Mercurial > repos > tduigou > parameters_maystro_workflow_0

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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
comparison
equal deleted inserted replaced
0:95f33fc513ad 1:6b3f7ebe4ddf
7 }, 7 },
8 "tests": [ 8 "tests": [
9 { 9 {
10 "data": { 10 "data": {
11 "inputs": { 11 "inputs": {
12 "DB|annotation_column": "annotation", 12 "annotation_column": "annotation",
13 "DB|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
14 "DB|execution": true,
15 "DB|fragment_column": "fragment",
16 "DB|sequence_column": "sequence",
17 "DB|table_name": "sample",
18 "DnaOptimizationProblemClass": "DnaOptimizationProblem",
19 "assembly_plan_name": "Type2sRestrictionAssembly", 13 "assembly_plan_name": "Type2sRestrictionAssembly",
20 "avoid_patterns": "BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer", 14 "avoid_patterns": "BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer",
15 "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
21 "enzyme": "auto", 16 "enzyme": "auto",
17 "execution": true,
18 "fragment_column": "fragment",
22 "gc_constraints": "mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100", 19 "gc_constraints": "mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100",
23 "hairpin_constraints": "stem_size=20, hairpin_window=200", 20 "hairpin_constraints": "stem_size=20, hairpin_window=200",
24 "kmer_size": "15", 21 "kmer_size": "15",
25 "methylation_protection": true, 22 "sequence_column": "sequence",
23 "table_name": "sample",
26 "topology": "circular" 24 "topology": "circular"
27 }, 25 },
28 "job": { 26 "job": {
29 "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'", 27 "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'",
30 "command_version": "", 28 "command_version": "",
31 "copied_from_job_id": null, 29 "copied_from_job_id": null,
32 "create_time": "2025-07-17T12:08:28.832103", 30 "create_time": "2025-07-31T08:57:00.548068",
33 "dependencies": [], 31 "dependencies": [],
34 "exit_code": 0, 32 "exit_code": 0,
35 "external_id": "135810", 33 "external_id": "205407",
36 "galaxy_version": "25.0", 34 "galaxy_version": "25.0",
37 "handler": null, 35 "handler": null,
38 "history_id": "d952758136b0c83c", 36 "history_id": "57c9e3825b6e5989",
39 "id": "d952758136b0c83c", 37 "id": "57c9e3825b6e5989",
40 "inputs": {}, 38 "inputs": {},
41 "job_messages": [], 39 "job_messages": [],
42 "job_metrics": [], 40 "job_metrics": [],
43 "job_runner_name": null, 41 "job_runner_name": null,
44 "job_stderr": "", 42 "job_stderr": "",
45 "job_stdout": "", 43 "job_stdout": "",
46 "model_class": "Job", 44 "model_class": "Job",
47 "output_collections": {}, 45 "output_collections": {},
48 "outputs": { 46 "outputs": {
49 "output_json": { 47 "output_json": {
50 "id": "d952758136b0c83c", 48 "id": "57c9e3825b6e5989",
51 "src": "hda", 49 "src": "hda",
52 "uuid": "53ffa695-5fab-48b3-b5f5-ff93f77bfc10" 50 "uuid": "1bfb5292-6b8f-4b66-9d74-cedaf9200451"
53 } 51 }
54 }, 52 },
55 "params": { 53 "params": {
56 "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}",
57 "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"",
58 "__input_ext": "\"input\"", 54 "__input_ext": "\"input\"",
59 "allow_edits": "true", 55 "annotation_column": "\"annotation\"",
60 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", 56 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
61 "avoid_patterns": "\"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\"", 57 "avoid_patterns": "\"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\"",
62 "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 58 "chromInfo": "\"/tmp/tmpt0l5fyog/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
59 "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
63 "dbkey": "\"?\"", 60 "dbkey": "\"?\"",
64 "enzyme": "\"auto\"", 61 "enzyme": "\"auto\"",
62 "execution": "true",
63 "fragment_column": "\"fragment\"",
65 "gc_constraints": "\"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\"", 64 "gc_constraints": "\"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\"",
66 "hairpin_constraints": "\"stem_size=20, hairpin_window=200\"", 65 "hairpin_constraints": "\"stem_size=20, hairpin_window=200\"",
67 "kmer_size": "\"15\"", 66 "kmer_size": "\"15\"",
68 "methylation_protection": "true", 67 "sequence_column": "\"sequence\"",
69 "topology": "\"circular\"" 68 "table_name": "\"sample\"",
69 "topology": "\"circular\"",
70 "user_json": null
70 }, 71 },
71 "state": "ok", 72 "state": "ok",
72 "stderr": "", 73 "stderr": "",
73 "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}", 74 "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}",
74 "tool_id": "parameters_maystro_workflow_2", 75 "tool_id": "parameters_maystro_workflow_1",
75 "tool_stderr": "", 76 "tool_stderr": "",
76 "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}", 77 "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}",
77 "update_time": "2025-07-17T12:08:33.771569", 78 "update_time": "2025-07-31T08:57:06.352395",
