--- a/output.json	Wed Jul 23 09:40:00 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,168 +0,0 @@
-{
-    "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