cloning_simulation: output.json comparison

comparison output.json @ 16:fbb241adf6c2 draft default tip

planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty

author	tduigou
date	Thu, 17 Jul 2025 10:17:24 +0000
parents	074a76e84b80
children

comparison

equal deleted inserted replaced

-:074a76e84b80
+:fbb241adf6c2
 {
 "summary": {
 "num_errors": 0,
 "num_failures": 0,
 "num_skips": 0,
-"num_tests": 7
+"num_tests": 8
 },
 "tests": [
 {
 "data": {
 "inputs": {
-"adv|use_file_names_as_ids": true,
 "assembly_csv": {
-"id": "1e8e6749bc68d8e8",
+"id": "54d710fc68386373",
 "src": "hda"
 },
-"assembly_plan_name": "Type2sRestrictionAssembly",
 "genbank_files": {
-"id": "e2ca7f14a85a8d44",
+"id": "986c9b47c580ae59",
 "src": "hdca"
 },
-"topology": "circular"
+"json_use|assembly_plan_name": "Type2sRestrictionAssembly",
+"json_use|topology": "circular",
+"json_use|use_json_paramers": false,
+"use_file_names_as_ids": true
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/2/0/d/dataset_20d4061a-81e4-4915-a841-ae8aa595c7b4.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/d/d/8/dataset_dd844d61-fc05-41d9-8179-21233649407d.dat,/tmp/tmpm1fyob3t/files/c/b/2/dataset_cb2362f3-4b32-46cc-a227-dc15742bf9e7.dat,/tmp/tmpm1fyob3t/files/6/d/7/dataset_6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a.dat,/tmp/tmpm1fyob3t/files/3/3/e/dataset_33e804b2-0fbe-4844-9b5d-420e8a2db772.dat,/tmp/tmpm1fyob3t/files/2/d/b/dataset_2db3825c-538b-483f-b6ff-8dc4ecc03780.dat,/tmp/tmpm1fyob3t/files/0/4/8/dataset_048ee7ed-5f4c-41ef-aed4-f2cf975aac92.dat,/tmp/tmpm1fyob3t/files/c/5/0/dataset_c505c12e-7089-4a17-a605-4f11dad6f1d7.dat,/tmp/tmpm1fyob3t/files/4/9/1/dataset_4912f12d-0842-46b7-8aaf-2a94a52f04f8.dat,/tmp/tmpm1fyob3t/files/b/2/b/dataset_b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027.dat,/tmp/tmpm1fyob3t/files/b/8/f/dataset_b8fd4610-2f6d-475c-8405-8bf8c2bc0306.dat,/tmp/tmpm1fyob3t/files/0/9/f/dataset_09f4b020-4e7b-4939-b3ba-348f91cb92bc.dat,/tmp/tmpm1fyob3t/files/e/b/7/dataset_eb730263-9442-4dca-a2dc-34b1cae450d7.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/d/d/8/dataset_dd844d61-fc05-41d9-8179-21233649407d.dat:part_A.gb,/tmp/tmpm1fyob3t/files/c/b/2/dataset_cb2362f3-4b32-46cc-a227-dc15742bf9e7.dat:part_B.gb,/tmp/tmpm1fyob3t/files/6/d/7/dataset_6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a.dat:part_C.gb,/tmp/tmpm1fyob3t/files/3/3/e/dataset_33e804b2-0fbe-4844-9b5d-420e8a2db772.dat:part_D.gb,/tmp/tmpm1fyob3t/files/2/d/b/dataset_2db3825c-538b-483f-b6ff-8dc4ecc03780.dat:part_E.gb,/tmp/tmpm1fyob3t/files/0/4/8/dataset_048ee7ed-5f4c-41ef-aed4-f2cf975aac92.dat:part_F.gb,/tmp/tmpm1fyob3t/files/c/5/0/dataset_c505c12e-7089-4a17-a605-4f11dad6f1d7.dat:part_G.gb,/tmp/tmpm1fyob3t/files/4/9/1/dataset_4912f12d-0842-46b7-8aaf-2a94a52f04f8.dat:part_H.gb,/tmp/tmpm1fyob3t/files/b/2/b/dataset_b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027.dat:part_I.gb,/tmp/tmpm1fyob3t/files/b/8/f/dataset_b8fd4610-2f6d-475c-8405-8bf8c2bc0306.dat:part_J.gb,/tmp/tmpm1fyob3t/files/0/9/f/dataset_09f4b020-4e7b-4939-b3ba-348f91cb92bc.dat:part_K.gb,/tmp/tmpm1fyob3t/files/e/b/7/dataset_eb730263-9442-4dca-a2dc-34b1cae450d7.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/tmpm1fyob3t/job_working_directory/000/14/outputs/dataset_64d1d8ac-32f0-4095-be30-22eee31e24a4.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/0/b/1/dataset_0b1d9a31-e124-42cf-b995-f7c136900f29.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/7/6/9/dataset_76952c3c-fc12-4748-87cb-b6af38db9d3e.dat,/tmp/tmpe6pmg7jw/files/9/a/6/dataset_9a60f4af-d7d4-4bce-ab79-3718dac468ed.dat,/tmp/tmpe6pmg7jw/files/f/e/c/dataset_fec08236-4b1b-4174-af9c-7c3a84487424.dat,/tmp/tmpe6pmg7jw/files/2/0/6/dataset_206ca419-7921-4fc1-9be0-12c35c84bd65.dat,/tmp/tmpe6pmg7jw/files/3/1/b/dataset_31bb0b24-e75c-493f-a016-3796d54eaa18.dat,/tmp/tmpe6pmg7jw/files/6/f/a/dataset_6fa953c7-a9a7-4ba7-a030-da147eadefdc.dat,/tmp/tmpe6pmg7jw/files/7/e/f/dataset_7ef147cb-f331-435c-9a1e-6f0e52abd102.dat,/tmp/tmpe6pmg7jw/files/9/b/6/dataset_9b611c55-c19e-42ce-b45c-40ac049b94cb.dat,/tmp/tmpe6pmg7jw/files/9/b/d/dataset_9bd8627e-0417-475f-b855-352bcd890630.dat,/tmp/tmpe6pmg7jw/files/1/6/4/dataset_164135c0-7b54-4ea0-86d3-e9e928cbc398.dat,/tmp/tmpe6pmg7jw/files/b/e/9/dataset_be927bb4-1a34-43bb-8680-81589459732b.dat,/tmp/tmpe6pmg7jw/files/8/a/4/dataset_8a4bab33-b3e8-4586-b375-ae904dc06793.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/7/6/9/dataset_76952c3c-fc12-4748-87cb-b6af38db9d3e.dat:part_A.gb,/tmp/tmpe6pmg7jw/files/9/a/6/dataset_9a60f4af-d7d4-4bce-ab79-3718dac468ed.dat:part_B.gb,/tmp/tmpe6pmg7jw/files/f/e/c/dataset_fec08236-4b1b-4174-af9c-7c3a84487424.dat:part_C.gb,/tmp/tmpe6pmg7jw/files/2/0/6/dataset_206ca419-7921-4fc1-9be0-12c35c84bd65.dat:part_D.gb,/tmp/tmpe6pmg7jw/files/3/1/b/dataset_31bb0b24-e75c-493f-a016-3796d54eaa18.dat:part_E.gb,/tmp/tmpe6pmg7jw/files/6/f/a/dataset_6fa953c7-a9a7-4ba7-a030-da147eadefdc.dat:part_F.gb,/tmp/tmpe6pmg7jw/files/7/e/f/dataset_7ef147cb-f331-435c-9a1e-6f0e52abd102.dat:part_G.gb,/tmp/tmpe6pmg7jw/files/9/b/6/dataset_9b611c55-c19e-42ce-b45c-40ac049b94cb.dat:part_H.gb,/tmp/tmpe6pmg7jw/files/9/b/d/dataset_9bd8627e-0417-475f-b855-352bcd890630.dat:part_I.gb,/tmp/tmpe6pmg7jw/files/1/6/4/dataset_164135c0-7b54-4ea0-86d3-e9e928cbc398.dat:part_J.gb,/tmp/tmpe6pmg7jw/files/b/e/9/dataset_be927bb4-1a34-43bb-8680-81589459732b.dat:part_K.gb,/tmp/tmpe6pmg7jw/files/8/a/4/dataset_8a4bab33-b3e8-4586-b375-ae904dc06793.dat:part_L.gb' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'Type2sRestrictionAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/14/outputs/dataset_95e21ebc-5bff-4544-a5d4-06db22e91066.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T12:02:32.643157",
+"create_time": "2025-07-17T10:10:24.406223",
 "dependencies": [],
 "exit_code": 0,
-"external_id": "172939",
+"external_id": "75641",
-"galaxy_version": "24.2",
+"galaxy_version": "25.0",
 "handler": null,
-"history_id": "e2ca7f14a85a8d44",
+"history_id": "986c9b47c580ae59",
-"id": "a36db940f4513bd9",
+"id": "98a2432f1cff4f91",
 "inputs": {
 "assembly_csv": {
-"id": "1e8e6749bc68d8e8",
+"id": "54d710fc68386373",
 "src": "hda",
-"uuid": "20d4061a-81e4-4915-a841-ae8aa595c7b4"
+"uuid": "0b1d9a31-e124-42cf-b995-f7c136900f29"
 },
 "genbank_files1": {
-"id": "e2ca7f14a85a8d44",
+"id": "986c9b47c580ae59",
 "src": "hda",
-"uuid": "dd844d61-fc05-41d9-8179-21233649407d"
+"uuid": "76952c3c-fc12-4748-87cb-b6af38db9d3e"
 },
 "genbank_files10": {
-"id": "fbec4a551130f847",
+"id": "8de66704b7df8b5e",
 "src": "hda",
-"uuid": "b8fd4610-2f6d-475c-8405-8bf8c2bc0306"
+"uuid": "164135c0-7b54-4ea0-86d3-e9e928cbc398"
 },
 "genbank_files11": {
-"id": "5bd8560352cb0b69",
+"id": "54c6d71c8dc7cb11",
 "src": "hda",
-"uuid": "09f4b020-4e7b-4939-b3ba-348f91cb92bc"
+"uuid": "be927bb4-1a34-43bb-8680-81589459732b"
 },
 "genbank_files12": {
-"id": "cb2fe7fb50f38553",
+"id": "2592d2c705ba0baa",
 "src": "hda",
-"uuid": "eb730263-9442-4dca-a2dc-34b1cae450d7"
+"uuid": "8a4bab33-b3e8-4586-b375-ae904dc06793"
 },
 "genbank_files2": {
-"id": "62e98d1a229b6ef5",
+"id": "8354ecc64d56337d",
 "src": "hda",
-"uuid": "cb2362f3-4b32-46cc-a227-dc15742bf9e7"
+"uuid": "9a60f4af-d7d4-4bce-ab79-3718dac468ed"
 },
 "genbank_files3": {
-"id": "f8fe24202fc5b2e5",
+"id": "c06bae188baa9490",
 "src": "hda",
-"uuid": "6d72dfe4-3e6b-4baf-b7b5-9fb2e843461a"
+"uuid": "fec08236-4b1b-4174-af9c-7c3a84487424"
 },
 "genbank_files4": {
-"id": "0d58e12bbe78a903",
+"id": "71d208f6d8b613ba",
 "src": "hda",
-"uuid": "33e804b2-0fbe-4844-9b5d-420e8a2db772"
+"uuid": "206ca419-7921-4fc1-9be0-12c35c84bd65"
 },
 "genbank_files5": {
-"id": "3937d5ff7c0e1373",
+"id": "58ad66a9f93223b8",
 "src": "hda",
-"uuid": "2db3825c-538b-483f-b6ff-8dc4ecc03780"
+"uuid": "31bb0b24-e75c-493f-a016-3796d54eaa18"
 },
 "genbank_files6": {
-"id": "473b1992d5f5b84f",
+"id": "e9003a596293e37c",
 "src": "hda",
-"uuid": "048ee7ed-5f4c-41ef-aed4-f2cf975aac92"
+"uuid": "6fa953c7-a9a7-4ba7-a030-da147eadefdc"
 },
 "genbank_files7": {
-"id": "9b5c1fe7a52a75e0",