78 "user_email": "planemo@galaxyproject.org", 79 "user_email": "planemo@galaxyproject.org",
79 "user_id": "d952758136b0c83c" 80 "user_id": "57c9e3825b6e5989"
80 }, 81 },
81 "status": "success", 82 "status": "success",
82 "test_index": 0, 83 "test_index": 0,
83 "time_seconds": 5.093859434127808, 84 "time_seconds": 6.245003700256348,
84 "tool_id": "parameters_maystro_workflow_2", 85 "tool_id": "parameters_maystro_workflow_1",
85 "tool_version": "0.1.0" 86 "tool_version": "0.1.0"
86 }, 87 },
87 "has_data": true, 88 "has_data": true,
88 "id": "parameters_maystro_workflow_2-0" 89 "id": "parameters_maystro_workflow_1-0"
89 }, 90 },
90 { 91 {
91 "data": { 92 "data": {
92 "inputs": { 93 "inputs": {
93 "DB|user_json": { 94 "user_json": {
94 "id": "b08444d846605ee4", 95 "id": "b8cd89e8131d3fe7",
95 "src": "hda" 96 "src": "hda"
96 } 97 }
97 }, 98 },
98 "job": { 99 "job": {
99 "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'", 100 "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'",
100 "command_version": "", 101 "command_version": "",
101 "copied_from_job_id": null, 102 "copied_from_job_id": null,
102 "create_time": "2025-07-17T12:08:43.857384", 103 "create_time": "2025-07-31T08:57:16.707828",
103 "dependencies": [], 104 "dependencies": [],
104 "exit_code": 0, 105 "exit_code": 0,
105 "external_id": "135995", 106 "external_id": "205636",
106 "galaxy_version": "25.0", 107 "galaxy_version": "25.0",
107 "handler": null, 108 "handler": null,
108 "history_id": "b08444d846605ee4", 109 "history_id": "b8cd89e8131d3fe7",
109 "id": "e67c2cbedbcb0da1", 110 "id": "abe44dd8383948e0",
110 "inputs": { 111 "inputs": {
111 "DB|user_json": { 112 "user_json": {
112 "id": "b08444d846605ee4", 113 "id": "b8cd89e8131d3fe7",
113 "src": "hda", 114 "src": "hda",
114 "uuid": "bbd9a440-a787-439e-9b36-2c1c45dae0a3" 115 "uuid": "d79830ca-f30e-4f82-8b67-150bf816c265"
115 } 116 }
116 }, 117 },
117 "job_messages": [], 118 "job_messages": [],
118 "job_metrics": [], 119 "job_metrics": [],
119 "job_runner_name": null, 120 "job_runner_name": null,
121 "job_stdout": "", 122 "job_stdout": "",
122 "model_class": "Job", 123 "model_class": "Job",
123 "output_collections": {}, 124 "output_collections": {},
124 "outputs": { 125 "outputs": {
125 "output_json": { 126 "output_json": {
126 "id": "e67c2cbedbcb0da1", 127 "id": "abe44dd8383948e0",
127 "src": "hda", 128 "src": "hda",
128 "uuid": "6eed7c7c-77ce-4d77-b2ef-0a367df7e250" 129 "uuid": "cd60237f-3d8d-4a7e-ac4c-b10728db646e"
129 } 130 }
130 }, 131 },
131 "params": { 132 "params": {
132 "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\"}]}}",
133 "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"",
134 "__input_ext": "\"input\"", 133 "__input_ext": "\"input\"",
135 "allow_edits": "true", 134 "annotation_column": null,
136 "assembly_plan_name": "\"Type2sRestrictionAssembly\"", 135 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
137 "avoid_patterns": null, 136 "avoid_patterns": null,
138 "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", 137 "chromInfo": "\"/tmp/tmpt0l5fyog/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
138 "db_uri": null,
139 "dbkey": "\"?\"", 139 "dbkey": "\"?\"",
140 "enzyme": "\"auto\"", 140 "enzyme": "\"auto\"",
141 "execution": "false",
142 "fragment_column": null,
141 "gc_constraints": null, 143 "gc_constraints": null,
142 "hairpin_constraints": null, 144 "hairpin_constraints": null,
143 "kmer_size": "\"\"", 145 "kmer_size": "\"\"",
144 "methylation_protection": "false", 146 "sequence_column": null,
147 "table_name": null,
145 "topology": "\"circular\"" 148 "topology": "\"circular\""
146 }, 149 },
147 "state": "ok", 150 "state": "ok",
148 "stderr": "", 151 "stderr": "",
149 "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", 152 "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",
150 "tool_id": "parameters_maystro_workflow_2", 153 "tool_id": "parameters_maystro_workflow_1",
151 "tool_stderr": "", 154 "tool_stderr": "",
152 "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", 155 "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",
153 "update_time": "2025-07-17T12:08:49.096516", 156 "update_time": "2025-07-31T08:57:22.628561",
154 "user_email": "planemo@galaxyproject.org", 157 "user_email": "planemo@galaxyproject.org",
155 "user_id": "d952758136b0c83c" 158 "user_id": "57c9e3825b6e5989"
156 }, 159 },
157 "status": "success", 160 "status": "success",
158 "test_index": 1, 161 "test_index": 1,
159 "time_seconds": 15.298557996749878, 162 "time_seconds": 15.919075965881348,
160 "tool_id": "parameters_maystro_workflow_2", 163 "tool_id": "parameters_maystro_workflow_1",
161 "tool_version": "0.1.0" 164 "tool_version": "0.1.0"
162 }, 165 },
163 "has_data": true, 166 "has_data": true,
164 "id": "parameters_maystro_workflow_2-1" 167 "id": "parameters_maystro_workflow_1-1"
165 } 168 }
166 ], 169 ],
167 "version": "0.1" 170 "version": "0.1"
168 } 171 }