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diff output.json @ 4:f78651af72e4 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 19 May 2025 13:01:50 +0000
parents bf8cd9487e33
children 70895bec2486
line wrap: on
line diff
--- a/output.json	Fri May 16 09:30:35 2025 +0000
+++ b/output.json	Mon May 19 13:01:50 2025 +0000
@@ -12,67 +12,67 @@
                     "adv|allow_edits": true,
                     "adv|use_file_names_as_ids": true,
                     "domestication_csv": {
-                        "id": "6c832fb8ac42860f",
+                        "id": "731d411caa07a047",
                         "src": "hda"
                     },
                     "genbank_files": {
-                        "id": "e660c01bdba47572",
+                        "id": "d14be99de3d080ed",
                         "src": "hdca"
                     },
                     "methylation_protection": false
                 },
                 "job": {
-                    "command_line": "mkdir 'outdir_gb' && mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmomj1390/files/9/8/e/dataset_98eaff26-0334-4311-b121-579c564457fa.dat,/tmp/tmpmomj1390/files/6/9/e/dataset_69e06834-aff3-45c0-8c8a-1b0951b3c58a.dat,/tmp/tmpmomj1390/files/a/4/3/dataset_a43d91b4-75bc-42ad-b3eb-3c2b8974849d.dat,/tmp/tmpmomj1390/files/b/8/4/dataset_b8425ed5-d152-443a-ab5e-d5e5d8e18685.dat,/tmp/tmpmomj1390/files/a/f/5/dataset_af5ff6ae-e7f3-4d04-9e27-2f4619b9a7f5.dat,/tmp/tmpmomj1390/files/d/f/b/dataset_dfbae617-1607-410e-ae63-95e367876898.dat,/tmp/tmpmomj1390/files/9/9/d/dataset_99d37e87-dd8a-4439-a03a-004433442d3f.dat' --csv_file '/tmp/tmpmomj1390/files/f/b/c/dataset_fbc30e96-b97e-4267-8ed5-5ceaa219759e.dat' --file_name_mapping '/tmp/tmpmomj1390/files/9/8/e/dataset_98eaff26-0334-4311-b121-579c564457fa.dat:p3_2_CAG.gb,/tmp/tmpmomj1390/files/6/9/e/dataset_69e06834-aff3-45c0-8c8a-1b0951b3c58a.dat:p7_gfp_sequence.gb,/tmp/tmpmomj1390/files/a/4/3/dataset_a43d91b4-75bc-42ad-b3eb-3c2b8974849d.dat:p14_CMVp.gb,/tmp/tmpmomj1390/files/b/8/4/dataset_b8425ed5-d152-443a-ab5e-d5e5d8e18685.dat:p16_bGHpolyA.gb,/tmp/tmpmomj1390/files/a/f/5/dataset_af5ff6ae-e7f3-4d04-9e27-2f4619b9a7f5.dat:p18_CMVp.gb,/tmp/tmpmomj1390/files/d/f/b/dataset_dfbae617-1607-410e-ae63-95e367876898.dat:p19_mNeoGreen.gb,/tmp/tmpmomj1390/files/9/9/d/dataset_99d37e87-dd8a-4439-a03a-004433442d3f.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_methprot 'outdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpmomj1390/job_working_directory/000/9/outputs/dataset_6e663eda-900f-4c38-aa98-8ed6be291879.dat'",
+                    "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpx7m35erq/files/f/a/a/dataset_faa3888b-c353-4955-a647-2de4e990aa04.dat,/tmp/tmpx7m35erq/files/9/9/a/dataset_99a9f317-902f-42e2-843e-bcf77f8d5e41.dat,/tmp/tmpx7m35erq/files/1/7/f/dataset_17f66eff-626e-418b-811d-23af40bcf421.dat,/tmp/tmpx7m35erq/files/3/7/a/dataset_37aee03e-9201-4898-90ed-08e269dcf307.dat,/tmp/tmpx7m35erq/files/f/9/7/dataset_f97defcc-6a78-48c0-adb8-dbc124814cc9.dat,/tmp/tmpx7m35erq/files/b/0/c/dataset_b0c757dd-f9dd-436c-8046-d848d6192506.dat,/tmp/tmpx7m35erq/files/4/0/4/dataset_40439379-7f50-4f5e-a329-f4be74549e95.dat' --csv_file '/tmp/tmpx7m35erq/files/2/9/c/dataset_29cd6651-90b3-43b3-91e3-c4cee6f32fd5.dat' --file_name_mapping '/tmp/tmpx7m35erq/files/f/a/a/dataset_faa3888b-c353-4955-a647-2de4e990aa04.dat:p3_2_CAG.gb,/tmp/tmpx7m35erq/files/9/9/a/dataset_99a9f317-902f-42e2-843e-bcf77f8d5e41.dat:p7_gfp_sequence.gb,/tmp/tmpx7m35erq/files/1/7/f/dataset_17f66eff-626e-418b-811d-23af40bcf421.dat:p14_CMVp.gb,/tmp/tmpx7m35erq/files/3/7/a/dataset_37aee03e-9201-4898-90ed-08e269dcf307.dat:p16_bGHpolyA.gb,/tmp/tmpx7m35erq/files/f/9/7/dataset_f97defcc-6a78-48c0-adb8-dbc124814cc9.dat:p18_CMVp.gb,/tmp/tmpx7m35erq/files/b/0/c/dataset_b0c757dd-f9dd-436c-8046-d848d6192506.dat:p19_mNeoGreen.gb,/tmp/tmpx7m35erq/files/4/0/4/dataset_40439379-7f50-4f5e-a329-f4be74549e95.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'false' && cp 'output_zip.zip' '/tmp/tmpx7m35erq/job_working_directory/000/9/outputs/dataset_4808d334-4a4b-4505-88c8-5b0be07a65f2.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-05-12T15:19:23.808194",