+"id": "8c39a9a410cc0a00",
 "src": "hda",
-"uuid": "c505c12e-7089-4a17-a605-4f11dad6f1d7"
+"uuid": "7ef147cb-f331-435c-9a1e-6f0e52abd102"
 },
 "genbank_files8": {
-"id": "c32c50a47ebf8564",
+"id": "f7b25594aba42961",
 "src": "hda",
-"uuid": "4912f12d-0842-46b7-8aaf-2a94a52f04f8"
+"uuid": "9b611c55-c19e-42ce-b45c-40ac049b94cb"
 },
 "genbank_files9": {
-"id": "5f035ce298b798b0",
+"id": "5f098a2d242af5ee",
 "src": "hda",
-"uuid": "b2b96d41-c7c8-49c1-9d35-ceaa1c7d3027"
+"uuid": "9bd8627e-0417-475f-b855-352bcd890630"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "62e98d1a229b6ef5",
+"id": "8354ecc64d56337d",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "182eefa577c2a56d",
+"id": "172543d29b19f394",
 "src": "hda",
-"uuid": "991437a5-bbe4-4adb-8831-c9a871adb17f"
+"uuid": "c12d7e47-49c5-4805-8a24-5d4fb0aa8cfa"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "979fd704a8b37879",
+"id": "018c827a8e5b161a",
 "src": "hda",
-"uuid": "9ebdb527-8609-4bc8-85a3-f8775156c356"
+"uuid": "be0c60c4-c33d-4855-95d4-ffdb53751eea"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "b53ff5232a859d40",
+"id": "494079827008dff1",
 "src": "hda",
-"uuid": "235361e4-93cc-4b56-ad81-c33ce8f593f0"
+"uuid": "77ec05f3-e147-4ff3-af59-1d173fbc6d27"
 },
 "__new_primary_file_construct_gb|construct_4__": {
-"id": "1ce0e68b6cd95b3c",
+"id": "665c2a499b613b70",
 "src": "hda",
-"uuid": "49100d5c-134b-4cb0-a86b-2cf03a336b1c"
+"uuid": "fd3ed880-c345-47d7-8a38-1ce5c507b417"
 },
 "output_zip": {
-"id": "a36db940f4513bd9",
+"id": "98a2432f1cff4f91",
 "src": "hda",
-"uuid": "64d1d8ac-32f0-4095-be30-22eee31e24a4"
+"uuid": "95e21ebc-5bff-4544-a5d4-06db22e91066"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
-"adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
+"chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
-"assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
-"topology": "\"circular\""
+"json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"Type2sRestrictionAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}",
+"use_file_names_as_ids": "true"
 },
 "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,  2.58it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.26it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.82it/s, now=None]\r                                                                 \r",
+"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,  2.23it/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": "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,  2.58it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.26it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.82it/s, now=None]\r                                                                 \r",
+"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,  2.23it/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": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T12:02:45.106475",
+"update_time": "2025-07-17T10:10:36.297958",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "e2ca7f14a85a8d44"
+"user_id": "986c9b47c580ae59"
 },
 "status": "success",
 "test_index": 0,
-"time_seconds": 53.48332858085632,
+"time_seconds": 52.21098494529724,
 "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": "035124d32eef3033",
+"id": "cf7d3dafd862f640",
 "src": "hda"
 },
-"assembly_plan_name": "GibsonAssembly",
 "genbank_files": {
-"id": "f8fe24202fc5b2e5",
+"id": "c06bae188baa9490",
 "src": "hdca"
 },
-"topology": "circular"
+"json_use|assembly_plan_name": "GibsonAssembly",
+"json_use|topology": "circular",
+"json_use|use_json_paramers": false,
+"use_file_names_as_ids": true
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/1/6/f/dataset_16f6d475-b614-4427-9c06-95a0d56d3c92.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/9/6/a/dataset_96a8f769-3544-4407-b064-04f24a733896.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'GibsonAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/9/6/a/dataset_96a8f769-3544-4407-b064-04f24a733896.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/tmpm1fyob3t/job_working_directory/000/17/outputs/dataset_505ecb2d-a6ca-40d3-864d-fc3e8bc7f9a1.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/2/a/d/dataset_2ad9afbb-7953-4cd9-bff3-482993791028.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/7/0/8/dataset_708e1901-be64-41f9-b767-b1749a71b785.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/7/0/8/dataset_708e1901-be64-41f9-b767-b1749a71b785.dat:gibson_sequences.fa' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'GibsonAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/17/outputs/dataset_9a58e169-47f4-4418-8a3b-0fec86242b5c.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T12:02:55.721992",
+"create_time": "2025-07-17T10:10:47.298570",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "173310",
+"external_id": "76029",
-"galaxy_version": "24.2",
+"galaxy_version": "25.0",
 "handler": null,
-"history_id": "62e98d1a229b6ef5",
+"history_id": "8354ecc64d56337d",
-"id": "b53ff5232a859d40",
+"id": "494079827008dff1",
 "inputs": {
 "assembly_csv": {
-"id": "035124d32eef3033",
+"id": "cf7d3dafd862f640",
 "src": "hda",
-"uuid": "16f6d475-b614-4427-9c06-95a0d56d3c92"
+"uuid": "2ad9afbb-7953-4cd9-bff3-482993791028"
 },
 "genbank_files1": {
-"id": "1fe688df02a38cc2",
+"id": "ccc90f05d17193c7",
 "src": "hda",
-"uuid": "96a8f769-3544-4407-b064-04f24a733896"
+"uuid": "708e1901-be64-41f9-b767-b1749a71b785"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "0d58e12bbe78a903",
+"id": "71d208f6d8b613ba",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "f970a04054a49348",
+"id": "5c63ea88ecac53b0",
 "src": "hda",
-"uuid": "ff8ea1a1-10ff-4416-b944-a78a4fd3e72e"
+"uuid": "bdd63ae3-8743-4fb8-b62e-15e2dd1b22fe"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "ae9b306409c7f353",
+"id": "56f89f48d02eaad8",
 "src": "hda",
-"uuid": "7afee741-2c2b-4e3b-a947-819ebb5b67b4"
+"uuid": "ae8106cf-202a-4ae6-b3be-0af4a59bf28b"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "791483eeafbe6bcb",
+"id": "a5c371b6918b1c88",
 "src": "hda",
-"uuid": "c820ba84-23dc-4e1c-b2de-abed54b17015"
+"uuid": "7085c961-0057-4a6f-93a5-e28a77e87a65"
 },
 "output_zip": {
-"id": "cd80768c91dddfb6",
+"id": "f0ec65f930df3348",
 "src": "hda",
-"uuid": "505ecb2d-a6ca-40d3-864d-fc3e8bc7f9a1"
+"uuid": "9a58e169-47f4-4418-8a3b-0fec86242b5c"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
-"adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
+"chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
-"assembly_plan_name": "\"GibsonAssembly\"",
-"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
-"topology": "\"circular\""
+"json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"GibsonAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}",
+"use_file_names_as_ids": "true"
 },
 "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,  4.35it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.33it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.31it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.53it/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,  4.37it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.38it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.38it/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",
 "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,  4.35it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.33it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.31it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 5/5 [00:01<00:00,  3.53it/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,  4.37it/s, now=None]\rassembly:  60%|\u2588\u2588\u2588\u2588\u2588\u2588    | 3/5 [00:00<00:00,  4.38it/s, now=None]\rassembly:  80%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588  | 4/5 [00:00<00:00,  4.38it/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_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 2, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T12:03:07.748084",
