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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 Tue, 27 May 2025 08:08:21 +0000
parents 4bfdec0be6b1
children
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{
    "summary": {
        "num_errors": 0,
        "num_failures": 0,
        "num_skips": 0,
        "num_tests": 2
    },
    "tests": [
        {
            "data": {
                "inputs": {
                    "adv|allow_edits": true,
                    "adv|use_file_names_as_ids": true,
                    "domestication_csv": {
                        "id": "df3910bf12e3ecf9",
                        "src": "hda"
                    },
                    "genbank_files": {
                        "id": "40971d80b8a8a53c",
                        "src": "hdca"
                    },
                    "methylation_protection": false
                },
                "job": {
                    "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpmo0pk3jj/files/6/1/a/dataset_61aea63f-fa8f-4855-b597-d298379d415c.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmo0pk3jj/files/2/f/f/dataset_2ff46bb9-5b06-4cad-b98f-afa1443697b5.dat,/tmp/tmpmo0pk3jj/files/9/9/c/dataset_99c508b5-234a-4eba-b9d2-05204eaa2ec8.dat,/tmp/tmpmo0pk3jj/files/0/a/0/dataset_0a0b7db9-a3ac-4999-b1c9-498618831d59.dat,/tmp/tmpmo0pk3jj/files/a/2/9/dataset_a2994595-0a40-48ba-a369-db577710e99a.dat,/tmp/tmpmo0pk3jj/files/c/8/b/dataset_c8b3e40f-a0a8-414e-a56c-bd71775b2218.dat,/tmp/tmpmo0pk3jj/files/c/8/1/dataset_c813a93e-97c6-4f6a-bcd0-dcdbd93728e2.dat,/tmp/tmpmo0pk3jj/files/3/6/8/dataset_368b2cf8-f34e-427d-888e-b431a4b28c87.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpmo0pk3jj/files/2/f/f/dataset_2ff46bb9-5b06-4cad-b98f-afa1443697b5.dat:p3_2_CAG.gb,/tmp/tmpmo0pk3jj/files/9/9/c/dataset_99c508b5-234a-4eba-b9d2-05204eaa2ec8.dat:p7_gfp_sequence.gb,/tmp/tmpmo0pk3jj/files/0/a/0/dataset_0a0b7db9-a3ac-4999-b1c9-498618831d59.dat:p14_CMVp.gb,/tmp/tmpmo0pk3jj/files/a/2/9/dataset_a2994595-0a40-48ba-a369-db577710e99a.dat:p16_bGHpolyA.gb,/tmp/tmpmo0pk3jj/files/c/8/b/dataset_c8b3e40f-a0a8-414e-a56c-bd71775b2218.dat:p18_CMVp.gb,/tmp/tmpmo0pk3jj/files/c/8/1/dataset_c813a93e-97c6-4f6a-bcd0-dcdbd93728e2.dat:p19_mNeoGreen.gb,/tmp/tmpmo0pk3jj/files/3/6/8/dataset_368b2cf8-f34e-427d-888e-b431a4b28c87.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/tmpmo0pk3jj/job_working_directory/000/9/outputs/dataset_598cd11f-0878-422d-b265-3e7d109f52d4.dat'",
                    "command_version": "",
                    "copied_from_job_id": null,
                    "create_time": "2025-05-27T08:07:08.549227",
                    "dependencies": [],
                    "exit_code": 0,
                    "external_id": "15664",
                    "galaxy_version": "24.2",
                    "handler": null,
                    "history_id": "40971d80b8a8a53c",
                    "id": "beecbc66855f4047",
                    "inputs": {
                        "domestication_csv": {
                            "id": "df3910bf12e3ecf9",
                            "src": "hda",
                            "uuid": "61aea63f-fa8f-4855-b597-d298379d415c"
                        },
                        "genbank_files1": {
                            "id": "40971d80b8a8a53c",
                            "src": "hda",
                            "uuid": "2ff46bb9-5b06-4cad-b98f-afa1443697b5"
                        },
                        "genbank_files2": {
                            "id": "722a3e09b8314bb2",
                            "src": "hda",
                            "uuid": "99c508b5-234a-4eba-b9d2-05204eaa2ec8"
                        },
                        "genbank_files3": {
                            "id": "1cc8aca787b2436a",
                            "src": "hda",
                            "uuid": "0a0b7db9-a3ac-4999-b1c9-498618831d59"
                        },
                        "genbank_files4": {
                            "id": "8026227525c5f951",
                            "src": "hda",
                            "uuid": "a2994595-0a40-48ba-a369-db577710e99a"
                        },
                        "genbank_files5": {
                            "id": "38afb044c6b21b09",
                            "src": "hda",
                            "uuid": "c8b3e40f-a0a8-414e-a56c-bd71775b2218"
                        },
                        "genbank_files6": {