+                    "create_time": "2025-05-19T12:58:14.187742",
                     "dependencies": [],
                     "exit_code": 0,
-                    "external_id": "300911",
+                    "external_id": "213747",
                     "galaxy_version": "24.2",
                     "handler": null,
-                    "history_id": "e660c01bdba47572",
-                    "id": "86d58b95f07edb2d",
+                    "history_id": "d14be99de3d080ed",
+                    "id": "fee508e1bcb0faa2",
                     "inputs": {
                         "domestication_csv": {
-                            "id": "6c832fb8ac42860f",
+                            "id": "731d411caa07a047",
                             "src": "hda",
-                            "uuid": "fbc30e96-b97e-4267-8ed5-5ceaa219759e"
+                            "uuid": "29cd6651-90b3-43b3-91e3-c4cee6f32fd5"
                         },
                         "genbank_files1": {
-                            "id": "e660c01bdba47572",
+                            "id": "d14be99de3d080ed",
                             "src": "hda",
-                            "uuid": "98eaff26-0334-4311-b121-579c564457fa"
+                            "uuid": "faa3888b-c353-4955-a647-2de4e990aa04"
                         },
                         "genbank_files2": {
-                            "id": "94d973d69c111d7f",
+                            "id": "333ca9fff0e09522",
                             "src": "hda",
-                            "uuid": "69e06834-aff3-45c0-8c8a-1b0951b3c58a"
+                            "uuid": "99a9f317-902f-42e2-843e-bcf77f8d5e41"
                         },
                         "genbank_files3": {
-                            "id": "6da151567610da58",
+                            "id": "b636088f5932061b",
                             "src": "hda",
-                            "uuid": "a43d91b4-75bc-42ad-b3eb-3c2b8974849d"
+                            "uuid": "17f66eff-626e-418b-811d-23af40bcf421"
                         },
                         "genbank_files4": {
-                            "id": "2cbbdad9a9ee38a7",
+                            "id": "95ac77ecc07de70b",
                             "src": "hda",
-                            "uuid": "b8425ed5-d152-443a-ab5e-d5e5d8e18685"
+                            "uuid": "37aee03e-9201-4898-90ed-08e269dcf307"
                         },
                         "genbank_files5": {
-                            "id": "8cbbf46d79fe2594",
+                            "id": "b67ddf0d29d01e70",
                             "src": "hda",
-                            "uuid": "af5ff6ae-e7f3-4d04-9e27-2f4619b9a7f5"
+                            "uuid": "f97defcc-6a78-48c0-adb8-dbc124814cc9"
                         },
                         "genbank_files6": {
-                            "id": "8e76e08000cb23f6",
+                            "id": "667facab024bf341",
                             "src": "hda",
-                            "uuid": "dfbae617-1607-410e-ae63-95e367876898"
+                            "uuid": "b0c757dd-f9dd-436c-8046-d848d6192506"
                         },
                         "genbank_files7": {
-                            "id": "c5a9d28d6cf64e0c",
+                            "id": "488fdb347c588432",
                             "src": "hda",
-                            "uuid": "99d37e87-dd8a-4439-a03a-004433442d3f"
+                            "uuid": "40439379-7f50-4f5e-a329-f4be74549e95"
                         }
                     },
                     "job_messages": [],
@@ -81,35 +81,75 @@
                     "job_stderr": "",