+"update_time": "2025-07-17T10:10:58.876561",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "e2ca7f14a85a8d44"
+"user_id": "986c9b47c580ae59"
 },
 "status": "success",
 "test_index": 1,
-"time_seconds": 22.338457345962524,
+"time_seconds": 22.198808431625366,
 "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": "c9169186136d0f27",
+"id": "9f199e72d4c8734c",
 "src": "hda"
 },
-"assembly_plan_name": "LigaseCyclingReactionAssembly",
 "genbank_files": {
-"id": "3937d5ff7c0e1373",
+"id": "58ad66a9f93223b8",
 "src": "hdca"
 },
-"topology": "circular"
+"json_use|assembly_plan_name": "LigaseCyclingReactionAssembly",
+"json_use|topology": "circular",
+"json_use|use_json_paramers": false,
+"use_file_names_as_ids": true
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/7/c/dataset_f7c9ad78-8e74-4a3c-9579-80a93ac923de.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/f/5/6/dataset_f56913bd-fc92-4122-8cf1-d9b1c60e8385.dat,/tmp/tmpm1fyob3t/files/3/b/4/dataset_3b4e75b3-e6a6-459a-a959-d43ce00c3701.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'LigaseCyclingReactionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/f/5/6/dataset_f56913bd-fc92-4122-8cf1-d9b1c60e8385.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpm1fyob3t/files/3/b/4/dataset_3b4e75b3-e6a6-459a-a959-d43ce00c3701.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/tmpm1fyob3t/job_working_directory/000/21/outputs/dataset_3fc625c8-722f-4efb-9c09-0d664dec2a9d.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/d/4/f/dataset_d4f42cf4-85ed-4eb7-ab79-944239671a0c.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/c/6/6/dataset_c66662f5-5307-40f5-b7d8-1ae34e9bc594.dat,/tmp/tmpe6pmg7jw/files/e/b/b/dataset_ebb77d89-fcaf-4aad-ae07-bd6df1cbc75d.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/c/6/6/dataset_c66662f5-5307-40f5-b7d8-1ae34e9bc594.dat:RFP_GFP_plasmid_BOs.fa,/tmp/tmpe6pmg7jw/files/e/b/b/dataset_ebb77d89-fcaf-4aad-ae07-bd6df1cbc75d.dat:RFP_GFP_plasmid_parts.fa' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'LigaseCyclingReactionAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/21/outputs/dataset_e37b2d54-bd4d-445c-9171-dd049f49ed36.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T12:03:18.983816",
+"create_time": "2025-07-17T10:11:10.098701",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "173689",
+"external_id": "76477",
-"galaxy_version": "24.2",
+"galaxy_version": "25.0",
 "handler": null,
-"history_id": "f8fe24202fc5b2e5",
+"history_id": "c06bae188baa9490",
-"id": "cd80768c91dddfb6",
+"id": "f0ec65f930df3348",
 "inputs": {
 "assembly_csv": {
-"id": "c9169186136d0f27",
+"id": "9f199e72d4c8734c",
 "src": "hda",
-"uuid": "f7c9ad78-8e74-4a3c-9579-80a93ac923de"
+"uuid": "d4f42cf4-85ed-4eb7-ab79-944239671a0c"
 },
 "genbank_files1": {
-"id": "f14f22136515e5fc",
+"id": "4eec6dacaee8b95b",
 "src": "hda",
-"uuid": "f56913bd-fc92-4122-8cf1-d9b1c60e8385"
+"uuid": "c66662f5-5307-40f5-b7d8-1ae34e9bc594"
 },
 "genbank_files2": {
-"id": "d00c2a698869e2f3",
+"id": "214d04ae88ac0b41",
 "src": "hda",
-"uuid": "3b4e75b3-e6a6-459a-a959-d43ce00c3701"
+"uuid": "ebb77d89-fcaf-4aad-ae07-bd6df1cbc75d"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "473b1992d5f5b84f",
+"id": "e9003a596293e37c",
 "src": "hdca"
 }
 },
 "outputs": {
 "output_zip": {
-"id": "0bb6e1adb7bbb7d6",
+"id": "1893df3b29988972",
 "src": "hda",
-"uuid": "3fc625c8-722f-4efb-9c09-0d664dec2a9d"
+"uuid": "e37b2d54-bd4d-445c-9171-dd049f49ed36"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
-"adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
+"chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
-"assembly_plan_name": "\"LigaseCyclingReactionAssembly\"",
-"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 5, \"src\": \"hdca\"}]}",
-"topology": "\"circular\""
+"json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"LigaseCyclingReactionAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}",
+"use_file_names_as_ids": "true"
 },
 "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,  2.40it/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,  2.40it/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": "2025-05-26T12:03:31.119796",
+"update_time": "2025-07-17T10:11:21.625362",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "e2ca7f14a85a8d44"
+"user_id": "986c9b47c580ae59"
 },
 "status": "success",
 "test_index": 2,
-"time_seconds": 23.440476655960083,
+"time_seconds": 22.644192218780518,
 "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": "b66a1bb5ed06a6bf",
+"id": "62b2e7c0b424e83e",
 "src": "hda"
 },
-"assembly_plan_name": "BASICAssembly",
 "genbank_files": {
-"id": "9b5c1fe7a52a75e0",
+"id": "8c39a9a410cc0a00",
 "src": "hdca"
 },
-"topology": "circular"
+"json_use|assembly_plan_name": "BASICAssembly",
+"json_use|topology": "circular",
+"json_use|use_json_paramers": false,
+"use_file_names_as_ids": true
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/b/4/dataset_fb426ceb-2615-447d-b04e-ae4253af648d.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/e/c/b/dataset_ecb057a2-dbf8-4105-b55e-d726ec1e9693.dat,/tmp/tmpm1fyob3t/files/4/9/8/dataset_498fe703-52c3-4162-be00-93f49f00689d.dat,/tmp/tmpm1fyob3t/files/d/4/0/dataset_d402c2ac-ca2d-46b6-b9d3-989739678de1.dat,/tmp/tmpm1fyob3t/files/1/1/2/dataset_1124ff36-f61b-4932-adc6-0b6de5a888ae.dat,/tmp/tmpm1fyob3t/files/8/f/e/dataset_8fe51091-39c5-4aa6-b0ec-fbc34712e405.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BASICAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/e/c/b/dataset_ecb057a2-dbf8-4105-b55e-d726ec1e9693.dat:GFP.gb,/tmp/tmpm1fyob3t/files/4/9/8/dataset_498fe703-52c3-4162-be00-93f49f00689d.dat:p15A_kan.gb,/tmp/tmpm1fyob3t/files/d/4/0/dataset_d402c2ac-ca2d-46b6-b9d3-989739678de1.dat:promoter.gb,/tmp/tmpm1fyob3t/files/1/1/2/dataset_1124ff36-f61b-4932-adc6-0b6de5a888ae.dat:RFP.gb,/tmp/tmpm1fyob3t/files/8/f/e/dataset_8fe51091-39c5-4aa6-b0ec-fbc34712e405.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/tmpm1fyob3t/job_working_directory/000/28/outputs/dataset_45ef7ed5-48aa-4286-ac51-3391b593eb7c.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/b/f/1/dataset_bf11bd3d-ca0e-4756-8106-142184dc57e7.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/a/f/3/dataset_af32db16-e6dc-493f-b6a7-5a3b6725a736.dat,/tmp/tmpe6pmg7jw/files/a/4/9/dataset_a4936e9b-d8be-4cf9-8d6c-1c625676bc58.dat,/tmp/tmpe6pmg7jw/files/0/3/c/dataset_03cda120-0c4d-4452-afab-925df4a5723a.dat,/tmp/tmpe6pmg7jw/files/3/b/1/dataset_3b164cad-fbab-47a9-8965-c95820826daf.dat,/tmp/tmpe6pmg7jw/files/a/b/3/dataset_ab35511d-2fbf-4014-b079-65b270bd9cc8.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/a/f/3/dataset_af32db16-e6dc-493f-b6a7-5a3b6725a736.dat:GFP.gb,/tmp/tmpe6pmg7jw/files/a/4/9/dataset_a4936e9b-d8be-4cf9-8d6c-1c625676bc58.dat:p15A_kan.gb,/tmp/tmpe6pmg7jw/files/0/3/c/dataset_03cda120-0c4d-4452-afab-925df4a5723a.dat:promoter.gb,/tmp/tmpe6pmg7jw/files/3/b/1/dataset_3b164cad-fbab-47a9-8965-c95820826daf.dat:RFP.gb,/tmp/tmpe6pmg7jw/files/a/b/3/dataset_ab35511d-2fbf-4014-b079-65b270bd9cc8.dat:oligos.fa' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'BASICAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/28/outputs/dataset_f130e84e-8140-449b-bb7e-8df370a421d1.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T12:03:51.986652",
+"create_time": "2025-07-17T10:11:42.348377",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "174270",
+"external_id": "77127",
-"galaxy_version": "24.2",
+"galaxy_version": "25.0",
 "handler": null,
-"history_id": "0d58e12bbe78a903",
+"history_id": "71d208f6d8b613ba",
-"id": "0bb6e1adb7bbb7d6",
+"id": "1893df3b29988972",
 "inputs": {
 "assembly_csv": {
-"id": "b66a1bb5ed06a6bf",
+"id": "62b2e7c0b424e83e",
 "src": "hda",
-"uuid": "fb426ceb-2615-447d-b04e-ae4253af648d"
+"uuid": "bf11bd3d-ca0e-4756-8106-142184dc57e7"
 },
 "genbank_files1": {
-"id": "4c26f2b3928e5c2b",
+"id": "b20d34fd097d655b",
 "src": "hda",
-"uuid": "ecb057a2-dbf8-4105-b55e-d726ec1e9693"