                            "id": "58f07e41a8a4674f",
                            "src": "hda",
                            "uuid": "c813a93e-97c6-4f6a-bcd0-dcdbd93728e2"
                        },
                        "genbank_files7": {
                            "id": "3e34fe414480d6bc",
                            "src": "hda",
                            "uuid": "368b2cf8-f34e-427d-888e-b431a4b28c87"
                        }
                    },
                    "job_messages": [],
                    "job_metrics": [],
                    "job_runner_name": null,
                    "job_stderr": "",
                    "job_stdout": "",
                    "model_class": "Job",
                    "output_collections": {
                        "domesticated_gb": {
                            "id": "722a3e09b8314bb2",
                            "src": "hdca"
                        }
                    },
                    "outputs": {
                        "__new_primary_file_domesticated_gb|p14_CMVp__": {
                            "id": "8b52218386489a1b",
                            "src": "hda",
                            "uuid": "9ec489c3-d7d2-4c8e-85ed-7c608bfffc49"
                        },
                        "__new_primary_file_domesticated_gb|p16_bGHpolyA__": {
                            "id": "7df4279c30fbf11a",
                            "src": "hda",
                            "uuid": "e56aa342-fc45-4a28-befa-290f5722a67c"
                        },
                        "__new_primary_file_domesticated_gb|p18_CMVp__": {
                            "id": "5a11a7ea1c4a0b78",
                            "src": "hda",
                            "uuid": "8beec3f0-36c6-4994-b890-35fbba7d1c32"
                        },
                        "__new_primary_file_domesticated_gb|p19_mNeoGreen__": {
                            "id": "f727b077209f6bea",
                            "src": "hda",
                            "uuid": "7309490c-224e-46b1-82d1-94102829a851"
                        },
                        "__new_primary_file_domesticated_gb|p22_PGKpolyA__": {
                            "id": "77c3effc68e335c0",
                            "src": "hda",
                            "uuid": "4d4c783f-d229-44b3-af52-0e6616cd140b"
                        },
                        "__new_primary_file_domesticated_gb|p3_2_CAG__": {
                            "id": "a5683b91f8081320",
                            "src": "hda",
                            "uuid": "08b3572e-4f1c-4fe3-ac3c-8dcf2ec05ce2"
                        },
                        "__new_primary_file_domesticated_gb|p7_gfp_sequence__": {
                            "id": "3e3b60188e62bb8d",
                            "src": "hda",
                            "uuid": "6fe9d54a-584a-470a-82a5-b16b0ed0b7e1"
                        },
                        "domesticated_zip": {
                            "id": "beecbc66855f4047",
                            "src": "hda",
                            "uuid": "598cd11f-0878-422d-b265-3e7d109f52d4"
                        }
                    },
                    "params": {
                        "__input_ext": "\"input\"",
                        "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
                        "chromInfo": "\"/tmp/tmpmo0pk3jj/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,  1.68it/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,  1.68it/s, now=None]\r                                                               \r",
                    "tool_stdout": "Part names were not truncated\n",
                    "update_time": "2025-05-27T08:07:20.210958",
                    "user_email": "planemo@galaxyproject.org",
                    "user_id": "40971d80b8a8a53c"
                },
                "status": "success",
                "test_index": 0,
                "time_seconds": 34.19329214096069,
                "tool_id": "domestication",
                "tool_version": "0.1.0+galaxy1"
            },
            "has_data": true,
            "id": "domestication-0"
        },
        {
            "data": {
                "inputs": {
                    "adv|allow_edits": true,
                    "adv|use_file_names_as_ids": true,
                    "domestication_csv": {
                        "id": "2d30278c16dd9bf8",