                     "job_stdout": "",
                     "model_class": "Job",
-                    "output_collections": {},
+                    "output_collections": {
+                        "domesticated_gb": {
+                            "id": "333ca9fff0e09522",
+                            "src": "hdca"
+                        }
+                    },
                     "outputs": {
+                        "__new_primary_file_domesticated_gb|p14_CMVp__": {
+                            "id": "4c892d88b39e70b4",
+                            "src": "hda",
+                            "uuid": "a10eb5bc-c1a0-4cfc-8924-27bd94e58726"
+                        },
+                        "__new_primary_file_domesticated_gb|p16_bGHpolyA__": {
+                            "id": "b253aa9b6cff5f9a",
+                            "src": "hda",
+                            "uuid": "4897e913-0f0f-4fdf-825b-d58bd898b1c1"
+                        },
+                        "__new_primary_file_domesticated_gb|p18_CMVp__": {
+                            "id": "2ce9c1583c06694d",
+                            "src": "hda",
+                            "uuid": "88be19e6-4d92-4fff-8e03-392746fab26d"
+                        },
+                        "__new_primary_file_domesticated_gb|p19_mNeoGreen__": {
+                            "id": "8cf63a87c95f5d66",
+                            "src": "hda",
+                            "uuid": "3b1aef51-8f63-4fcb-af4d-869261c9a74c"
+                        },
+                        "__new_primary_file_domesticated_gb|p22_PGKpolyA__": {
+                            "id": "c76711703fd2ebee",
+                            "src": "hda",
+                            "uuid": "e5cefba7-b68e-4988-a7c6-24e0d4216ac4"
+                        },
+                        "__new_primary_file_domesticated_gb|p3_2_CAG__": {
+                            "id": "7084b37a971d5f6b",
+                            "src": "hda",
+                            "uuid": "cfff458f-c165-403e-a848-21a5b17769f6"
+                        },
+                        "__new_primary_file_domesticated_gb|p7_gfp_sequence__": {
+                            "id": "bdbb8b37b6fe9de4",
+                            "src": "hda",
+                            "uuid": "58043ea5-16c9-4600-9de1-17b7e32466b3"
+                        },
                         "output_zip": {
-                            "id": "86d58b95f07edb2d",
+                            "id": "fee508e1bcb0faa2",
                             "src": "hda",
-                            "uuid": "6e663eda-900f-4c38-aa98-8ed6be291879"
+                            "uuid": "4808d334-4a4b-4505-88c8-5b0be07a65f2"
                         }
                     },
                     "params": {
                         "__input_ext": "\"input\"",
                         "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
-                        "chromInfo": "\"/tmp/tmpmomj1390/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "chromInfo": "\"/tmp/tmpx7m35erq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
                         "dbkey": "\"?\"",
                         "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}",
                         "methylation_protection": "false"
                     },
                     "state": "ok",
-                    "stderr": "\rrecord:   0%|          | 0/7 [00:00<?, ?it/s, now=None]\rrecord:  43%|\u2588\u2588\u2588\u2588\u258e     | 3/7 [00:01<00:02,  1.73it/s, now=None]\r                                                               \r",
+                    "stderr": "\rrecord:   0%|          | 0/7 [00:00<?, ?it/s, now=None]\rrecord:  43%|\u2588\u2588\u2588\u2588\u258e     | 3/7 [00:01<00:02,  1.77it/s, now=None]\r                                                               \r",
                     "stdout": "Part names were not truncated\n",