+"uuid": "af32db16-e6dc-493f-b6a7-5a3b6725a736"
 },
 "genbank_files2": {
-"id": "7f1b25c57f1b4097",
+"id": "38d1a5747f8e5978",
 "src": "hda",
-"uuid": "498fe703-52c3-4162-be00-93f49f00689d"
+"uuid": "a4936e9b-d8be-4cf9-8d6c-1c625676bc58"
 },
 "genbank_files3": {
-"id": "cbd9b7f3981a10ff",
+"id": "aa0c2bc050c99399",
 "src": "hda",
-"uuid": "d402c2ac-ca2d-46b6-b9d3-989739678de1"
+"uuid": "03cda120-0c4d-4452-afab-925df4a5723a"
 },
 "genbank_files4": {
-"id": "8f1ec376bf339086",
+"id": "7696fc7f810474ba",
 "src": "hda",
-"uuid": "1124ff36-f61b-4932-adc6-0b6de5a888ae"
+"uuid": "3b164cad-fbab-47a9-8965-c95820826daf"
 },
 "genbank_files5": {
-"id": "a91e9fd0ce2e3c53",
+"id": "bf4065b67294e257",
 "src": "hda",
-"uuid": "8fe51091-39c5-4aa6-b0ec-fbc34712e405"
+"uuid": "ab35511d-2fbf-4014-b079-65b270bd9cc8"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "c32c50a47ebf8564",
+"id": "f7b25594aba42961",
 "src": "hdca"
 }
 },
 "outputs": {
 "output_zip": {
-"id": "2be24ce9bdbc87e1",
+"id": "1f477a8cb4ab1699",
 "src": "hda",
-"uuid": "45ef7ed5-48aa-4286-ac51-3391b593eb7c"
+"uuid": "f130e84e-8140-449b-bb7e-8df370a421d1"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
-"adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
+"chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
-"assembly_plan_name": "\"BASICAssembly\"",
-"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 7, \"src\": \"hdca\"}]}",
-"topology": "\"circular\""
+"json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"BASICAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}",
+"use_file_names_as_ids": "true"
 },
 "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:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 6/8 [00:00<00:00, 48.97it/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, 49.66it/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:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 6/8 [00:00<00:00, 48.97it/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, 49.66it/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": "2025-05-26T12:04:01.978111",
+"update_time": "2025-07-17T10:11:52.291581",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "e2ca7f14a85a8d44"
+"user_id": "986c9b47c580ae59"
 },
 "status": "success",
 "test_index": 3,
-"time_seconds": 30.717636823654175,
+"time_seconds": 30.479472160339355,
 "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": "5493159c7d57114c",
+"id": "38b6c0c549bf284f",
 "src": "hda"
 },
-"assembly_plan_name": "BioBrickStandardAssembly",
 "genbank_files": {
-"id": "5f035ce298b798b0",
+"id": "5f098a2d242af5ee",
 "src": "hdca"
 },
-"topology": "circular"
+"json_use|assembly_plan_name": "BioBrickStandardAssembly",
+"json_use|topology": "circular",
+"json_use|use_json_paramers": false,
+"use_file_names_as_ids": true
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/4/9/a/dataset_49af2c08-3ad4-4940-ae84-f93df3c0dd8a.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/8/9/4/dataset_894d0a5e-2d87-4861-85cb-b5cae83b19cb.dat,/tmp/tmpm1fyob3t/files/3/1/5/dataset_315f1808-e9c5-45fb-8cb8-b71e8e1c8366.dat,/tmp/tmpm1fyob3t/files/b/6/7/dataset_b67a6264-6208-4b44-8fd4-47ba3f96faee.dat,/tmp/tmpm1fyob3t/files/c/e/3/dataset_ce3a0b5e-0344-4422-b84a-84904818396b.dat,/tmp/tmpm1fyob3t/files/b/7/d/dataset_b7dcace3-2dbd-49db-94ac-98485bf522aa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'BioBrickStandardAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/8/9/4/dataset_894d0a5e-2d87-4861-85cb-b5cae83b19cb.dat:BBa_E0040_GFP.gb,/tmp/tmpm1fyob3t/files/3/1/5/dataset_315f1808-e9c5-45fb-8cb8-b71e8e1c8366.dat:BBa_J23119_prom.gb,/tmp/tmpm1fyob3t/files/b/6/7/dataset_b67a6264-6208-4b44-8fd4-47ba3f96faee.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpm1fyob3t/files/c/e/3/dataset_ce3a0b5e-0344-4422-b84a-84904818396b.dat:BBa_J61048_term.gb,/tmp/tmpm1fyob3t/files/b/7/d/dataset_b7dcace3-2dbd-49db-94ac-98485bf522aa.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/tmpm1fyob3t/job_working_directory/000/35/outputs/dataset_3f72ea64-02f3-413e-9d9a-5c43eaaadf14.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/3/0/7/dataset_307ff774-78e5-410b-926b-396bf0346f5f.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/8/7/9/dataset_879f6c49-14f5-4f78-8b32-f06d098a7f4f.dat,/tmp/tmpe6pmg7jw/files/a/3/c/dataset_a3cb8cea-16ad-4a33-8e41-a9b378b2974a.dat,/tmp/tmpe6pmg7jw/files/c/7/b/dataset_c7bca70e-0ae9-4062-b185-1e0e5ed116a6.dat,/tmp/tmpe6pmg7jw/files/b/3/a/dataset_b3a11bc9-4c29-470c-8985-d845c2f9e183.dat,/tmp/tmpe6pmg7jw/files/0/8/1/dataset_08129340-240c-4349-af6c-0379d32cae9c.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/8/7/9/dataset_879f6c49-14f5-4f78-8b32-f06d098a7f4f.dat:BBa_E0040_GFP.gb,/tmp/tmpe6pmg7jw/files/a/3/c/dataset_a3cb8cea-16ad-4a33-8e41-a9b378b2974a.dat:BBa_J23119_prom.gb,/tmp/tmpe6pmg7jw/files/c/7/b/dataset_c7bca70e-0ae9-4062-b185-1e0e5ed116a6.dat:BBa_J23119_prom_flawed.gb,/tmp/tmpe6pmg7jw/files/b/3/a/dataset_b3a11bc9-4c29-470c-8985-d845c2f9e183.dat:BBa_J61048_term.gb,/tmp/tmpe6pmg7jw/files/0/8/1/dataset_08129340-240c-4349-af6c-0379d32cae9c.dat:BBa_K611094_bar.gb' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'BioBrickStandardAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/35/outputs/dataset_c2f7d71f-de27-48c6-bc1f-b656bc8d53f1.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T12:04:23.734013",
+"create_time": "2025-07-17T10:12:13.370696",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "174889",
+"external_id": "77757",
-"galaxy_version": "24.2",
+"galaxy_version": "25.0",
 "handler": null,
-"history_id": "3937d5ff7c0e1373",
+"history_id": "58ad66a9f93223b8",
-"id": "2be24ce9bdbc87e1",
+"id": "1f477a8cb4ab1699",
 "inputs": {
 "assembly_csv": {
-"id": "5493159c7d57114c",
+"id": "38b6c0c549bf284f",
 "src": "hda",
-"uuid": "49af2c08-3ad4-4940-ae84-f93df3c0dd8a"
+"uuid": "307ff774-78e5-410b-926b-396bf0346f5f"
 },
 "genbank_files1": {
-"id": "8d7d89366ae6734b",
+"id": "de5166318ad7499c",
 "src": "hda",
-"uuid": "894d0a5e-2d87-4861-85cb-b5cae83b19cb"
+"uuid": "879f6c49-14f5-4f78-8b32-f06d098a7f4f"
 },
 "genbank_files2": {
-"id": "30133c2583e745a4",
+"id": "0a0976316513f675",
 "src": "hda",
-"uuid": "315f1808-e9c5-45fb-8cb8-b71e8e1c8366"
+"uuid": "a3cb8cea-16ad-4a33-8e41-a9b378b2974a"
 },
 "genbank_files3": {
-"id": "d3fd00b679818750",
+"id": "88f51edac3b2f70e",
 "src": "hda",
-"uuid": "b67a6264-6208-4b44-8fd4-47ba3f96faee"
+"uuid": "c7bca70e-0ae9-4062-b185-1e0e5ed116a6"
 },
 "genbank_files4": {
-"id": "a5593c3e02c9d8f6",
+"id": "6974b4f354e9f36a",
 "src": "hda",
-"uuid": "ce3a0b5e-0344-4422-b84a-84904818396b"
+"uuid": "b3a11bc9-4c29-470c-8985-d845c2f9e183"
 },
 "genbank_files5": {
-"id": "fb42640a8a596816",
+"id": "5b088a1dc26c39a4",
 "src": "hda",
-"uuid": "b7dcace3-2dbd-49db-94ac-98485bf522aa"
+"uuid": "08129340-240c-4349-af6c-0379d32cae9c"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "fbec4a551130f847",
+"id": "8de66704b7df8b5e",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|C1_prom_barcode__": {
-"id": "f1bdbab1d80457ac",
+"id": "79e58137b38a96f5",
 "src": "hda",
-"uuid": "8a7dec58-9e11-4bbf-a945-3910d02c89d9"
+"uuid": "8b1ffa40-fda8-4629-a843-4a17c7d9e983"
 },
 "__new_primary_file_construct_gb|C2_gfp_term__": {
-"id": "588795470b41a739",
+"id": "b5ab7a1e4a941d0d",
 "src": "hda",
-"uuid": "ee52fe89-63a0-498c-bdbb-ec9fe5b72eca"
+"uuid": "ef840f10-be08-4855-858c-ee696e852624"
 },
 "__new_primary_file_construct_gb|C3_final__": {
-"id": "de619fffe043835f",
+"id": "76e4f31bf12269ab",
 "src": "hda",
-"uuid": "6b8fe4a1-1743-4ec5-a12e-6b7b267efa08"
+"uuid": "0eba0e00-8261-4ff7-a40e-46d7fd0b9f62"
 },
 "output_zip": {
-"id": "a072914da4208f87",
+"id": "8380aea1f9c6b8c9",
 "src": "hda",
-"uuid": "3f72ea64-02f3-413e-9d9a-5c43eaaadf14"
+"uuid": "c2f7d71f-de27-48c6-bc1f-b656bc8d53f1"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
-"adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
+"chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
