b2dfe524"
+},
+"domesticated_input12": {
+"id": "b1f9d845e51287f2",
+"src": "hda",
+"uuid": "226889a1-0543-4052-9d94-3276acdbd8ad"
+},
+"domesticated_input2": {
+"id": "24ad2b10f2de1c15",
+"src": "hda",
+"uuid": "4c6b4c02-8f84-4314-8a13-682a855005e0"
+},
+"domesticated_input3": {
+"id": "6bd3728894d22921",
+"src": "hda",
+"uuid": "29c207fc-3958-40b7-8d3a-29486ebe729e"
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+"domesticated_input4": {
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+"src": "hda",
+"uuid": "c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c"
+},
+"domesticated_input5": {
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+"src": "hda",
+"uuid": "cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd"
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+"domesticated_input6": {
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+"src": "hda",
+"uuid": "eb6733f2-ea91-4ce2-878c-0bca789bfe95"
+},
+"domesticated_input7": {
+"id": "01a8e5946ae7b883",
+"src": "hda",
+"uuid": "dea7a300-b098-41a1-863d-ec55e3b78bda"
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+"domesticated_input8": {
+"id": "348481ce28d8892f",
+"src": "hda",
+"uuid": "13300353-8b8d-4bd4-9d25-88dceda7594b"
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+"domesticated_input9": {
+"id": "c53526ace39ecb75",
+"src": "hda",
+"uuid": "61ffb7d6-856a-4e4a-9da3-48a419455e92"
+},
+"genbank_files1": {
+"id": "515ae798a3a66959",
+"src": "hda",
+"uuid": "4c7c671b-5fc3-4e96-b7f2-7e309d53588d"
+},
+"genbank_files10": {
+"id": "ad6435740a2af171",
+"src": "hda",
+"uuid": "e6431634-077e-451e-afa3-b12c08fc5c7c"
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+"genbank_files11": {
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+"src": "hda",
+"uuid": "758b4a45-c17d-4d1a-a289-79d3b2dfe524"
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+"genbank_files12": {
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+"src": "hda",
+"uuid": "226889a1-0543-4052-9d94-3276acdbd8ad"
+},
+"genbank_files2": {
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+"src": "hda",
+"uuid": "4c6b4c02-8f84-4314-8a13-682a855005e0"
+},
+"genbank_files3": {
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+"src": "hda",
+"uuid": "29c207fc-3958-40b7-8d3a-29486ebe729e"
+},
+"genbank_files4": {
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+"src": "hda",
+"uuid": "c6e14abc-4cc3-4027-bb1b-cf87b4df2e4c"
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+"genbank_files5": {
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+"src": "hda",
+"uuid": "cb90c0ec-c5d5-4a0c-a2a8-82bdf58a4dcd"
+},
+"genbank_files6": {
+"id": "dac5f4fe4fc9d2c5",
+"src": "hda",
+"uuid": "eb6733f2-ea91-4ce2-878c-0bca789bfe95"
+},
+"genbank_files7": {
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+"src": "hda",
+"uuid": "dea7a300-b098-41a1-863d-ec55e3b78bda"
+},
+"genbank_files8": {
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+"src": "hda",
+"uuid": "13300353-8b8d-4bd4-9d25-88dceda7594b"
+},
+"genbank_files9": {
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+"src": "hda",
+"uuid": "61ffb7d6-856a-4e4a-9da3-48a419455e92"
+}
+},
+"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": "fae073f924dc0737",
+"src": "hdca"
+}
+},
+"outputs": {
+"output_zip": {
+"id": "24ef522ceac5a910",
+"src": "hda",
+"uuid": "7ec4ccea-6d53-4d2c-b343-476013e8c0d9"
+}
+},
+"params": {
+"__input_ext": "\"input\"",
+"adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
+"assembly_plan_name": "\"Type2sRestrictionAssembly\"",
+"chromInfo": "\"/tmp/tmpo3npfzdk/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"dbkey": "\"?\"",
+"domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}",
+"genbank_files": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}",
+"topology": "\"circular\""
+},
+"state": "error",
+"stderr": "Traceback (most recent call last):\n  File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, 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 22, in cloning_simulation\n    repository.import_records(files=domesticated_files,\n    ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n                                 use_file_names_as_ids=use_file_names_as_id,\n                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n                                 topology=topology)\n                                 ^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n    self.add_records(records, collection=collection)\n    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n    self.add_record(record, collection=collection)\n    ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n    raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in  in repo\n",
+"stdout": "",
+"tool_id": "cloning_simulation",
+"tool_stderr": "Traceback (most recent call last):\n  File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, 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 22, in cloning_simulation\n    repository.import_records(files=domesticated_files,\n    ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n                                 use_file_names_as_ids=use_file_names_as_id,\n                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n                                 topology=topology)\n                                 ^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n    self.add_records(records, collection=collection)\n    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n    self.add_record(record, collection=collection)\n    ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n    raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in  in repo\n",
+"tool_stdout": "",
+"update_time": "2025-05-21T14:51:18.877985",
+"user_email": "planemo@galaxyproject.org",
+"user_id": "9f2c11a06c2c8bb2"
+},
+"output_problems": [
+"Job in error state.. tool_id: cloning_simulation, exit_code: 1, stderr: Traceback (most recent call last):\n  File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, 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 22, in cloning_simulation\n    repository.import_records(files=domesticated_files,\n    ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n                                 use_file_names_as_ids=use_file_names_as_id,\n                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n                                 topology=topology)\n                                 ^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n    self.add_records(records, collection=collection)\n    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n    self.add_record(record, collection=collection)\n    ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n    raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in  in repo\n.",
+"Job in error state.. tool_id: cloning_simulation, exit_code: 1, stderr: Traceback (most recent call last):\n  File \"/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py\", line 165, 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 22, in cloning_simulation\n    repository.import_records(files=domesticated_files,\n    ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^\n                                 use_file_names_as_ids=use_file_names_as_id,\n                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n                                 topology=topology)\n                                 ^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 170, in import_records\n    self.add_records(records, collection=collection)\n    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 96, in add_records\n    self.add_record(record, collection=collection)\n    ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/rkhaled/miniconda3/envs/mulled-v1-6c2b9ebb475a37bd0d9ca7857474e8574719e546de882810f7828fe5993a8adf/lib/python3.13/site-packages/dnacauldron/SequenceRepository.py\", line 85, in add_record\n    raise RepositoryDuplicateError([record.id], repository=self)\ndnacauldron.SequenceRepository.RepositoryDuplicateError: Part ID dataset_4c7c671b-5fc3-4e96-b7f2-7e309d53588d duplicated in  in repo\n.",
+"Output collection 'construct_gb': expected to have 4 elements, but it had 0."
+],
+"status": "failure",
+"test_index": 6,
+"time_seconds": 49.28661274909973,
+"tool_id": "cloning_simulation",
+"tool_version": "0.1.0+galaxy0"
+},
+"has_data": true,
+"id": "cloning_simulation-6"
 }
 ],
 "version": "0.1"
 }

Mercurial > repos > tduigou > cloning_simulation

comparison output.json @ 6:e1e985913204 draft