Mercurial > repos > tduigou > parameters_maystro
diff output.json @ 1:34135dac85b0 draft default tip
planemo upload for repository https://github.com/brsynth commit d8cc8b87fdb0374745b5420f2da7f08ae905c222-dirty
| author | tduigou |
|---|---|
| date | Wed, 16 Jul 2025 14:28:21 +0000 |
| parents | 1a766d8d3883 |
| children |
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--- a/output.json Fri Jul 11 10:10:16 2025 +0000 +++ b/output.json Wed Jul 16 14:28:21 2025 +0000 @@ -9,45 +9,104 @@ { "data": { "inputs": { - "distribute_json": false, - "json_from_workflow": [ - { - "id": "051ed7ff50845d8c", - "src": "hda" - }, - { - "id": "25656ddfec77a3b3", - "src": "hda" - } - ] + "annotation_column": "annotation", + "avoid_patterns": "BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer", + "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", + "execution": true, + "fragment_column": "fragment", + "gc_constraints": "mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100", + "hairpin_constraints": "stem_size=20, hairpin_window=200", + "kmer_size": "15", + "sequence_column": "sequence", + "table_name": "sample" }, "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/parameters_maystro/maystro.py' --distribute_json 'false' --json_from_workflow \"/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat\" \"/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat\" --json_from_user 'None' --json_name_mapping /tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat:seq_from_db_param.json,/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat:seq_to_db_param.json --output_workflow '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_d100f4ee-f845-4a68-be68-004c7af9679d.dat' --output_user '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat' && echo 'DEBUB' && cat '/tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat'", + "command_line": "python3 -c \"import json; params = { 'avoid_patterns': 'BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer', 'hairpin_constraints': 'stem_size=20, hairpin_window=200', 'gc_constraints': 'mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100', 'kmer_size': '15', 'execution': 'true', 'db_uri': 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db', 'table': 'sample', 'fragment_column': 'fragment', 'sequence_column': 'sequence', 'annotation_column': 'annotation' }; f = open('/tmp/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat' && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/1/outputs/dataset_ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-07-11T09:42:39.854743", + "create_time": "2025-07-16T14:25:13.835798", "dependencies": [], "exit_code": 0, - "external_id": "79277", + "external_id": "153937", "galaxy_version": "25.0", "handler": null, - "history_id": "051ed7ff50845d8c", - "id": "d66447d427a79ce4", - "inputs": { - "json_from_workflow": { - "id": "051ed7ff50845d8c", + "history_id": "479ca6463d0132e0", + "id": "479ca6463d0132e0", + "inputs": {}, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_json": { + "id": "479ca6463d0132e0", "src": "hda", - "uuid": "2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6" - }, - "json_from_workflow1": { - "id": "051ed7ff50845d8c", + "uuid": "ba54b8e6-58da-4f46-ab17-8f0c4d46bb3c" + } + }, + "params": { + "__input_ext": "\"input\"", + "annotation_column": "\"annotation\"", + "avoid_patterns": "\"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\"", + "chromInfo": "\"/tmp/tmpojrs64js/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", + "dbkey": "\"?\"", + "execution": "true", + "fragment_column": "\"fragment\"", + "gc_constraints": "\"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\"", + "hairpin_constraints": "\"stem_size=20, hairpin_window=200\"", + "kmer_size": "\"15\"", + "sequence_column": "\"sequence\"", + "table_name": "\"sample\"", + "user_json": null + }, + "state": "ok", + "stderr": "", + "stdout": "DEBG\n{\n \"avoid_patterns\": \"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}DEBG\n{\n \"avoid_patterns\": \"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}", + "tool_id": "parameters_maystro", + "tool_stderr": "", + "tool_stdout": "DEBG\n{\n \"avoid_patterns\": \"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}DEBG\n{\n \"avoid_patterns\": \"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}", + "update_time": "2025-07-16T14:25:27.820187", + "user_email": "planemo@galaxyproject.org", + "user_id": "479ca6463d0132e0" + }, + "status": "success", + "test_index": 0, + "time_seconds": 14.118565320968628, + "tool_id": "parameters_maystro", + "tool_version": "1.1.0+galaxy3" + }, + "has_data": true, + "id": "parameters_maystro-0" + }, + { + "data": { + "inputs": { + "user_json": { + "id": "0311cb8bec9eec65", + "src": "hda" + } + }, + "job": { + "command_line": "cp '/tmp/tmpojrs64js/files/a/6/4/dataset_a64b8b4b-290b-4b2e-bf77-d0d4ebc35137.dat' '/tmp/tmpojrs64js/job_working_directory/000/3/outputs/dataset_0dedeb7c-7969-452f-a162-25e70662b775.dat' && echo DEBG && cat '/tmp/tmpojrs64js/job_working_directory/000/3/outputs/dataset_0dedeb7c-7969-452f-a162-25e70662b775.dat'", + "command_version": "", + "copied_from_job_id": null, + "create_time": "2025-07-16T14:25:36.982208", + "dependencies": [], + "exit_code": 0, + "external_id": "154115", + "galaxy_version": "25.0", + "handler": null, + "history_id": "0311cb8bec9eec65", + "id": "da029efde06939a6", + "inputs": { + "user_json": { + "id": "0311cb8bec9eec65", "src": "hda", - "uuid": "2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6" - }, - "json_from_workflow2": { - "id": "25656ddfec77a3b3", - "src": "hda", - "uuid": "960eac8e-fb66-4982-8009-4896c9e57b38" + "uuid": "a64b8b4b-290b-4b2e-bf77-d0d4ebc35137" } }, "job_messages": [], @@ -58,136 +117,42 @@ "model_class": "Job", "output_collections": {}, "outputs": { - "output_user": { - "id": "39496c7f8d685f43", + "output_json": { + "id": "da029efde06939a6", "src": "hda", - "uuid": "1e2a9024-ad29-4d18-b95d-645817393383" - }, - "output_workflow": { - "id": "d66447d427a79ce4", - "src": "hda", - "uuid": "d100f4ee-f845-4a68-be68-004c7af9679d" + "uuid": "0dedeb7c-7969-452f-a162-25e70662b775" } }, "params": { "__input_ext": "\"input\"", - "chromInfo": "\"/tmp/tmpfpd6tei1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "annotation_column": null, + "avoid_patterns": null, + "chromInfo": "\"/tmp/tmpojrs64js/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": null, "dbkey": "\"?\"", - "distribute_json": "false", - "json_from_user": null + "execution": "false", + "fragment_column": null, + "gc_constraints": null, + "hairpin_constraints": null, + "kmer_size": "\"\"", + "sequence_column": null, + "table_name": null }, "state": "ok", "stderr": "", - "stdout": "[INFO] Watching temp dir for new JSONs: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\n[INFO] Initial JSONs from workflow: ['/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat', '/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat']\n[INFO] Added data under key: seq_from_db_param\n[INFO] Added data under key: seq_to_db_param\n[INFO] Merged JSON written to: /tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat\n[INFO] Cleaning up: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\nDEBUB\n{\n \"seq_from_db_param\": {\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n },\n \"seq_to_db_param\": {\n \"execution\": true,\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n }\n}", + "stdout": "DEBG\n{\n \"avoid_patterns\": \"BsaI_site\\nBsmBI_site\\nBbsI_site\\nSapI_site\\n8x1mer\\n5x3mer\\n9x2mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100\\nmini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}\n", "tool_id": "parameters_maystro", "tool_stderr": "", - "tool_stdout": "[INFO] Watching temp dir for new JSONs: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\n[INFO] Initial JSONs from workflow: ['/tmp/tmpfpd6tei1/files/2/f/4/dataset_2f4ca6ae-77d6-4bfe-8e39-0051c294e4f6.dat', '/tmp/tmpfpd6tei1/files/9/6/0/dataset_960eac8e-fb66-4982-8009-4896c9e57b38.dat']\n[INFO] Added data under key: seq_from_db_param\n[INFO] Added data under key: seq_to_db_param\n[INFO] Merged JSON written to: /tmp/tmpfpd6tei1/job_working_directory/000/3/outputs/dataset_1e2a9024-ad29-4d18-b95d-645817393383.dat\n[INFO] Cleaning up: /tmp/tmpfpd6tei1/tmp/maystro_merge_xd06s1et\nDEBUB\n{\n \"seq_from_db_param\": {\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n },\n \"seq_to_db_param\": {\n \"execution\": true,\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n }\n}", - "update_time": "2025-07-11T09:42:45.494563", + "tool_stdout": "DEBG\n{\n \"avoid_patterns\": \"BsaI_site\\nBsmBI_site\\nBbsI_site\\nSapI_site\\n8x1mer\\n5x3mer\\n9x2mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\",\n \"gc_constraints\": \"mini=0.3, maxi=0.7, window=100\\nmini=0.1, maxi=0.9, window=100\",\n \"kmer_size\": \"15\",\n \"execution\": \"true\",\n \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\",\n \"table\": \"sample\",\n \"fragment_column\": \"fragment\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\"\n}\n", + "update_time": "2025-07-16T14:25:42.101497", "user_email": "planemo@galaxyproject.org", - "user_id": "051ed7ff50845d8c" - }, - "status": "success", - "test_index": 0, - "time_seconds": 16.301273107528687, - "tool_id": "parameters_maystro", - "tool_version": "0.1.0+galaxy1" - }, - "has_data": true, - "id": "parameters_maystro-0" - }, - { - "data": { - "inputs": { - "distribute_json": true, - "json_from_user": { - "id": "10ea9be91661a5fd", - "src": "hda" - }, - "json_from_workflow": [ - { - "id": "b7e19a053756efb9", - "src": "hda" - }, - { - "id": "45e8a4dfb17d83f9", - "src": "hda" - } - ] - }, - "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/parameters_maystro/maystro.py' --distribute_json 'true' --json_from_workflow \"/tmp/tmpfpd6tei1/files/c/1/e/dataset_c1e98b32-965c-4a0d-9c7f-26973a7e0fe6.dat\" \"/tmp/tmpfpd6tei1/files/3/a/5/dataset_3a560c20-0d3f-4aae-abd4-4a460698f28f.dat\" --json_from_user '/tmp/tmpfpd6tei1/files/0/a/b/dataset_0abf65a6-bd5b-47fc-94ba-a6a97fa6d88b.dat' --json_name_mapping /tmp/tmpfpd6tei1/files/c/1/e/dataset_c1e98b32-965c-4a0d-9c7f-26973a7e0fe6.dat:seq_from_db_param.json,/tmp/tmpfpd6tei1/files/3/a/5/dataset_3a560c20-0d3f-4aae-abd4-4a460698f28f.dat:seq_to_db_param.json --output_workflow '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_5254084b-4d71-4098-b933-f73a9e7d5a28.dat' --output_user '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_04c60445-2ff4-4b59-bcbc-75f08b68625a.dat' && echo 'DEBUB' && cat '/tmp/tmpfpd6tei1/job_working_directory/000/7/outputs/dataset_04c60445-2ff4-4b59-bcbc-75f08b68625a.dat'", - "command_version": "", - "copied_from_job_id": null, - "create_time": "2025-07-11T09:42:56.883885", - "dependencies": [], - "exit_code": 0, - "external_id": "79598", - "galaxy_version": "25.0", - "handler": null, - "history_id": "25656ddfec77a3b3", - "id": "10ea9be91661a5fd", - "inputs": { - "json_from_user": { - "id": "10ea9be91661a5fd", - "src": "hda", - "uuid": "0abf65a6-bd5b-47fc-94ba-a6a97fa6d88b" - }, - "json_from_workflow": { - "id": "b7e19a053756efb9", - "src": "hda", - "uuid": "c1e98b32-965c-4a0d-9c7f-26973a7e0fe6" - }, - "json_from_workflow1": { - "id": "b7e19a053756efb9", - "src": "hda", - "uuid": "c1e98b32-965c-4a0d-9c7f-26973a7e0fe6" - }, - "json_from_workflow2": { - "id": "45e8a4dfb17d83f9", - "src": "hda", - "uuid": "3a560c20-0d3f-4aae-abd4-4a460698f28f" - } - }, - "job_messages": [], - "job_metrics": [], - "job_runner_name": null, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_collections": {}, - "outputs": { - "output_user": { - "id": "295d652904818249", - "src": "hda", - "uuid": "04c60445-2ff4-4b59-bcbc-75f08b68625a" - }, - "output_workflow": { - "id": "8c61ed432685cfe0", - "src": "hda", - "uuid": "5254084b-4d71-4098-b933-f73a9e7d5a28" - } - }, - "params": { - "__input_ext": "\"input\"", - "chromInfo": "\"/tmp/tmpfpd6tei1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "dbkey": "\"?\"", - "distribute_json": "true" - }, - "state": "ok", - "stderr": "", - "stdout": "DEBUB\n", - "tool_id": "parameters_maystro", - "tool_stderr": "", - "tool_stdout": "DEBUB\n", - "update_time": "2025-07-11T09:43:02.149865", - "user_email": "planemo@galaxyproject.org", - "user_id": "051ed7ff50845d8c" + "user_id": "479ca6463d0132e0" }, "status": "success", "test_index": 1, - "time_seconds": 16.54760479927063, + "time_seconds": 14.252628803253174, "tool_id": "parameters_maystro", - "tool_version": "0.1.0+galaxy1" + "tool_version": "1.1.0+galaxy3" }, "has_data": true, "id": "parameters_maystro-1"