-"assembly_plan_name": "\"BioBrickStandardAssembly\"",
-"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": null,
 "genbank_files": "{\"values\": [{\"id\": 9, \"src\": \"hdca\"}]}",
-"topology": "\"circular\""
+"json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"BioBrickStandardAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}",
+"use_file_names_as_ids": "true"
 },
 "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 [00:00<00:00,  2.04it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.66it/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,  1.93it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.59it/s, now=None]\r                                                                 \r",
 "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 [00:00<00:00,  2.04it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.66it/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,  1.93it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 3/3 [00:01<00:00,  1.59it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 3}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T12:04:36.963198",
+"update_time": "2025-07-17T10:12:26.209759",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "e2ca7f14a85a8d44"
+"user_id": "986c9b47c580ae59"
 },
 "status": "success",
 "test_index": 4,
-"time_seconds": 34.648075580596924,
+"time_seconds": 33.86248016357422,
 "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": "d61e70858d065388",
+"id": "7b8a6e6b82f35567",
 "src": "hda"
 },
-"assembly_plan_name": "Type2sRestrictionAssembly",
 "domesticated_input": {
-"id": "5bd8560352cb0b69",
+"id": "54c6d71c8dc7cb11",
 "src": "hdca"
 },
 "genbank_files": {
-"id": "cb2fe7fb50f38553",
+"id": "2592d2c705ba0baa",
 "src": "hdca"
 },
-"topology": "circular"
+"json_use|assembly_plan_name": "Type2sRestrictionAssembly",
+"json_use|topology": "circular",
+"json_use|use_json_paramers": false,
+"use_file_names_as_ids": true
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/f/2/3/dataset_f2390ba6-b891-4c75-b5b4-881fabe15212.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/d/f/e/dataset_dfe71b71-2603-48cf-bf59-772724abea0f.dat,/tmp/tmpm1fyob3t/files/0/9/2/dataset_09260017-ac9e-4868-b386-27ef07ca03a8.dat,/tmp/tmpm1fyob3t/files/8/4/e/dataset_84e57026-4e85-4a63-b66a-8bae5b767f0c.dat,/tmp/tmpm1fyob3t/files/7/d/2/dataset_7d26d36d-bb1c-4f83-be4f-3311e4ec2441.dat,/tmp/tmpm1fyob3t/files/8/a/0/dataset_8a0ff1e5-aaf7-461e-b642-b60e5cf13132.dat,/tmp/tmpm1fyob3t/files/f/9/4/dataset_f94fb7c9-761b-4dc1-8caa-a02ee7892c59.dat,/tmp/tmpm1fyob3t/files/c/7/e/dataset_c7e408b5-927b-4966-8d1f-08de3b41fc34.dat' --domesticated_seq '/tmp/tmpm1fyob3t/files/b/2/6/dataset_b263e11f-1d52-45d4-8679-8bb23668154a.dat,/tmp/tmpm1fyob3t/files/c/4/c/dataset_c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee.dat,/tmp/tmpm1fyob3t/files/d/d/c/dataset_ddcb9f93-9b4f-41e3-a1df-5537b6326a78.dat,/tmp/tmpm1fyob3t/files/9/9/b/dataset_99bac98d-1cbf-4ab1-a680-49cdb721e447.dat,/tmp/tmpm1fyob3t/files/6/8/5/dataset_685cd571-80b5-4c03-b247-4fb51e199639.dat' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/d/f/e/dataset_dfe71b71-2603-48cf-bf59-772724abea0f.dat:part_A.gb,/tmp/tmpm1fyob3t/files/0/9/2/dataset_09260017-ac9e-4868-b386-27ef07ca03a8.dat:part_B.gb,/tmp/tmpm1fyob3t/files/8/4/e/dataset_84e57026-4e85-4a63-b66a-8bae5b767f0c.dat:part_C.gb,/tmp/tmpm1fyob3t/files/7/d/2/dataset_7d26d36d-bb1c-4f83-be4f-3311e4ec2441.dat:part_D.gb,/tmp/tmpm1fyob3t/files/8/a/0/dataset_8a0ff1e5-aaf7-461e-b642-b60e5cf13132.dat:part_E.gb,/tmp/tmpm1fyob3t/files/f/9/4/dataset_f94fb7c9-761b-4dc1-8caa-a02ee7892c59.dat:part_F.gb,/tmp/tmpm1fyob3t/files/c/7/e/dataset_c7e408b5-927b-4966-8d1f-08de3b41fc34.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpm1fyob3t/files/b/2/6/dataset_b263e11f-1d52-45d4-8679-8bb23668154a.dat:part_H.gb,/tmp/tmpm1fyob3t/files/c/4/c/dataset_c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee.dat:part_I.gb,/tmp/tmpm1fyob3t/files/d/d/c/dataset_ddcb9f93-9b4f-41e3-a1df-5537b6326a78.dat:part_J.gb,/tmp/tmpm1fyob3t/files/9/9/b/dataset_99bac98d-1cbf-4ab1-a680-49cdb721e447.dat:part_K.gb,/tmp/tmpm1fyob3t/files/6/8/5/dataset_685cd571-80b5-4c03-b247-4fb51e199639.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/tmpm1fyob3t/job_working_directory/000/49/outputs/dataset_b5c1d918-9a86-47ac-9fd0-0d1eeecb3515.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/9/b/5/dataset_9b53e736-9aa4-428b-866b-72d2f525f99e.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/d/1/5/dataset_d15ff026-babf-41d1-b9e0-e701e0a51b6b.dat,/tmp/tmpe6pmg7jw/files/2/9/8/dataset_298d983c-3e5c-4b93-944c-b372d4295740.dat,/tmp/tmpe6pmg7jw/files/4/e/3/dataset_4e3c0103-dbb8-465c-abbf-7f9b66a8263b.dat,/tmp/tmpe6pmg7jw/files/1/5/4/dataset_15452284-bc19-43d6-8367-2753056a96ec.dat,/tmp/tmpe6pmg7jw/files/0/f/3/dataset_0f36b33d-8c1c-472b-abbd-c3f63418174a.dat,/tmp/tmpe6pmg7jw/files/a/d/d/dataset_adde970f-87a8-45b0-9303-acf0d7ed7c2e.dat,/tmp/tmpe6pmg7jw/files/9/6/b/dataset_96bd86f4-cd0a-4a34-a1cf-3044a62f77a2.dat' --domesticated_seq '/tmp/tmpe6pmg7jw/files/5/5/8/dataset_5587676a-8c81-4954-bf33-2c965bf7635d.dat,/tmp/tmpe6pmg7jw/files/b/f/b/dataset_bfb815a2-67c8-4cb5-afb8-ea35cfa372eb.dat,/tmp/tmpe6pmg7jw/files/2/1/6/dataset_216a998c-35de-48c2-a017-c3fed9787319.dat,/tmp/tmpe6pmg7jw/files/8/9/1/dataset_89112e3f-e936-4419-938d-b4b4daa68e40.dat,/tmp/tmpe6pmg7jw/files/5/3/2/dataset_53218d73-0f61-4527-b279-62ced98701d1.dat' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/d/1/5/dataset_d15ff026-babf-41d1-b9e0-e701e0a51b6b.dat:part_A.gb,/tmp/tmpe6pmg7jw/files/2/9/8/dataset_298d983c-3e5c-4b93-944c-b372d4295740.dat:part_B.gb,/tmp/tmpe6pmg7jw/files/4/e/3/dataset_4e3c0103-dbb8-465c-abbf-7f9b66a8263b.dat:part_C.gb,/tmp/tmpe6pmg7jw/files/1/5/4/dataset_15452284-bc19-43d6-8367-2753056a96ec.dat:part_D.gb,/tmp/tmpe6pmg7jw/files/0/f/3/dataset_0f36b33d-8c1c-472b-abbd-c3f63418174a.dat:part_E.gb,/tmp/tmpe6pmg7jw/files/a/d/d/dataset_adde970f-87a8-45b0-9303-acf0d7ed7c2e.dat:part_F.gb,/tmp/tmpe6pmg7jw/files/9/6/b/dataset_96bd86f4-cd0a-4a34-a1cf-3044a62f77a2.dat:part_G.gb' --file_name_mapping_dom '/tmp/tmpe6pmg7jw/files/5/5/8/dataset_5587676a-8c81-4954-bf33-2c965bf7635d.dat:part_H.gb,/tmp/tmpe6pmg7jw/files/b/f/b/dataset_bfb815a2-67c8-4cb5-afb8-ea35cfa372eb.dat:part_I.gb,/tmp/tmpe6pmg7jw/files/2/1/6/dataset_216a998c-35de-48c2-a017-c3fed9787319.dat:part_J.gb,/tmp/tmpe6pmg7jw/files/8/9/1/dataset_89112e3f-e936-4419-938d-b4b4daa68e40.dat:part_K.gb,/tmp/tmpe6pmg7jw/files/5/3/2/dataset_53218d73-0f61-4527-b279-62ced98701d1.dat:part_L.gb' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'Type2sRestrictionAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/49/outputs/dataset_85657c38-c9be-421a-8d2e-3ba54dcd1ee1.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T12:05:17.468278",
+"create_time": "2025-07-17T10:13:06.053332",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "176006",
+"external_id": "78856",
-"galaxy_version": "24.2",
+"galaxy_version": "25.0",
 "handler": null,
-"history_id": "473b1992d5f5b84f",
+"history_id": "e9003a596293e37c",
-"id": "52d2dbb7944a53fc",
+"id": "c4dd95e8260a7aca",
 "inputs": {
 "assembly_csv": {
-"id": "d61e70858d065388",
+"id": "7b8a6e6b82f35567",
 "src": "hda",
-"uuid": "f2390ba6-b891-4c75-b5b4-881fabe15212"
+"uuid": "9b53e736-9aa4-428b-866b-72d2f525f99e"
 },
 "domesticated_input1": {
-"id": "201ce005b4eba284",
+"id": "3cae7d055c6a8b90",
 "src": "hda",
-"uuid": "b263e11f-1d52-45d4-8679-8bb23668154a"
+"uuid": "5587676a-8c81-4954-bf33-2c965bf7635d"
 },
 "domesticated_input2": {
-"id": "ccacdf94e033958e",
+"id": "eb3eeb1f7f0d700b",
 "src": "hda",
-"uuid": "c4c08e8f-3ffc-40d0-8a27-1bee8b5f6fee"
+"uuid": "bfb815a2-67c8-4cb5-afb8-ea35cfa372eb"
 },
 "domesticated_input3": {
-"id": "71f633fb8d250097",
+"id": "0a842033366cb6f4",
 "src": "hda",
-"uuid": "ddcb9f93-9b4f-41e3-a1df-5537b6326a78"
+"uuid": "216a998c-35de-48c2-a017-c3fed9787319"
 },
 "domesticated_input4": {
-"id": "23971c9dcf22198b",
+"id": "3b0ecfffcd65a433",
