Mercurial > repos > tduigou > domestication
diff output.json @ 0:8fd9af4cb080 draft
planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Mon, 12 May 2025 10:21:24 +0000 |
| parents | |
| children | bf8cd9487e33 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output.json Mon May 12 10:21:24 2025 +0000 @@ -0,0 +1,530 @@ +{ + "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": "aaa883914c50d913", + "src": "hda" + }, + "genbank_files": [ + { + "id": "f16125b2a7e364b6", + "src": "hda" + }, + { + "id": "723c01d174904c31", + "src": "hda" + }, + { + "id": "6f9854c84e6fb32c", + "src": "hda" + }, + { + "id": "ac6038717ee9c106", + "src": "hda" + }, + { + "id": "1b3b4b31ea959cca", + "src": "hda" + }, + { + "id": "7144c3d02f40c0d6", + "src": "hda" + }, + { + "id": "9d14f67ce73d06b8", + "src": "hda" + } + ], + "methylation_protection": false + }, + "job": { + "command_line": "mkdir 'outdir_gb' && mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpbjg5_060/files/1/7/7/dataset_1773336e-37c8-467a-932e-47c5d4bc7247.dat,/tmp/tmpbjg5_060/files/e/e/4/dataset_ee4defe5-2762-48fb-b10b-350bfbb4b71d.dat,/tmp/tmpbjg5_060/files/4/0/4/dataset_4041b0a0-86b9-4a81-9e95-77031b1fb96f.dat,/tmp/tmpbjg5_060/files/f/a/8/dataset_fa8e14e1-6c87-4a13-801f-ecb72b5e9517.dat,/tmp/tmpbjg5_060/files/0/7/b/dataset_07b8841b-22ef-4142-8931-7ae4111f1887.dat,/tmp/tmpbjg5_060/files/a/6/5/dataset_a653f705-9192-485d-94f3-22b66714c9fb.dat,/tmp/tmpbjg5_060/files/1/e/a/dataset_1ea79cfa-b478-4c9b-b906-9b08526c85f4.dat' --csv_file '/tmp/tmpbjg5_060/files/8/d/0/dataset_8d08fc90-ab45-4d65-8912-1edef99b50e5.dat' --file_name_mapping '/tmp/tmpbjg5_060/files/1/7/7/dataset_1773336e-37c8-467a-932e-47c5d4bc7247.dat:p3_2_CAG.gb,/tmp/tmpbjg5_060/files/e/e/4/dataset_ee4defe5-2762-48fb-b10b-350bfbb4b71d.dat:p7_gfp_sequence.gb,/tmp/tmpbjg5_060/files/4/0/4/dataset_4041b0a0-86b9-4a81-9e95-77031b1fb96f.dat:p14_CMVp.gb,/tmp/tmpbjg5_060/files/f/a/8/dataset_fa8e14e1-6c87-4a13-801f-ecb72b5e9517.dat:p16_bGHpolyA.gb,/tmp/tmpbjg5_060/files/0/7/b/dataset_07b8841b-22ef-4142-8931-7ae4111f1887.dat:p18_CMVp.gb,/tmp/tmpbjg5_060/files/a/6/5/dataset_a653f705-9192-485d-94f3-22b66714c9fb.dat:p19_mNeoGreen.gb,/tmp/tmpbjg5_060/files/1/e/a/dataset_1ea79cfa-b478-4c9b-b906-9b08526c85f4.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/tmpbjg5_060/job_working_directory/000/9/outputs/dataset_3bd2c885-c568-4c63-8f50-4d3f470c77a5.dat'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-05-12T10:19:22.845477", + "dependencies": [], + "exit_code": 0, + "external_id": "151742", + "galaxy_version": "24.2", + "handler": null, + "history_id": "f16125b2a7e364b6", + "id": "711290ccc3448dbe", + "inputs": { + "domestication_csv": { + "id": "aaa883914c50d913", + "src": "hda", + "uuid": "8d08fc90-ab45-4d65-8912-1edef99b50e5" + }, + "genbank_files": { + "id": "f16125b2a7e364b6", + "src": "hda", + "uuid": "1773336e-37c8-467a-932e-47c5d4bc7247" + }, + "genbank_files1": { + "id": "f16125b2a7e364b6", + "src": "hda", + "uuid": "1773336e-37c8-467a-932e-47c5d4bc7247" + }, + "genbank_files2": { + "id": "723c01d174904c31", + "src": "hda", + "uuid": "ee4defe5-2762-48fb-b10b-350bfbb4b71d" + }, + "genbank_files3": { + "id": "6f9854c84e6fb32c", + "src": "hda", + "uuid": "4041b0a0-86b9-4a81-9e95-77031b1fb96f" + }, + "genbank_files4": { + "id": "ac6038717ee9c106", + "src": "hda", + "uuid": "fa8e14e1-6c87-4a13-801f-ecb72b5e9517" + }, + "genbank_files5": { + "id": "1b3b4b31ea959cca", + "src": "hda", + "uuid": "07b8841b-22ef-4142-8931-7ae4111f1887" + }, + "genbank_files6": { + "id": "7144c3d02f40c0d6", + "src": "hda", + "uuid": "a653f705-9192-485d-94f3-22b66714c9fb" + }, + "genbank_files7": { + "id": "9d14f67ce73d06b8", + "src": "hda", + "uuid": "1ea79cfa-b478-4c9b-b906-9b08526c85f4" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_zip": { + "id": "711290ccc3448dbe", + "src": "hda", + "uuid": "3bd2c885-c568-4c63-8f50-4d3f470c77a5" + } + }, + "params": { + "__input_ext": "\"input\"", + "adv": "{\"allow_edits\": true, \"use_file_names_as_ids\": true}", + "chromInfo": "\"/tmp/tmpbjg5_060/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "dbkey": "\"?