                     "tool_id": "domestication",
-                    "tool_stderr": "\rrecord:   0%|          | 0/7 [00:00<?, ?it/s, now=None]\rrecord:  43%|\u2588\u2588\u2588\u2588\u258e     | 3/7 [00:01<00:02,  1.73it/s, now=None]\r                                                               \r",
+                    "tool_stderr": "\rrecord:   0%|          | 0/7 [00:00<?, ?it/s, now=None]\rrecord:  43%|\u2588\u2588\u2588\u2588\u258e     | 3/7 [00:01<00:02,  1.77it/s, now=None]\r                                                               \r",
                     "tool_stdout": "Part names were not truncated\n",
-                    "update_time": "2025-05-12T15:19:35.066496",
+                    "update_time": "2025-05-19T12:58:25.364417",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "e660c01bdba47572"
+                    "user_id": "d14be99de3d080ed"
                 },
                 "status": "success",
                 "test_index": 0,
-                "time_seconds": 33.88110899925232,
+                "time_seconds": 33.631378173828125,
                 "tool_id": "domestication",
                 "tool_version": "0.1.0+galaxy1"
             },
@@ -122,20 +162,20 @@
                     "adv|allow_edits": true,
                     "adv|use_file_names_as_ids": true,
                     "domestication_csv": {
-                        "id": "ff21cf4b5818da45",
+                        "id": "d60a40c52e891f81",
                         "src": "hda"
                     },
                     "genbank_files": {
-                        "id": "94d973d69c111d7f",
+                        "id": "b636088f5932061b",
                         "src": "hdca"
                     },
                     "methylation_protection": true
                 },
                 "job": {
-                    "command_line": "mkdir 'outdir_gb' && mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmomj1390/files/b/1/3/dataset_b13b6d1b-090f-499c-b64b-c1630dcc675b.dat,/tmp/tmpmomj1390/files/c/5/0/dataset_c5065ec8-dc8a-4bd5-ad78-8b6925b1e13a.dat,/tmp/tmpmomj1390/files/5/c/6/dataset_5c6a4082-6f02-474d-be70-1263d3220dcb.dat,/tmp/tmpmomj1390/files/a/b/1/dataset_ab14cebb-85b9-4fff-9cb1-1056c9701e21.dat,/tmp/tmpmomj1390/files/6/f/e/dataset_6fe23d92-e2c0-4888-b627-d413e61b1d61.dat,/tmp/tmpmomj1390/files/e/9/9/dataset_e990dda1-9ebf-4414-a79c-9cf220f81ca3.dat,/tmp/tmpmomj1390/files/b/4/0/dataset_b40f7a77-27cd-4422-b821-eecc5774e6e6.dat' --csv_file '/tmp/tmpmomj1390/files/0/b/1/dataset_0b1c2aef-600f-4d98-afa3-a2243e337da1.dat' --file_name_mapping '/tmp/tmpmomj1390/files/b/1/3/dataset_b13b6d1b-090f-499c-b64b-c1630dcc675b.dat:p3_2_CAG.gb,/tmp/tmpmomj1390/files/c/5/0/dataset_c5065ec8-dc8a-4bd5-ad78-8b6925b1e13a.dat:p7_gfp_sequence.gb,/tmp/tmpmomj1390/files/5/c/6/dataset_5c6a4082-6f02-474d-be70-1263d3220dcb.dat:p14_CMVp.gb,/tmp/tmpmomj1390/files/a/b/1/dataset_ab14cebb-85b9-4fff-9cb1-1056c9701e21.dat:p16_bGHpolyA.gb,/tmp/tmpmomj1390/files/6/f/e/dataset_6fe23d92-e2c0-4888-b627-d413e61b1d61.dat:p18_CMVp.gb,/tmp/tmpmomj1390/files/e/9/9/dataset_e990dda1-9ebf-4414-a79c-9cf220f81ca3.dat:p19_mNeoGreen.gb,/tmp/tmpmomj1390/files/b/4/0/dataset_b40f7a77-27cd-4422-b821-eecc5774e6e6.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_methprot 'outdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpmomj1390/job_working_directory/000/18/outputs/dataset_e5fbb54d-ef6f-4bd9-9a45-a16d722f41f1.dat'",