 "src": "hda",
-"uuid": "99bac98d-1cbf-4ab1-a680-49cdb721e447"
+"uuid": "89112e3f-e936-4419-938d-b4b4daa68e40"
 },
 "domesticated_input5": {
-"id": "60438d790668bc40",
+"id": "7b7bd43bd69db4da",
 "src": "hda",
-"uuid": "685cd571-80b5-4c03-b247-4fb51e199639"
+"uuid": "53218d73-0f61-4527-b279-62ced98701d1"
 },
 "genbank_files1": {
-"id": "562cdacb0f854350",
+"id": "b2f60919761cbe66",
 "src": "hda",
-"uuid": "dfe71b71-2603-48cf-bf59-772724abea0f"
+"uuid": "d15ff026-babf-41d1-b9e0-e701e0a51b6b"
 },
 "genbank_files2": {
-"id": "b5f666ac47f1f830",
+"id": "99a09fce7ce0f899",
 "src": "hda",
-"uuid": "09260017-ac9e-4868-b386-27ef07ca03a8"
+"uuid": "298d983c-3e5c-4b93-944c-b372d4295740"
 },
 "genbank_files3": {
-"id": "316b2bf479d3691f",
+"id": "f6b26195fd7f7f3e",
 "src": "hda",
-"uuid": "84e57026-4e85-4a63-b66a-8bae5b767f0c"
+"uuid": "4e3c0103-dbb8-465c-abbf-7f9b66a8263b"
 },
 "genbank_files4": {
-"id": "52d2dbb7944a53fc",
+"id": "c4dd95e8260a7aca",
 "src": "hda",
-"uuid": "7d26d36d-bb1c-4f83-be4f-3311e4ec2441"
+"uuid": "15452284-bc19-43d6-8367-2753056a96ec"
 },
 "genbank_files5": {
-"id": "6d0420a098f813ba",
+"id": "03de0919cac4bbd5",
 "src": "hda",
-"uuid": "8a0ff1e5-aaf7-461e-b642-b60e5cf13132"
+"uuid": "0f36b33d-8c1c-472b-abbd-c3f63418174a"
 },
 "genbank_files6": {
-"id": "98086fd4fda4fb74",
+"id": "8b133a938a16d94a",
 "src": "hda",
-"uuid": "f94fb7c9-761b-4dc1-8caa-a02ee7892c59"
+"uuid": "adde970f-87a8-45b0-9303-acf0d7ed7c2e"
 },
 "genbank_files7": {
-"id": "1e3f8509b9833e4e",
+"id": "de8340ef2cf62a09",
 "src": "hda",
-"uuid": "c7e408b5-927b-4966-8d1f-08de3b41fc34"
+"uuid": "96bd86f4-cd0a-4a34-a1cf-3044a62f77a2"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "1e8e6749bc68d8e8",
+"id": "54d710fc68386373",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "825e5e92a55932c1",
+"id": "955be7be95972849",
 "src": "hda",
-"uuid": "fd97fd7a-08b9-42ba-ae2a-022c8be1b219"
+"uuid": "14602eef-eda6-4c3a-8f13-f1cac1adca78"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "4a8ace5529c8c3e9",
+"id": "535a274eb83bb714",
 "src": "hda",
-"uuid": "b9201d86-ee66-45ac-99a5-09d3ca161d8b"
+"uuid": "c94a01f0-fd44-4112-be7e-0cc5c48e541d"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "f0d76a7bda3035c9",
+"id": "b79f0249bac52469",
 "src": "hda",
-"uuid": "7c74cbab-8a62-43a2-95f3-00919cc11fa7"
+"uuid": "a4df015a-0bc4-4cec-b8be-67681da9f1b7"
 },
 "__new_primary_file_construct_gb|construct_4__": {
-"id": "640790f555d03105",
+"id": "3cafb1bf19a56844",
 "src": "hda",
-"uuid": "a450e128-38e8-4eb5-82a1-304b04c68510"
+"uuid": "d38c7640-aa80-4ddd-b16b-6c71f3aaf195"
 },
 "output_zip": {
-"id": "50943f113f3eedaf",
+"id": "0d8c106f64e9b667",
 "src": "hda",
-"uuid": "b5c1d918-9a86-47ac-9fd0-0d1eeecb3515"
+"uuid": "85657c38-c9be-421a-8d2e-3ba54dcd1ee1"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
-"adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
+"chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
-"assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpm1fyob3t/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\""
+"json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"Type2sRestrictionAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}",
+"use_file_names_as_ids": "true"
 },
 "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,  2.40it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.81it/s, now=None]\r                                                                 \r",
+"stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.43it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.82it/s, now=None]\r                                                                 \r",
 "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,  2.40it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.81it/s, now=None]\r                                                                 \r",
+"tool_stderr": "\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\r                                                         \r\rassembly:   0%|          | 0/4 [00:00<?, ?it/s, now=None]\rassembly:  50%|\u2588\u2588\u2588\u2588\u2588     | 2/4 [00:00<00:00,  2.43it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.22it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.82it/s, now=None]\r                                                                 \r",
 "tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
-"update_time": "2025-05-26T12:05:29.989306",
+"update_time": "2025-07-17T10:13:18.198417",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "e2ca7f14a85a8d44"
+"user_id": "986c9b47c580ae59"
 },
 "status": "success",
 "test_index": 5,
-"time_seconds": 53.09692740440369,
+"time_seconds": 51.96266531944275,
 "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": "d71403ee85b47d8d",
+"id": "6cceecf1bcab0d5e",
 "src": "hda"
 },
-"assembly_plan_name": "Type2sRestrictionAssembly",
 "domesticated_input": {
-"id": "a36db940f4513bd9",
+"id": "98a2432f1cff4f91",
 "src": "hdca"
 },
-"topology": "circular"
+"json_use|assembly_plan_name": "Type2sRestrictionAssembly",
+"json_use|topology": "circular",
+"json_use|use_json_paramers": false,
+"use_file_names_as_ids": true
 },
 "job": {
-"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpm1fyob3t/files/3/c/1/dataset_3c1221bc-ba53-4ede-899c-e4defbe838eb.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpm1fyob3t/files/6/8/e/dataset_68ee2e69-c2d9-43cd-851e-0b660884cac2.dat,/tmp/tmpm1fyob3t/files/5/c/2/dataset_5c298af3-9cdb-4837-8054-8903c2683f85.dat,/tmp/tmpm1fyob3t/files/9/c/1/dataset_9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e.dat,/tmp/tmpm1fyob3t/files/e/7/7/dataset_e77c955d-e9b5-4175-a061-81b9a781d2ff.dat,/tmp/tmpm1fyob3t/files/3/5/d/dataset_35df1ceb-416b-4c2d-b20a-3efe96b6770f.dat,/tmp/tmpm1fyob3t/files/c/0/2/dataset_c02fc9fb-dc4e-49e1-b99f-8199fd97d795.dat,/tmp/tmpm1fyob3t/files/3/3/9/dataset_339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a.dat,/tmp/tmpm1fyob3t/files/2/2/4/dataset_2246947a-dbb7-4ed2-855a-56a42a899aab.dat,/tmp/tmpm1fyob3t/files/0/a/9/dataset_0a935c03-48a7-4c8a-8077-aea407e5285d.dat,/tmp/tmpm1fyob3t/files/0/4/b/dataset_04bcf9c1-ccc8-4d52-a739-fb3630f90b05.dat,/tmp/tmpm1fyob3t/files/4/0/2/dataset_402aaabe-0ea9-4519-998b-11cf6b07a1df.dat,/tmp/tmpm1fyob3t/files/9/c/f/dataset_9cf71985-a62d-4d89-845c-2b996d8096fa.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --assembly_plan_name 'Type2sRestrictionAssembly' --file_name_mapping '/tmp/tmpm1fyob3t/files/6/8/e/dataset_68ee2e69-c2d9-43cd-851e-0b660884cac2.dat:part_A.gb,/tmp/tmpm1fyob3t/files/5/c/2/dataset_5c298af3-9cdb-4837-8054-8903c2683f85.dat:part_B.gb,/tmp/tmpm1fyob3t/files/9/c/1/dataset_9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e.dat:part_C.gb,/tmp/tmpm1fyob3t/files/e/7/7/dataset_e77c955d-e9b5-4175-a061-81b9a781d2ff.dat:part_D.gb,/tmp/tmpm1fyob3t/files/3/5/d/dataset_35df1ceb-416b-4c2d-b20a-3efe96b6770f.dat:part_E.gb,/tmp/tmpm1fyob3t/files/c/0/2/dataset_c02fc9fb-dc4e-49e1-b99f-8199fd97d795.dat:part_F.gb,/tmp/tmpm1fyob3t/files/3/3/9/dataset_339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a.dat:part_G.gb,/tmp/tmpm1fyob3t/files/2/2/4/dataset_2246947a-dbb7-4ed2-855a-56a42a899aab.dat:part_H.gb,/tmp/tmpm1fyob3t/files/0/a/9/dataset_0a935c03-48a7-4c8a-8077-aea407e5285d.dat:part_I.gb,/tmp/tmpm1fyob3t/files/0/4/b/dataset_04bcf9c1-ccc8-4d52-a739-fb3630f90b05.dat:part_J.gb,/tmp/tmpm1fyob3t/files/4/0/2/dataset_402aaabe-0ea9-4519-998b-11cf6b07a1df.dat:part_K.gb,/tmp/tmpm1fyob3t/files/9/c/f/dataset_9cf71985-a62d-4d89-845c-2b996d8096fa.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/tmpm1fyob3t/job_working_directory/000/63/outputs/dataset_02e7ea5e-6c8f-419d-82de-476bccc550ec.dat'",