\"", + "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, 1.57it/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, 1.57it/s, now=None]\r \r", + "tool_stdout": "Part names were not truncated\n", + "update_time": "2025-05-12T10:19:34.231647", + "user_email": "planemo@galaxyproject.org", + "user_id": "f16125b2a7e364b6" + }, + "status": "success", + "test_index": 0, + "time_seconds": 34.99027061462402, + "tool_id": "domestication", + "tool_version": "0.1.0+galaxy0" + }, + "has_data": true, + "id": "domestication-0" + }, + { + "data": { + "inputs": { + "adv|allow_edits": true, + "adv|use_file_names_as_ids": true, + "domestication_csv": { + "id": "0712ecd128ea57d7", + "src": "hda" + }, + "genbank_files": [ + { + "id": "4e411fc6241b00c0", + "src": "hda" + }, + { + "id": "53c1d5da63e22734", + "src": "hda" + }, + { + "id": "918757d2d9059ecb", + "src": "hda" + }, + { + "id": "3d0b1ede0f9f407d", + "src": "hda" + }, + { + "id": "d67f207c70f90bba", + "src": "hda" + }, + { + "id": "5c88b35f288963f6", + "src": "hda" + }, + { + "id": "3e3b5a8a813595d7", + "src": "hda" + } + ], + "methylation_protection": true + }, + "job": { + "command_line": "mkdir 'outdir_gb' && mkdir 'outdir_zip' && python '/home/rkhaled/galaxytools/tools/domestication/domestication.py' --files_to_domestication '/tmp/tmpbjg5_060/files/b/f/f/dataset_bff36fb4-2ddc-497c-a812-b821fcafcaf6.dat,/tmp/tmpbjg5_060/files/c/9/4/dataset_c94619a2-c571-4719-8d77-fe8e5566092f.dat,/tmp/tmpbjg5_060/files/a/8/e/dataset_a8edcb78-9ec5-45f1-b05f-17b619e372a7.dat,/tmp/tmpbjg5_060/files/b/c/6/dataset_bc62ddd0-de10-42c4-9aa4-c62010af835d.dat,/tmp/tmpbjg5_060/files/5/5/a/dataset_55aa74b8-36ca-474d-ac73-bda39d9e5e01.dat,/tmp/tmpbjg5_060/files/7/0/9/dataset_7098d987-4200-4111-9508-bbe109fec271.dat,/tmp/tmpbjg5_060/files/7/8/1/dataset_781da4ba-2cb5-4cc3-aebb-e066475dfaef.dat' --csv_file '/tmp/tmpbjg5_060/files/6/2/b/dataset_62b232e6-6915-467a-9e55-febd6b17d9d7.dat' --file_name_mapping '/tmp/tmpbjg5_060/files/b/f/f/dataset_bff36fb4-2ddc-497c-a812-b821fcafcaf6.dat:p3_2_CAG.gb,/tmp/tmpbjg5_060/files/c/9/4/dataset_c94619a2-c571-4719-8d77-fe8e5566092f.dat:p7_gfp_sequence.gb,/tmp/tmpbjg5_060/files/a/8/e/dataset_a8edcb78-9ec5-45f1-b05f-17b619e372a7.dat:p14_CMVp.gb,/tmp/tmpbjg5_060/files/b/c/6/dataset_bc62ddd0-de10-42c4-9aa4-c62010af835d.dat:p16_bGHpolyA.gb,/tmp/tmpbjg5_060/files/5/5/a/dataset_55aa74b8-36ca-474d-ac73-bda39d9e5e01.dat:p18_CMVp.gb,/tmp/tmpbjg5_060/files/7/0/9/dataset_7098d987-4200-4111-9508-bbe109fec271.dat:p19_mNeoGreen.gb,/tmp/tmpbjg5_060/files/7/8/1/dataset_781da4ba-2cb5-4cc3-aebb-e066475dfaef.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/tmpbjg5_060/job_working_directory/000/18/outputs/dataset_8986a1c0-102c-469b-b20d-012bfab02e3a.dat'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-05-12T10:19:57.856904", + "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-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", + "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-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", + "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-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", + "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-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "genedom", + "version": "0.2.1" + }, + { + "cacheable": false, + "dependency_resolver": { + "auto_init": true, + 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"versionless": false + }, + "dependency_type": "conda", + "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-bdd4a85f8bf182a44b33909cd353bfe9976ca4f7cd7e03cfde43ddec0191410c", + "exact": true, + "model_class": "MergedCondaDependency", + "name": "dna_features_viewer", + "version": "3.1.4" + } + ], + "exit_code": 0, + "external_id": "152624", + "galaxy_version": "24.2", + "handler": null, + "history_id": "723c01d174904c31", + "id": "297141c205679f60", + "inputs": { + "domestication_csv": { + "id": "0712ecd128ea57d7", + "src": "hda", + "uuid": "62b232e6-6915-467a-9e55-febd6b17d9d7" + }, + "genbank_files": { + "id": "4e411fc6241b00c0", + "src": "hda", + "uuid": "bff36fb4-2ddc-497c-a812-b821fcafcaf6" + }, + "genbank_files1": { + "id": "4e411fc6241b00c0", + "src": "hda", + "uuid": "bff36fb4-2ddc-497c-a812-b821fcafcaf6" + }, + "genbank_files2": { + "id": "53c1d5da63e22734", + "src": "hda", + "uuid": "c94619a2-c571-4719-8d77-fe8e5566092f" + }, + "genbank_files3": { + "id": 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