+                    "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpx7m35erq/files/6/0/f/dataset_60f65d19-207d-4b98-bd4e-e96fedce54f9.dat,/tmp/tmpx7m35erq/files/a/0/3/dataset_a0327351-822f-434b-9419-5be863a9860c.dat,/tmp/tmpx7m35erq/files/b/8/b/dataset_b8ba71c8-c407-4ef2-8d62-9e4424abb738.dat,/tmp/tmpx7m35erq/files/1/c/f/dataset_1cf7eb8e-2756-4a32-8528-feed753df170.dat,/tmp/tmpx7m35erq/files/d/9/a/dataset_d9a3d440-744f-42d7-b237-1d660611b50f.dat,/tmp/tmpx7m35erq/files/9/4/2/dataset_94214037-a224-48c0-a020-d65d129c7991.dat,/tmp/tmpx7m35erq/files/8/4/7/dataset_847ef527-7ddf-4e84-a946-7ee7a299b19e.dat' --csv_file '/tmp/tmpx7m35erq/files/3/7/8/dataset_378455ea-e8e0-4a2f-a6fc-b74871efe332.dat' --file_name_mapping '/tmp/tmpx7m35erq/files/6/0/f/dataset_60f65d19-207d-4b98-bd4e-e96fedce54f9.dat:p3_2_CAG.gb,/tmp/tmpx7m35erq/files/a/0/3/dataset_a0327351-822f-434b-9419-5be863a9860c.dat:p7_gfp_sequence.gb,/tmp/tmpx7m35erq/files/b/8/b/dataset_b8ba71c8-c407-4ef2-8d62-9e4424abb738.dat:p14_CMVp.gb,/tmp/tmpx7m35erq/files/1/c/f/dataset_1cf7eb8e-2756-4a32-8528-feed753df170.dat:p16_bGHpolyA.gb,/tmp/tmpx7m35erq/files/d/9/a/dataset_d9a3d440-744f-42d7-b237-1d660611b50f.dat:p18_CMVp.gb,/tmp/tmpx7m35erq/files/9/4/2/dataset_94214037-a224-48c0-a020-d65d129c7991.dat:p19_mNeoGreen.gb,/tmp/tmpx7m35erq/files/8/4/7/dataset_847ef527-7ddf-4e84-a946-7ee7a299b19e.dat:p22_PGKpolyA.gb' --use_file_names_as_id 'true' --allow_edits 'true' --output_dom 'output_zip.zip' --output_gb_dom 'outdir_gb' --output_methprot 'metoutdir_gb' --methylation_protection 'true' && cp 'output_zip.zip' '/tmp/tmpx7m35erq/job_working_directory/000/18/outputs/dataset_13e409d9-b579-4ded-8f9a-1587cf692ef3.dat'",
                     "command_version": "",
                     "copied_from_job_id": null,
-                    "create_time": "2025-05-12T15:19:57.567258",
+                    "create_time": "2025-05-19T12:58:48.405152",
                     "dependencies": [
                         {
                             "cacheable": false,
@@ -153,7 +193,7 @@
                                 "versionless": false
                             },
                             "dependency_type": "conda",
-                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
+                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ebf0296502565ba7d0f6435a4c3184b56b9905bb762f63578baf4e839a11ad14",
                             "exact": true,
                             "model_class": "MergedCondaDependency",
                             "name": "flametree",
@@ -175,7 +215,7 @@
                                 "versionless": false
                             },
                             "dependency_type": "conda",
-                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
+                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ebf0296502565ba7d0f6435a4c3184b56b9905bb762f63578baf4e839a11ad14",
                             "exact": true,
                             "model_class": "MergedCondaDependency",
                             "name": "biopython",
@@ -197,7 +237,7 @@
                                 "versionless": false
                             },
                             "dependency_type": "conda",
-                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
+                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ebf0296502565ba7d0f6435a4c3184b56b9905bb762f63578baf4e839a11ad14",
                             "exact": true,
                             "model_class": "MergedCondaDependency",
                             "name": "proglog",
@@ -219,11 +259,11 @@
                                 "versionless": false
                             },
                             "dependency_type": "conda",
-                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
+                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ebf0296502565ba7d0f6435a4c3184b56b9905bb762f63578baf4e839a11ad14",
                             "exact": true,
                             "model_class": "MergedCondaDependency",
                             "name": "genedom",
-                            "version": "0.2.1"
+                            "version": "0.2.2"
                         },
                         {
                             "cacheable": false,
@@ -241,7 +281,7 @@
                                 "versionless": false
                             },
                             "dependency_type": "conda",
