Mercurial > repos > tduigou > parameters_maystro_workflow_0
diff output.json @ 1:6b3f7ebe4ddf draft default tip
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
| author | tduigou |
|---|---|
| date | Thu, 31 Jul 2025 08:57:56 +0000 |
| parents | 95f33fc513ad |
| children |
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--- a/output.json Thu Jul 17 14:01:09 2025 +0000 +++ b/output.json Thu Jul 31 08:57:56 2025 +0000 @@ -9,34 +9,32 @@ { "data": { "inputs": { - "DB|annotation_column": "annotation", - "DB|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", - "DB|execution": true, - "DB|fragment_column": "fragment", - "DB|sequence_column": "sequence", - "DB|table_name": "sample", - "DnaOptimizationProblemClass": "DnaOptimizationProblem", + "annotation_column": "annotation", "assembly_plan_name": "Type2sRestrictionAssembly", - "avoid_patterns": "BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer", + "avoid_patterns": "BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer", + "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", "enzyme": "auto", + "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", - "methylation_protection": true, + "sequence_column": "sequence", + "table_name": "sample", "topology": "circular" }, "job": { - "command_line": "python3 -c \"import json; params = { 'DnaOptimizationProblemClass': 'DnaOptimizationProblem', 'methylation_protection': 'true', 'allow_edits': 'true', 'avoid_patterns': 'BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer', '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', 'assembly_plan_name': 'Type2sRestrictionAssembly', 'topology': 'circular', 'enzyme': 'auto', '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/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.dat' && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/1/outputs/dataset_53ffa695-5fab-48b3-b5f5-ff93f77bfc10.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', 'assembly_plan_name': 'Type2sRestrictionAssembly', 'topology': 'circular', 'enzyme': 'auto', '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/tmpt0l5fyog/job_working_directory/000/1/outputs/dataset_1bfb5292-6b8f-4b66-9d74-cedaf9200451.dat', 'w'); json.dump(params, f, indent=4); f.close()\" && echo DEBG && cat '/tmp/tmpt0l5fyog/job_working_directory/000/1/outputs/dataset_1bfb5292-6b8f-4b66-9d74-cedaf9200451.dat' && echo DEBG && cat '/tmp/tmpt0l5fyog/job_working_directory/000/1/outputs/dataset_1bfb5292-6b8f-4b66-9d74-cedaf9200451.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-07-17T12:08:28.832103", + "create_time": "2025-07-31T08:57:00.548068", "dependencies": [], "exit_code": 0, - "external_id": "135810", + "external_id": "205407", "galaxy_version": "25.0", "handler": null, - "history_id": "d952758136b0c83c", - "id": "d952758136b0c83c", + "history_id": "57c9e3825b6e5989", + "id": "57c9e3825b6e5989", "inputs": {}, "job_messages": [], "job_metrics": [], @@ -47,71 +45,74 @@ "output_collections": {}, "outputs": { "output_json": { - "id": "d952758136b0c83c", + "id": "57c9e3825b6e5989", "src": "hda", - "uuid": "53ffa695-5fab-48b3-b5f5-ff93f77bfc10" + "uuid": "1bfb5292-6b8f-4b66-9d74-cedaf9200451" } }, "params": { - "DB": "{\"annotation_column\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"execution\": true, \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table_name\": \"sample\", \"user_json\": null}", - "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"", "__input_ext": "\"input\"", - "allow_edits": "true", + "annotation_column": "\"annotation\"", "assembly_plan_name": "\"Type2sRestrictionAssembly\"", - "avoid_patterns": "\"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\"", - "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "avoid_patterns": "\"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\"", + "chromInfo": "\"/tmp/tmpt0l5fyog/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", "dbkey": "\"?\"", "enzyme": "\"auto\"", + "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\"", - "methylation_protection": "true", - "topology": "\"circular\"" + "sequence_column": "\"sequence\"", + "table_name": "\"sample\"", + "topology": "\"circular\"", + "user_json": null }, "state": "ok", "stderr": "", - "stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\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 \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\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 \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\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 \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\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_workflow_2", + "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 \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\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 \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\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_workflow_1", "tool_stderr": "", - "tool_stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\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 \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\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 \"DnaOptimizationProblemClass\": \"DnaOptimizationProblem\",\n \"methylation_protection\": \"true\",\n \"allow_edits\": \"true\",\n \"avoid_patterns\": \"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\",\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 \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\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": "2025-07-17T12:08:33.771569", + "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 \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\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 \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\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": "2025-07-31T08:57:06.352395", "user_email": "planemo@galaxyproject.org", - "user_id": "d952758136b0c83c" + "user_id": "57c9e3825b6e5989" }, "status": "success", "test_index": 0, - "time_seconds": 5.093859434127808, - "tool_id": "parameters_maystro_workflow_2", + "time_seconds": 6.245003700256348, + "tool_id": "parameters_maystro_workflow_1", "tool_version": "0.1.0" }, "has_data": true, - "id": "parameters_maystro_workflow_2-0" + "id": "parameters_maystro_workflow_1-0" }, { "data": { "inputs": { - "DB|user_json": { - "id": "b08444d846605ee4", + "user_json": { + "id": "b8cd89e8131d3fe7", "src": "hda" } }, "job": { - "command_line": "cp '/tmp/tmpnxavcgf5/files/b/b/d/dataset_bbd9a440-a787-439e-9b36-2c1c45dae0a3.dat' '/tmp/tmpnxavcgf5/job_working_directory/000/3/outputs/dataset_6eed7c7c-77ce-4d77-b2ef-0a367df7e250.dat' && echo DEBG && cat '/tmp/tmpnxavcgf5/job_working_directory/000/3/outputs/dataset_6eed7c7c-77ce-4d77-b2ef-0a367df7e250.dat'", + "command_line": "cp '/tmp/tmpt0l5fyog/files/d/7/9/dataset_d79830ca-f30e-4f82-8b67-150bf816c265.dat' '/tmp/tmpt0l5fyog/job_working_directory/000/3/outputs/dataset_cd60237f-3d8d-4a7e-ac4c-b10728db646e.dat' && echo DEBG && cat '/tmp/tmpt0l5fyog/job_working_directory/000/3/outputs/dataset_cd60237f-3d8d-4a7e-ac4c-b10728db646e.dat'", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-07-17T12:08:43.857384", + "create_time": "2025-07-31T08:57:16.707828", "dependencies": [], "exit_code": 0, - "external_id": "135995", + "external_id": "205636", "galaxy_version": "25.0", "handler": null, - "history_id": "b08444d846605ee4", - "id": "e67c2cbedbcb0da1", + "history_id": "b8cd89e8131d3fe7", + "id": "abe44dd8383948e0", "inputs": { - "DB|user_json": { - "id": "b08444d846605ee4", + "user_json": { + "id": "b8cd89e8131d3fe7", "src": "hda", - "uuid": "bbd9a440-a787-439e-9b36-2c1c45dae0a3" + "uuid": "d79830ca-f30e-4f82-8b67-150bf816c265" } }, "job_messages": [], @@ -123,45 +124,47 @@ "output_collections": {}, "outputs": { "output_json": { - "id": "e67c2cbedbcb0da1", + "id": "abe44dd8383948e0", "src": "hda", - "uuid": "6eed7c7c-77ce-4d77-b2ef-0a367df7e250" + "uuid": "cd60237f-3d8d-4a7e-ac4c-b10728db646e" } }, "params": { - "DB": "{\"annotation_column\": null, \"db_uri\": null, \"execution\": false, \"fragment_column\": null, \"sequence_column\": null, \"table_name\": null, \"user_json\": {\"values\": [{\"id\": 2, \"src\": \"hda\"}]}}", - "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"", "__input_ext": "\"input\"", - "allow_edits": "true", + "annotation_column": null, "assembly_plan_name": "\"Type2sRestrictionAssembly\"", "avoid_patterns": null, - "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "chromInfo": "\"/tmp/tmpt0l5fyog/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "db_uri": null, "dbkey": "\"?\"", "enzyme": "\"auto\"", + "execution": "false", + "fragment_column": null, "gc_constraints": null, "hairpin_constraints": null, "kmer_size": "\"\"", - "methylation_protection": "false", + "sequence_column": null, + "table_name": null, "topology": "\"circular\"" }, "state": "ok", "stderr": "", - "stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\":\"DnaOptimizationProblem\",\n \"avoid_patterns\": \"BsaI_site\\nNotI_site\\nXbaI_site\\nClaI_site\\n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\\nstem_size=10, hairpin_window=100\",\n \"gc_constraints\": \"mini=0.1, maxi=0.9\\nmini-0.3, maxi=0.7, window=50\",\n \"kmer_size\": \"15\",\n \"methylation_protection\":\"methylation_protection\",\n \"allow_edits\":\"True\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\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_workflow_2", + "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=0.1, maxi=0.9,, window=100\\nmini=0.3, maxi=0.7, 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 \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\"\n}\n", + "tool_id": "parameters_maystro_workflow_1", "tool_stderr": "", - "tool_stdout": "DEBG\n{\n \"DnaOptimizationProblemClass\":\"DnaOptimizationProblem\",\n \"avoid_patterns\": \"BsaI_site\\nNotI_site\\nXbaI_site\\nClaI_site\\n8x1mer\",\n \"hairpin_constraints\": \"stem_size=20, hairpin_window=200\\nstem_size=10, hairpin_window=100\",\n \"gc_constraints\": \"mini=0.1, maxi=0.9\\nmini-0.3, maxi=0.7, window=50\",\n \"kmer_size\": \"15\",\n \"methylation_protection\":\"methylation_protection\",\n \"allow_edits\":\"True\",\n \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\",\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": "2025-07-17T12:08:49.096516", + "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=0.1, maxi=0.9,, window=100\\nmini=0.3, maxi=0.7, 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 \"assembly_plan_name\": \"Type2sRestrictionAssembly\",\n \"topology\": \"circular\",\n \"enzyme\": \"auto\"\n}\n", + "update_time": "2025-07-31T08:57:22.628561", "user_email": "planemo@galaxyproject.org", - "user_id": "d952758136b0c83c" + "user_id": "57c9e3825b6e5989" }, "status": "success", "test_index": 1, - "time_seconds": 15.298557996749878, - "tool_id": "parameters_maystro_workflow_2", + "time_seconds": 15.919075965881348, + "tool_id": "parameters_maystro_workflow_1", "tool_version": "0.1.0" }, "has_data": true, - "id": "parameters_maystro_workflow_2-1" + "id": "parameters_maystro_workflow_1-1" } ], "version": "0.1"