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/2/8/4/dataset_2844fc99-3db2-458b-9656-9c18962aed13.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/3/6/7/dataset_367c8adb-623b-4fc2-8710-1402b90dc27a.dat,/tmp/tmpe6pmg7jw/files/b/8/c/dataset_b8c15683-a369-4b52-b94d-52e823e2dbc4.dat,/tmp/tmpe6pmg7jw/files/7/b/7/dataset_7b71197b-9cec-4ebc-a0ab-9a9070856680.dat,/tmp/tmpe6pmg7jw/files/0/8/2/dataset_08203bf4-e285-4e41-845d-c7db10709a14.dat,/tmp/tmpe6pmg7jw/files/b/1/7/dataset_b174f6f8-eb0c-44b9-9d1b-89b7a62bc494.dat,/tmp/tmpe6pmg7jw/files/c/5/9/dataset_c598d3b6-58ab-4695-99a5-5fb6197a4823.dat,/tmp/tmpe6pmg7jw/files/0/9/e/dataset_09eec457-37de-4c2c-8b7e-1be1dfbaffd6.dat,/tmp/tmpe6pmg7jw/files/e/8/4/dataset_e84bc66f-f327-4070-8511-c5734161ea4b.dat,/tmp/tmpe6pmg7jw/files/d/b/0/dataset_db0c0f17-0973-48f2-a70a-2760c7521af3.dat,/tmp/tmpe6pmg7jw/files/a/f/1/dataset_af171625-0bb7-4a5f-a858-f92983e9f54e.dat,/tmp/tmpe6pmg7jw/files/3/5/1/dataset_3515fd31-0758-4e14-a6ac-b01ba9941850.dat,/tmp/tmpe6pmg7jw/files/f/2/1/dataset_f2119eb4-c9ca-461f-8d40-6284effbefa1.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/3/6/7/dataset_367c8adb-623b-4fc2-8710-1402b90dc27a.dat:part_A.gb,/tmp/tmpe6pmg7jw/files/b/8/c/dataset_b8c15683-a369-4b52-b94d-52e823e2dbc4.dat:part_B.gb,/tmp/tmpe6pmg7jw/files/7/b/7/dataset_7b71197b-9cec-4ebc-a0ab-9a9070856680.dat:part_C.gb,/tmp/tmpe6pmg7jw/files/0/8/2/dataset_08203bf4-e285-4e41-845d-c7db10709a14.dat:part_D.gb,/tmp/tmpe6pmg7jw/files/b/1/7/dataset_b174f6f8-eb0c-44b9-9d1b-89b7a62bc494.dat:part_E.gb,/tmp/tmpe6pmg7jw/files/c/5/9/dataset_c598d3b6-58ab-4695-99a5-5fb6197a4823.dat:part_F.gb,/tmp/tmpe6pmg7jw/files/0/9/e/dataset_09eec457-37de-4c2c-8b7e-1be1dfbaffd6.dat:part_G.gb,/tmp/tmpe6pmg7jw/files/e/8/4/dataset_e84bc66f-f327-4070-8511-c5734161ea4b.dat:part_H.gb,/tmp/tmpe6pmg7jw/files/d/b/0/dataset_db0c0f17-0973-48f2-a70a-2760c7521af3.dat:part_I.gb,/tmp/tmpe6pmg7jw/files/a/f/1/dataset_af171625-0bb7-4a5f-a858-f92983e9f54e.dat:part_J.gb,/tmp/tmpe6pmg7jw/files/3/5/1/dataset_3515fd31-0758-4e14-a6ac-b01ba9941850.dat:part_K.gb,/tmp/tmpe6pmg7jw/files/f/2/1/dataset_f2119eb4-c9ca-461f-8d40-6284effbefa1.dat:part_L.gb' --file_name_mapping_dom '' --use_json_paramers 'false' --enzyme 'auto' --topology 'circular' --assembly_plan_name 'Type2sRestrictionAssembly' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/63/outputs/dataset_fc4a95ba-4368-4457-b175-ebf26af659aa.dat'",
 "command_version": "",
 "copied_from_job_id": null,
-"create_time": "2025-05-26T12:06:09.749817",
+"create_time": "2025-07-17T10:13:57.903413",
 "dependencies": [
 {
 "cacheable": false,
 "dependency_resolver": {
 "auto_init": true,
 "name": "dna_features_viewer",
 "version": "3.1.5"
 }
 ],
 "exit_code": 0,
-"external_id": "177047",
+"external_id": "80009",
-"galaxy_version": "24.2",
+"galaxy_version": "25.0",
 "handler": null,
-"history_id": "9b5c1fe7a52a75e0",
+"history_id": "8c39a9a410cc0a00",
-"id": "640790f555d03105",
+"id": "3cafb1bf19a56844",
 "inputs": {
 "assembly_csv": {
-"id": "d71403ee85b47d8d",
+"id": "6cceecf1bcab0d5e",
 "src": "hda",
-"uuid": "3c1221bc-ba53-4ede-899c-e4defbe838eb"
+"uuid": "2844fc99-3db2-458b-9656-9c18962aed13"
 },
 "domesticated_input1": {
-"id": "740094ed962e7335",
+"id": "95f8e30291b4c724",
 "src": "hda",
-"uuid": "68ee2e69-c2d9-43cd-851e-0b660884cac2"
+"uuid": "367c8adb-623b-4fc2-8710-1402b90dc27a"
 },
 "domesticated_input10": {
-"id": "06981e06b6149081",
+"id": "5dc7959fa599d57d",
 "src": "hda",
-"uuid": "04bcf9c1-ccc8-4d52-a739-fb3630f90b05"
+"uuid": "af171625-0bb7-4a5f-a858-f92983e9f54e"
 },
 "domesticated_input11": {
-"id": "343d33e0d7549cb9",
+"id": "d309b7113a9d8008",
 "src": "hda",
-"uuid": "402aaabe-0ea9-4519-998b-11cf6b07a1df"
+"uuid": "3515fd31-0758-4e14-a6ac-b01ba9941850"
 },
 "domesticated_input12": {
-"id": "2c330e522704b0f9",
+"id": "f558e884d7fd7d56",
 "src": "hda",
-"uuid": "9cf71985-a62d-4d89-845c-2b996d8096fa"
+"uuid": "f2119eb4-c9ca-461f-8d40-6284effbefa1"
 },
 "domesticated_input2": {
-"id": "839c90adaefe5f3f",
+"id": "e51e45ceb8fc2cce",
 "src": "hda",
-"uuid": "5c298af3-9cdb-4837-8054-8903c2683f85"
+"uuid": "b8c15683-a369-4b52-b94d-52e823e2dbc4"
 },
 "domesticated_input3": {
-"id": "1f56aa824e7dde43",
+"id": "7a147471a754feaa",
 "src": "hda",
-"uuid": "9c1fd651-de1e-4ba9-a8e1-ee78953b0c8e"
+"uuid": "7b71197b-9cec-4ebc-a0ab-9a9070856680"
 },
 "domesticated_input4": {
-"id": "26b32a65097dcc1d",
+"id": "980ee860844f9585",
 "src": "hda",
-"uuid": "e77c955d-e9b5-4175-a061-81b9a781d2ff"
+"uuid": "08203bf4-e285-4e41-845d-c7db10709a14"
 },
 "domesticated_input5": {
-"id": "60327bfb8991788f",
+"id": "fbc8779ea7cd6ed6",
 "src": "hda",
-"uuid": "35df1ceb-416b-4c2d-b20a-3efe96b6770f"
+"uuid": "b174f6f8-eb0c-44b9-9d1b-89b7a62bc494"
 },
 "domesticated_input6": {
-"id": "ac528058169ea450",
+"id": "185e1f0b9b0a67b3",
 "src": "hda",
-"uuid": "c02fc9fb-dc4e-49e1-b99f-8199fd97d795"
+"uuid": "c598d3b6-58ab-4695-99a5-5fb6197a4823"
 },
 "domesticated_input7": {
-"id": "8d7c8aec2b1ab229",
+"id": "37c673ee68b5c3ed",
 "src": "hda",
-"uuid": "339b4cbf-4ca2-4c49-9cc4-9796c5b9ba8a"
+"uuid": "09eec457-37de-4c2c-8b7e-1be1dfbaffd6"
 },
 "domesticated_input8": {
-"id": "f996cb18f164a451",
+"id": "8a3a0f65c762008d",
 "src": "hda",
-"uuid": "2246947a-dbb7-4ed2-855a-56a42a899aab"
+"uuid": "e84bc66f-f327-4070-8511-c5734161ea4b"
 },
 "domesticated_input9": {
-"id": "f3c4f2ef486441ac",
+"id": "5033875e970a3799",
 "src": "hda",
-"uuid": "0a935c03-48a7-4c8a-8077-aea407e5285d"
+"uuid": "db0c0f17-0973-48f2-a70a-2760c7521af3"
 }
 },
 "job_messages": [],
 "job_metrics": [],
 "job_runner_name": null,
 "job_stderr": "",
 "job_stdout": "",
 "model_class": "Job",
 "output_collections": {
 "construct_gb": {
-"id": "182eefa577c2a56d",
+"id": "172543d29b19f394",
 "src": "hdca"
 }
 },
 "outputs": {
 "__new_primary_file_construct_gb|construct_1__": {
-"id": "613a1bff017ef479",
+"id": "6665d38e10ff581d",
 "src": "hda",
-"uuid": "a0c57d2e-8ac7-48d8-b9c5-f01b728ebba7"
+"uuid": "30a2a28d-9d1b-4332-8d5a-acda885308dd"
 },
 "__new_primary_file_construct_gb|construct_2__": {
-"id": "1a8ab2437d7e496f",
+"id": "0788ac4ba66a0bdd",
 "src": "hda",
-"uuid": "d7804ee2-c9a8-46c2-b057-7f25a8002f55"
+"uuid": "49f11bec-1e54-49fe-8c44-7cc25273d54d"
 },
 "__new_primary_file_construct_gb|construct_3__": {
-"id": "af3c5f81417a677c",
+"id": "f41d1a7bd862df72",
 "src": "hda",
-"uuid": "71c1f25b-f43d-43f7-9893-bfd3bc967517"
+"uuid": "a01def58-86a8-48c3-aabc-d9d5a9367927"
 },
 "__new_primary_file_construct_gb|construct_4__": {
-"id": "b5b1a9766aab456e",
+"id": "a371069cf8561e3f",
 "src": "hda",
-"uuid": "f23f1069-e4c4-4a9e-9787-5b2b5e905e24"
+"uuid": "7fd4fd46-1149-4dbe-aaa4-531dc7db5adb"
 },
 "output_zip": {
-"id": "7d40cd3e06526c58",
+"id": "9df6b2b003837432",
 "src": "hda",
-"uuid": "02e7ea5e-6c8f-419d-82de-476bccc550ec"
+"uuid": "fc4a95ba-4368-4457-b175-ebf26af659aa"
 }
 },
 "params": {
 "__input_ext": "\"input\"",
-"adv": "{\"enzyme\": \"auto\", \"use_file_names_as_ids\": true}",
+"chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
-"assembly_plan_name": "\"Type2sRestrictionAssembly\"",
-"chromInfo": "\"/tmp/tmpm1fyob3t/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
 "dbkey": "\"?\"",
 "domesticated_input": "{\"values\": [{\"id\": 14, \"src\": \"hdca\"}]}",
 "genbank_files": null,
-"topology": "\"circular\""
+"json_use": "{\"__current_case__\": 0, \"assembly_plan_name\": \"Type2sRestrictionAssembly\", \"enzyme\": \"auto\", \"topology\": \"circular\", \"use_json_paramers\": false}",
+"use_file_names_as_ids": "true"
 },
 "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,  2.43it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.81it/s, now=None]\r                                                                 \r",
+"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,  2.40it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.19it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.80it/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,  2.43it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.21it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.81it/s, now=None]\r                                                                 \r",