-                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
+                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ebf0296502565ba7d0f6435a4c3184b56b9905bb762f63578baf4e839a11ad14",
                             "exact": true,
                             "model_class": "MergedCondaDependency",
                             "name": "pandas",
@@ -263,11 +303,11 @@
                                 "versionless": false
                             },
                             "dependency_type": "conda",
-                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
+                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ebf0296502565ba7d0f6435a4c3184b56b9905bb762f63578baf4e839a11ad14",
                             "exact": true,
                             "model_class": "MergedCondaDependency",
                             "name": "dnacauldron",
-                            "version": "2.0.11"
+                            "version": "2.0.12"
                         },
                         {
                             "cacheable": false,
@@ -285,7 +325,7 @@
                                 "versionless": false
                             },
                             "dependency_type": "conda",
-                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
+                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ebf0296502565ba7d0f6435a4c3184b56b9905bb762f63578baf4e839a11ad14",
                             "exact": true,
                             "model_class": "MergedCondaDependency",
                             "name": "pdf-reports",
@@ -307,7 +347,7 @@
                                 "versionless": false
                             },
                             "dependency_type": "conda",
-                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
+                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ebf0296502565ba7d0f6435a4c3184b56b9905bb762f63578baf4e839a11ad14",
                             "exact": true,
                             "model_class": "MergedCondaDependency",
                             "name": "sequenticon",
@@ -329,59 +369,59 @@
                                 "versionless": false
                             },
                             "dependency_type": "conda",
-                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-f05e814ead139eea2d366bbe58573083f8fc211e23465a99188722aaf9b8befd",
+                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ebf0296502565ba7d0f6435a4c3184b56b9905bb762f63578baf4e839a11ad14",
                             "exact": true,
                             "model_class": "MergedCondaDependency",
                             "name": "dna_features_viewer",
-                            "version": "3.1.4"
+                            "version": "3.1.5"
                         }
                     ],
                     "exit_code": 0,
-                    "external_id": "301662",
+                    "external_id": "214552",
                     "galaxy_version": "24.2",
                     "handler": null,
-                    "history_id": "94d973d69c111d7f",
-                    "id": "3a6ea217cbbcfeb3",
+                    "history_id": "333ca9fff0e09522",
+                    "id": "d6319365b3f15bc0",
                     "inputs": {
                         "domestication_csv": {
-                            "id": "ff21cf4b5818da45",
+                            "id": "d60a40c52e891f81",
                             "src": "hda",
-                            "uuid": "0b1c2aef-600f-4d98-afa3-a2243e337da1"
+                            "uuid": "378455ea-e8e0-4a2f-a6fc-b74871efe332"
                         },
                         "genbank_files1": {
-                            "id": "58b9ec2cc51a7bbc",
+                            "id": "a5542bcb255f1fe3",
