Mercurial > repos > tduigou > parameters_maystro_workflow_0
diff output.json @ 0:9ab8b3673816 draft default tip
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
| author | tduigou |
|---|---|
| date | Wed, 23 Jul 2025 09:39:39 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output.json Wed Jul 23 09:39:39 2025 +0000 @@ -0,0 +1,168 @@ +{ + "summary": { + "num_errors": 0, + "num_failures": 0, + "num_skips": 0, + "num_tests": 2 + }, + "tests": [ + { + "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", + "assembly_plan_name": "Type2sRestrictionAssembly", + "avoid_patterns": "BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer", + "enzyme": "auto", + "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" + }, + "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_version": "", + "copied_from_job_id": null, + "create_time": "2025-07-17T12:08:28.832103", + "dependencies": [], + "exit_code": 0, + "external_id": "135810", + "galaxy_version": "25.0", + "handler": null, + "history_id": "d952758136b0c83c", + "id": "d952758136b0c83c", + "inputs": {}, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_json": { + "id": "d952758136b0c83c", + "src": "hda", + "uuid": "53ffa695-5fab-48b3-b5f5-ff93f77bfc10" + } + }, + "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", + "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\"", + "dbkey": "\"?\"", + "enzyme": "\"auto\"", + "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\"" + }, + "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", + "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", + "user_email": "planemo@galaxyproject.org", + "user_id": "d952758136b0c83c" + }, + "status": "success", + "test_index": 0, + "time_seconds": 5.093859434127808, + "tool_id": "parameters_maystro_workflow_2", + "tool_version": "0.1.0" + }, + "has_data": true, + "id": "parameters_maystro_workflow_2-0" + }, + { + "data": { + "inputs": { + "DB|user_json": { + "id": "b08444d846605ee4", + "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_version": "", + "copied_from_job_id": null, + "create_time": "2025-07-17T12:08:43.857384", + "dependencies": [], + "exit_code": 0, + "external_id": "135995", + "galaxy_version": "25.0", + "handler": null, + "history_id": "b08444d846605ee4", + "id": "e67c2cbedbcb0da1", + "inputs": { + "DB|user_json": { + "id": "b08444d846605ee4", + "src": "hda", + "uuid": "bbd9a440-a787-439e-9b36-2c1c45dae0a3" + } + }, + "job_messages": [], + "job_metrics": [], + "job_runner_name": null, + "job_stderr": "", + "job_stdout": "", + "model_class": "Job", + "output_collections": {}, + "outputs": { + "output_json": { + "id": "e67c2cbedbcb0da1", + "src": "hda", + "uuid": "6eed7c7c-77ce-4d77-b2ef-0a367df7e250" + } + }, + "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", + "assembly_plan_name": "\"Type2sRestrictionAssembly\"", + "avoid_patterns": null, + "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", + "dbkey": "\"?\"", + "enzyme": "\"auto\"", + "gc_constraints": null, + "hairpin_constraints": null, + "kmer_size": "\"\"", + "methylation_protection": "false", + "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", + "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", + "user_email": "planemo@galaxyproject.org", + "user_id": "d952758136b0c83c" + }, + "status": "success", + "test_index": 1, + "time_seconds": 15.298557996749878, + "tool_id": "parameters_maystro_workflow_2", + "tool_version": "0.1.0" + }, + "has_data": true, + "id": "parameters_maystro_workflow_2-1" + } + ], + "version": "0.1" +} \ No newline at end of file