+"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,  2.40it/s, now=None]\rassembly:  75%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u258c  | 3/4 [00:01<00:00,  2.19it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.80it/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": "2025-05-26T12:06:22.164674",
+"update_time": "2025-07-17T10:14:10.606776",
 "user_email": "planemo@galaxyproject.org",
-"user_id": "e2ca7f14a85a8d44"
+"user_id": "986c9b47c580ae59"
 },
 "status": "success",
 "test_index": 6,
-"time_seconds": 52.117783308029175,
+"time_seconds": 52.30599284172058,
 "tool_id": "cloning_simulation",
 "tool_version": "0.1.0+galaxy0"
 },
 "has_data": true,
 "id": "cloning_simulation-6"
+},
+{
+"data": {
+"inputs": {
+"assembly_csv": {
+"id": "1a15f75791a9be7d",
+"src": "hda"
+},
+"genbank_files": {
+"id": "018c827a8e5b161a",
+"src": "hdca"
+},
+"json_use|json_conf": {
+"id": "9736c9b0f355f9e7",
+"src": "hda"
+},
+"json_use|use_json_paramers": true,
+"use_file_names_as_ids": true
+},
+"job": {
+"command_line": "mkdir 'outdir_zip' && mkdir 'outdir_gb' && cp '/tmp/tmpe6pmg7jw/files/1/5/e/dataset_15e76393-8b6d-44a4-ad54-61e9090f2281.dat' 'assembly_csv.csv' && python '/home/rkhaled/galaxytools/tools/cloning_simulation/cloning_simulation.py' --parts_files '/tmp/tmpe6pmg7jw/files/5/9/5/dataset_5952eac7-72c5-4e87-bac4-94a6eb3d7258.dat,/tmp/tmpe6pmg7jw/files/c/6/c/dataset_c6caf0b6-8d07-4998-8d0d-29b5d76faf46.dat,/tmp/tmpe6pmg7jw/files/c/3/e/dataset_c3e1ef9d-d877-4423-9f6d-0c1d109c0101.dat,/tmp/tmpe6pmg7jw/files/8/6/a/dataset_86a24365-6eed-4415-b56f-d0ff9854f0db.dat,/tmp/tmpe6pmg7jw/files/6/9/6/dataset_69698749-ab10-4865-b19a-ef4c5cb47996.dat,/tmp/tmpe6pmg7jw/files/8/e/d/dataset_8eda50dc-6b4b-4af8-9087-c6473e345a47.dat,/tmp/tmpe6pmg7jw/files/f/9/9/dataset_f99ec108-a3c6-4e80-8eff-68d9b8e9f67c.dat,/tmp/tmpe6pmg7jw/files/1/8/7/dataset_187c2c93-0a63-41ce-bf4f-88b7c770557b.dat,/tmp/tmpe6pmg7jw/files/3/d/7/dataset_3d7f0627-ba1c-4541-95f7-27ed41e601fa.dat,/tmp/tmpe6pmg7jw/files/4/c/1/dataset_4c18d9a5-e37c-428e-a5a3-8f698bbd9b3f.dat,/tmp/tmpe6pmg7jw/files/c/d/2/dataset_cd21525e-d4e4-4e03-a632-5a7152529d82.dat,/tmp/tmpe6pmg7jw/files/c/a/a/dataset_caa4a166-f30b-45f5-b1a9-cdacc6b40073.dat' --domesticated_seq '' --assembly_csv 'assembly_csv.csv' --file_name_mapping '/tmp/tmpe6pmg7jw/files/5/9/5/dataset_5952eac7-72c5-4e87-bac4-94a6eb3d7258.dat:part_A.gb,/tmp/tmpe6pmg7jw/files/c/6/c/dataset_c6caf0b6-8d07-4998-8d0d-29b5d76faf46.dat:part_B.gb,/tmp/tmpe6pmg7jw/files/c/3/e/dataset_c3e1ef9d-d877-4423-9f6d-0c1d109c0101.dat:part_C.gb,/tmp/tmpe6pmg7jw/files/8/6/a/dataset_86a24365-6eed-4415-b56f-d0ff9854f0db.dat:part_D.gb,/tmp/tmpe6pmg7jw/files/6/9/6/dataset_69698749-ab10-4865-b19a-ef4c5cb47996.dat:part_E.gb,/tmp/tmpe6pmg7jw/files/8/e/d/dataset_8eda50dc-6b4b-4af8-9087-c6473e345a47.dat:part_F.gb,/tmp/tmpe6pmg7jw/files/f/9/9/dataset_f99ec108-a3c6-4e80-8eff-68d9b8e9f67c.dat:part_G.gb,/tmp/tmpe6pmg7jw/files/1/8/7/dataset_187c2c93-0a63-41ce-bf4f-88b7c770557b.dat:part_H.gb,/tmp/tmpe6pmg7jw/files/3/d/7/dataset_3d7f0627-ba1c-4541-95f7-27ed41e601fa.dat:part_I.gb,/tmp/tmpe6pmg7jw/files/4/c/1/dataset_4c18d9a5-e37c-428e-a5a3-8f698bbd9b3f.dat:part_J.gb,/tmp/tmpe6pmg7jw/files/c/d/2/dataset_cd21525e-d4e4-4e03-a632-5a7152529d82.dat:part_K.gb,/tmp/tmpe6pmg7jw/files/c/a/a/dataset_caa4a166-f30b-45f5-b1a9-cdacc6b40073.dat:part_L.gb' --file_name_mapping_dom '' --use_json_paramers 'true' --json_conf '/tmp/tmpe6pmg7jw/files/9/b/8/dataset_9b899aff-2835-4f10-84f3-52034c55b5dc.dat' --use_file_names_as_id 'true' --outdir_simulation 'outdir_zip' --outdir_gb 'outdir_gb' --output_simulation 'output_zip.zip' && cp 'output_zip.zip' '/tmp/tmpe6pmg7jw/job_working_directory/000/78/outputs/dataset_6ee2cd5c-d43c-4fc7-9ebc-265f89a87696.dat'",
+"command_version": "",
+"copied_from_job_id": null,
+"create_time": "2025-07-17T10:14:50.961634",
+"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": "81204",
+"galaxy_version": "25.0",
+"handler": null,
+"history_id": "f7b25594aba42961",
+"id": "6665d38e10ff581d",
+"inputs": {
+"assembly_csv": {
+"id": "1a15f75791a9be7d",
+"src": "hda",
+"uuid": "15e76393-8b6d-44a4-ad54-61e9090f2281"
+},
+"genbank_files1": {
+"id": "59c39a1f7cd89b1b",
+"src": "hda",
+"uuid": "5952eac7-72c5-4e87-bac4-94a6eb3d7258"
+},
+"genbank_files10": {
+"id": "e01657e1b61da6f3",
+"src": "hda",
+"uuid": "4c18d9a5-e37c-428e-a5a3-8f698bbd9b3f"
+},
+"genbank_files11": {
+"id": "ca4aa85e07d14f5a",
+"src": "hda",
+"uuid": "cd21525e-d4e4-4e03-a632-5a7152529d82"
+},
+"genbank_files12": {
+"id": "c041165b2b3d8e70",
+"src": "hda",
+"uuid": "caa4a166-f30b-45f5-b1a9-cdacc6b40073"
+},
+"genbank_files2": {
+"id": "a6194e007a63df57",
+"src": "hda",
+"uuid": "c6caf0b6-8d07-4998-8d0d-29b5d76faf46"
+},
+"genbank_files3": {
+"id": "fa554b79bf343ee0",
+"src": "hda",
+"uuid": "c3e1ef9d-d877-4423-9f6d-0c1d109c0101"
+},
+"genbank_files4": {
+"id": "5a80b8b59c71bb8c",
+"src": "hda",
+"uuid": "86a24365-6eed-4415-b56f-d0ff9854f0db"
+},
+"genbank_files5": {
+"id": "e0d49f429b51fe72",
+"src": "hda",
+"uuid": "69698749-ab10-4865-b19a-ef4c5cb47996"
+},
+"genbank_files6": {
+"id": "78e04b973431c16b",
+"src": "hda",
+"uuid": "8eda50dc-6b4b-4af8-9087-c6473e345a47"
+},
+"genbank_files7": {
+"id": "0582b59361b7ebfc",
+"src": "hda",
+"uuid": "f99ec108-a3c6-4e80-8eff-68d9b8e9f67c"
+},
+"genbank_files8": {
+"id": "d65ee033f23e8216",
+"src": "hda",
+"uuid": "187c2c93-0a63-41ce-bf4f-88b7c770557b"
+},
+"genbank_files9": {
+"id": "eb35258b10e09e8e",
+"src": "hda",
+"uuid": "3d7f0627-ba1c-4541-95f7-27ed41e601fa"
+},
+"json_use|json_conf": {
+"id": "9736c9b0f355f9e7",
+"src": "hda",
+"uuid": "9b899aff-2835-4f10-84f3-52034c55b5dc"
+}
+},
+"job_messages": [],
+"job_metrics": [],
+"job_runner_name": null,
+"job_stderr": "",
+"job_stdout": "",
+"model_class": "Job",
+"output_collections": {
+"construct_gb": {
+"id": "494079827008dff1",
+"src": "hdca"
+}
+},
+"outputs": {
+"__new_primary_file_construct_gb|construct_1__": {
+"id": "042ef984f231298e",
+"src": "hda",
+"uuid": "88d735c2-5600-4ed7-942c-07e0ce3b5b4a"
+},
+"__new_primary_file_construct_gb|construct_2__": {
+"id": "ec93ee31e9126c50",
+"src": "hda",
+"uuid": "7b9fee32-94aa-421d-a905-a8a5863047e3"
+},
+"__new_primary_file_construct_gb|construct_3__": {
+"id": "5cf69b6cb189d4a3",
+"src": "hda",
+"uuid": "001a91be-d900-4196-b6b0-fa5ac8e97946"
+},
+"__new_primary_file_construct_gb|construct_4__": {
+"id": "84d3b22c61ad807e",
+"src": "hda",
+"uuid": "e567ccf6-ed3b-4dcb-85e8-8456952d28cc"
+},
+"output_zip": {
+"id": "985e51699d0cdeaa",
+"src": "hda",
+"uuid": "6ee2cd5c-d43c-4fc7-9ebc-265f89a87696"
+}
+},
+"params": {
+"__input_ext": "\"input\"",
+"chromInfo": "\"/tmp/tmpe6pmg7jw/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+"dbkey": "\"?\"",
+"domesticated_input": null,
+"genbank_files": "{\"values\": [{\"id\": 16, \"src\": \"hdca\"}]}",
+"json_use": "{\"__current_case__\": 1, \"json_conf\": {\"values\": [{\"id\": 95, \"src\": \"hda\"}]}, \"use_json_paramers\": true}",
+"use_file_names_as_ids": "true"
+},
+"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,  2.19it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.81it/s, now=None]\r                                                                 \r",
+"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,  2.19it/s, now=None]\rassembly: 100%|\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588\u2588| 4/4 [00:02<00:00,  1.81it/s, now=None]\r                                                                 \r",
+"tool_stdout": "Simulating assembly plan assambly...\n{'cancelled_assemblies': 0, 'errored_assemblies': 0, 'valid_assemblies': 4}\nGenerating assemblies reports...\n",
+"update_time": "2025-07-17T10:15:03.707417",
+"user_email": "planemo@galaxyproject.org",
+"user_id": "986c9b47c580ae59"
+},
+"status": "success",
+"test_index": 7,
+"time_seconds": 52.973809242248535,
+"tool_id": "cloning_simulation",
+"tool_version": "0.1.0+galaxy0"
+},
+"has_data": true,
+"id": "cloning_simulation-7"
 }
 ],
 "version": "0.1"
 }

Mercurial > repos > tduigou > cloning_simulation

comparison output.json @ 16:fbb241adf6c2 draft default tip