                             "src": "hda",
-                            "uuid": "b13b6d1b-090f-499c-b64b-c1630dcc675b"
+                            "uuid": "60f65d19-207d-4b98-bd4e-e96fedce54f9"
                         },
                         "genbank_files2": {
-                            "id": "dfd200964bc0e0b3",
+                            "id": "d6319365b3f15bc0",
                             "src": "hda",
-                            "uuid": "c5065ec8-dc8a-4bd5-ad78-8b6925b1e13a"
+                            "uuid": "a0327351-822f-434b-9419-5be863a9860c"
                         },
                         "genbank_files3": {
-                            "id": "728ee4548f790253",
+                            "id": "e8bbe2c6fd185fe3",
                             "src": "hda",
-                            "uuid": "5c6a4082-6f02-474d-be70-1263d3220dcb"
+                            "uuid": "b8ba71c8-c407-4ef2-8d62-9e4424abb738"
                         },
                         "genbank_files4": {
-                            "id": "8ec4d60703928c0b",
+                            "id": "898df5142a61135b",
                             "src": "hda",
-                            "uuid": "ab14cebb-85b9-4fff-9cb1-1056c9701e21"
+                            "uuid": "1cf7eb8e-2756-4a32-8528-feed753df170"
                         },
                         "genbank_files5": {
-                            "id": "0ea49e46b3b36fc8",
+                            "id": "e17cef8ccd4f9c47",
                             "src": "hda",
-                            "uuid": "6fe23d92-e2c0-4888-b627-d413e61b1d61"
+                            "uuid": "d9a3d440-744f-42d7-b237-1d660611b50f"
                         },
                         "genbank_files6": {
-                            "id": "fa15c2af129b8b76",
+                            "id": "8d21e5a48c50c737",
                             "src": "hda",
-                            "uuid": "e990dda1-9ebf-4414-a79c-9cf220f81ca3"
+                            "uuid": "94214037-a224-48c0-a020-d65d129c7991"
                         },
                         "genbank_files7": {
-                            "id": "e23a32c230113bee",
+                            "id": "90d918ed95474b27",
                             "src": "hda",
-                            "uuid": "b40f7a77-27cd-4422-b821-eecc5774e6e6"
+                            "uuid": "847ef527-7ddf-4e84-a946-7ee7a299b19e"
                         }
                     },
                     "job_messages": [],
@@ -392,58 +432,58 @@
                     "model_class": "Job",
                     "output_collections": {
                         "methprot_gb": {
-                            "id": "6da151567610da58",
+                            "id": "95ac77ecc07de70b",
                             "src": "hdca"
                         }
                     },
                     "outputs": {
                         "__new_primary_file_methprot_gb|p14_CMVp__": {
-                            "id": "ff56119d03b36f7e",
+                            "id": "489ec5bc1516ecd5",
                             "src": "hda",
-                            "uuid": "4ce1c883-a9a0-4d2f-893d-1367d70461a9"
+                            "uuid": "0d2af719-3628-40af-a6c1-a5e90137381f"
                         },
                         "__new_primary_file_methprot_gb|p16_bGHpolyA__": {
-                            "id": "23c852ea5c29414c",
+                            "id": "99e717225525c9eb",
                             "src": "hda",
-                            "uuid": "1db47dfa-c46a-47cd-bd6e-cb373414291a"
+                            "uuid": "33425e71-0bff-46f4-8c23-e744a45602ca"
                         },
                         "__new_primary_file_methprot_gb|p18_CMVp__": {
-                            "id": "2a13f3a02c150685",
+                            "id": "656b6ec7223fbf1e",