                        "src": "hda"
                    },
                    "genbank_files": {
                        "id": "1cc8aca787b2436a",
                        "src": "hdca"
                    },
                    "methylation_protection": true
                },
                "job": {
                    "command_line": "mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&& cp '/tmp/tmpmo0pk3jj/files/8/8/c/dataset_88ce7dbb-b512-47e2-b4c4-a33e25f510f5.dat' 'domestication_csv.csv' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpmo0pk3jj/files/3/e/0/dataset_3e0edcaf-c663-4aaa-833b-4d28d353ff86.dat,/tmp/tmpmo0pk3jj/files/c/b/e/dataset_cbeb8071-98da-4bcd-829a-3eebaaec359e.dat,/tmp/tmpmo0pk3jj/files/1/9/9/dataset_199870d8-d8a6-4437-8843-802fe43f55a3.dat,/tmp/tmpmo0pk3jj/files/5/8/2/dataset_582e346f-d990-4e67-aa16-75c5854a9c4e.dat,/tmp/tmpmo0pk3jj/files/5/a/9/dataset_5a962295-b81c-4eac-95f9-cb9b715227ec.dat,/tmp/tmpmo0pk3jj/files/a/d/6/dataset_ad62bd0c-a6a8-40dc-b75e-5caff07b002f.dat,/tmp/tmpmo0pk3jj/files/2/4/6/dataset_2462927e-bb24-4865-b0d7-233193737d9b.dat' --csv_file 'domestication_csv.csv' --file_name_mapping '/tmp/tmpmo0pk3jj/files/3/e/0/dataset_3e0edcaf-c663-4aaa-833b-4d28d353ff86.dat:p3_2_CAG.gb,/tmp/tmpmo0pk3jj/files/c/b/e/dataset_cbeb8071-98da-4bcd-829a-3eebaaec359e.dat:p7_gfp_sequence.gb,/tmp/tmpmo0pk3jj/files/1/9/9/dataset_199870d8-d8a6-4437-8843-802fe43f55a3.dat:p14_CMVp.gb,/tmp/tmpmo0pk3jj/files/5/8/2/dataset_582e346f-d990-4e67-aa16-75c5854a9c4e.dat:p16_bGHpolyA.gb,/tmp/tmpmo0pk3jj/files/5/a/9/dataset_5a962295-b81c-4eac-95f9-cb9b715227ec.dat:p18_CMVp.gb,/tmp/tmpmo0pk3jj/files/a/d/6/dataset_ad62bd0c-a6a8-40dc-b75e-5caff07b002f.dat:p19_mNeoGreen.gb,/tmp/tmpmo0pk3jj/files/2/4/6/dataset_2462927e-bb24-4865-b0d7-233193737d9b.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/tmpmo0pk3jj/job_working_directory/000/18/outputs/dataset_b8f77694-af17-44c7-8ca7-94039b4f9f10.dat'",
                    "command_version": "",
                    "copied_from_job_id": null,
                    "create_time": "2025-05-27T08:07:43.266253",
                    "dependencies": [
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                            "dependency_type": "conda",
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                            },
                            "dependency_type": "conda",
                            "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ebf0296502565ba7d0f6435a4c3184b56b9905bb762f63578baf4e839a11ad14",
                            "exact": true,
                            "model_class": "MergedCondaDependency",
                            "name": "dna_features_viewer",
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                    ],
                    "exit_code": 0,
                    "external_id": "16351",
                    "galaxy_version": "24.2",
                    "handler": null,
                    "history_id": "722a3e09b8314bb2",
                    "id": "6c90a7736cfec646",
                    "inputs": {
                        "domestication_csv": {
                            "id": "2d30278c16dd9bf8",
                            "src": "hda",
                            "uuid": "88ce7dbb-b512-47e2-b4c4-a33e25f510f5"
                        },
                        "genbank_files1": {
                            "id": "92861e8424eabf5a",
                            "src": "hda",
                            "uuid": "3e0edcaf-c663-4aaa-833b-4d28d353ff86"
                        },
                        "genbank_files2": {
                            "id": "6c90a7736cfec646",
                            "src": "hda",
                            "uuid": "cbeb8071-98da-4bcd-829a-3eebaaec359e"
                        },
                        "genbank_files3": {
                            "id": "d833721564461fe0",
                            "src": "hda",
                            "uuid": "199870d8-d8a6-4437-8843-802fe43f55a3"
                        },
                        "genbank_files4": {
                            "id": "bc67cca121169b32",
                            "src": "hda",
                            "uuid": "582e346f-d990-4e67-aa16-75c5854a9c4e"
                        },
                        "genbank_files5": {
                            "id": "2c119c7d607245b7",
                            "src": "hda",
                            "uuid": "5a962295-b81c-4eac-95f9-cb9b715227ec"
                        },
                        "genbank_files6": {
                            "id": "654b689f382d7faf",
                            "src": "hda",
                            "uuid": "ad62bd0c-a6a8-40dc-b75e-5caff07b002f"
                        },
                        "genbank_files7": {
                            "id": "848a7ec9db54f91c",
                            "src": "hda",
                            "uuid": "2462927e-bb24-4865-b0d7-233193737d9b"
                        }
                    },
                    "job_messages": [],
                    "job_metrics": [],
                    "job_runner_name": null,
                    "job_stderr": "",
                    "job_stdout": "",
                    "model_class": "Job",
                    "output_collections": {
                        "methprot_gb": {
                            "id": "8026227525c5f951",
                            "src": "hdca"
                        }
                    },
                    "outputs": {
                        "__new_primary_file_methprot_gb|p14_CMVp__": {
                            "id": "552487cd77e5739b",
                            "src": "hda",
                            "uuid": "47a78a3c-f714-4a3b-baf6-db74ec3e57ec"
                        },
                        "__new_primary_file_methprot_gb|p16_bGHpolyA__": {
                            "id": "c150df1632d3bf7a",
                            "src": "hda",
                            "uuid": "9ec7ff7e-c752-40ab-8e30-d00bce534323"
                        },
                        "__new_primary_file_methprot_gb|p18_CMVp__": {
                            "id": "3b8df2fa2b4da081",
                            "src": "hda",
                            "uuid": "ef3876f0-595c-4e36-b1d2-424ac4f3c495"
                        },
                        "__new_primary_file_methprot_gb|p19_mNeoGreen__": {
                            "id": "ea8abe36fc9e84c6",
                            "src": "hda",
                            "uuid": "d9db4707-d9a0-4578-861a-4536b24e3d55"
                        },
                        "__new_primary_file_methprot_gb|p22_PGKpolyA__": {
                            "id": "195917444a0d1fd3",
                            "src": "hda",
                            "uuid": "ebcddc78-8aec-4aa7-a99f-1f6c98312abf"
                        },
                        "__new_primary_file_methprot_gb|p3_2_CAG__": {
                            "id": "07090fd15ab7700f",
                            "src": "hda",
                            "uuid": "f565adba-00b9-4476-a1dc-f917d7695ed7"
                        },
                        "__new_primary_file_methprot_gb|p7_gfp_sequence__": {
                            "id": "181ca79c6e3f2d04",
                            "src": "hda",
                            "uuid": "d36b2983-c229-453a-b3c5-d6e44ab877f5"
                        },
                        "domesticated_zip": {
                            "id": "bbfdb6491da014b1",
                            "src": "hda",
                            "uuid": "b8f77694-af17-44c7-8ca7-94039b4f9f10"
                        }
                    },
                    "params": {
                        "__input_ext": "\"input\"",
                        "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}",
                        "chromInfo": "\"/tmp/tmpmo0pk3jj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
                        "dbkey": "\"?\"",
                        "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}",
                        "methylation_protection": "true"
                    },
                    "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",
                    "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_stdout": "Part names were not truncated\n",
                    "update_time": "2025-05-27T08:07:54.372698",
                    "user_email": "planemo@galaxyproject.org",
                    "user_id": "40971d80b8a8a53c"
                },
                "status": "success",
                "test_index": 1,
                "time_seconds": 34.02547550201416,
                "tool_id": "domestication",
                "tool_version": "0.1.0+galaxy1"
            },
            "has_data": true,
            "id": "domestication-1"
        }
    ],
    "version": "0.1"
}