                             "src": "hda",
-                            "uuid": "974bb633-efcf-4a64-8b65-ccd2e02c7fc7"
+                            "uuid": "48cda26f-cfea-44f6-9e8b-50eff2717750"
                         },
                         "__new_primary_file_methprot_gb|p19_mNeoGreen__": {
-                            "id": "0d219ad454277643",
+                            "id": "113c9cc0c15058bb",
                             "src": "hda",
-                            "uuid": "bc97a0eb-f620-4e9c-8d54-f538c86a1a84"
+                            "uuid": "bab0b5c7-fc74-4ad4-b663-705a673522bb"
                         },
                         "__new_primary_file_methprot_gb|p22_PGKpolyA__": {
-                            "id": "8ba22fe1db24a1dd",
+                            "id": "0c6048baa6a25748",
                             "src": "hda",
-                            "uuid": "f2082e29-29a9-44b5-8090-88d82b96fab7"
+                            "uuid": "ee56e78a-0a85-47c9-a059-0a61413e55ed"
                         },
                         "__new_primary_file_methprot_gb|p3_2_CAG__": {
-                            "id": "eeb9f7bb54b54cc1",
+                            "id": "05295ab3ba4727fb",
                             "src": "hda",
-                            "uuid": "996aeeed-114f-4e88-a3e8-ac6ca810bd5a"
+                            "uuid": "3c5e8804-dfd5-4294-8122-6bcbc027f815"
                         },
                         "__new_primary_file_methprot_gb|p7_gfp_sequence__": {
-                            "id": "a067f4d569f90edf",
+                            "id": "ae0a3b89507f75f1",
                             "src": "hda",
-                            "uuid": "938ac53e-c913-4c4e-99b5-0ed92e4114d4"
+                            "uuid": "ab9d3d90-d1f0-48ed-b8de-988762521355"
                         },
                         "output_zip": {
-                            "id": "3a6ea217cbbcfeb3",
+                            "id": "891630a60c9b70b3",
                             "src": "hda",
-                            "uuid": "e5fbb54d-ef6f-4bd9-9a45-a16d722f41f1"
+                            "uuid": "13e409d9-b579-4ded-8f9a-1587cf692ef3"
                         }
                     },
                     "params": {
                         "__input_ext": "\"input\"",
                         "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
-                        "chromInfo": "\"/tmp/tmpmomj1390/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
+                        "chromInfo": "\"/tmp/tmpx7m35erq/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
                         "dbkey": "\"?\"",
-                        "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}",
+                        "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
                         "methylation_protection": "true"
                     },
                     "state": "ok",
@@ -452,13 +492,13 @@
                     "tool_id": "domestication",
                     "tool_stderr": "\rrecord:   0%|          | 0/7 [00:00<?, ?it/s, now=None]\rrecord:  43%|\u2588\u2588\u2588\u2588\u258e     | 3/7 [00:01<00:02,  1.76it/s, now=None]\r                                                               \r",
                     "tool_stdout": "Part names were not truncated\n",
-                    "update_time": "2025-05-12T15:20:08.233126",
+                    "update_time": "2025-05-19T12:58:58.703537",
                     "user_email": "planemo@galaxyproject.org",
-                    "user_id": "e660c01bdba47572"
+                    "user_id": "d14be99de3d080ed"
                 },
                 "status": "success",
                 "test_index": 1,
-                "time_seconds": 33.191433906555176,
+                "time_seconds": 33.25414228439331,
                 "tool_id": "domestication",
                 "tool_version": "0.1.0+galaxy1"
             },