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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
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9ab8b3673816 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
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1 {
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2 "summary": {
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3 "num_errors": 0,
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4 "num_failures": 0,
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5 "num_skips": 0,
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6 "num_tests": 2
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7 },
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8 "tests": [
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9 {
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10 "data": {
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11 "inputs": {
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12 "DB|annotation_column": "annotation",
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13 "DB|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
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14 "DB|execution": true,
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15 "DB|fragment_column": "fragment",
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16 "DB|sequence_column": "sequence",
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17 "DB|table_name": "sample",
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18 "DnaOptimizationProblemClass": "DnaOptimizationProblem",
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19 "assembly_plan_name": "Type2sRestrictionAssembly",
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20 "avoid_patterns": "BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer",
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21 "enzyme": "auto",
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22 "gc_constraints": "mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100",
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23 "hairpin_constraints": "stem_size=20, hairpin_window=200",
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24 "kmer_size": "15",
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25 "methylation_protection": true,
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26 "topology": "circular"
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27 },
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28 "job": {
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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'",
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30 "command_version": "",
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31 "copied_from_job_id": null,
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32 "create_time": "2025-07-17T12:08:28.832103",
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33 "dependencies": [],
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34 "exit_code": 0,
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35 "external_id": "135810",
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36 "galaxy_version": "25.0",
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37 "handler": null,
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38 "history_id": "d952758136b0c83c",
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39 "id": "d952758136b0c83c",
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40 "inputs": {},
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41 "job_messages": [],
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42 "job_metrics": [],
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43 "job_runner_name": null,
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44 "job_stderr": "",
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45 "job_stdout": "",
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46 "model_class": "Job",
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47 "output_collections": {},
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48 "outputs": {
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49 "output_json": {
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50 "id": "d952758136b0c83c",
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51 "src": "hda",
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52 "uuid": "53ffa695-5fab-48b3-b5f5-ff93f77bfc10"
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53 }
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54 },
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55 "params": {
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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}",
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57 "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"",
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58 "__input_ext": "\"input\"",
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59 "allow_edits": "true",
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60 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
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61 "avoid_patterns": "\"BsaI_site nNotI_site nXbaI_site nClaI_site n8x1mer\"",
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62 "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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63 "dbkey": "\"?\"",
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64 "enzyme": "\"auto\"",
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65 "gc_constraints": "\"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\"",
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66 "hairpin_constraints": "\"stem_size=20, hairpin_window=200\"",
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67 "kmer_size": "\"15\"",
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68 "methylation_protection": "true",
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69 "topology": "\"circular\""
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70 },
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71 "state": "ok",
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72 "stderr": "",
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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}",
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74 "tool_id": "parameters_maystro_workflow_2",
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75 "tool_stderr": "",
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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}",
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77 "update_time": "2025-07-17T12:08:33.771569",
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78 "user_email": "planemo@galaxyproject.org",
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79 "user_id": "d952758136b0c83c"
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80 },
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81 "status": "success",
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82 "test_index": 0,
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83 "time_seconds": 5.093859434127808,
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84 "tool_id": "parameters_maystro_workflow_2",
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85 "tool_version": "0.1.0"
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86 },
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87 "has_data": true,
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88 "id": "parameters_maystro_workflow_2-0"
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89 },
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90 {
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91 "data": {
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92 "inputs": {
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93 "DB|user_json": {
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94 "id": "b08444d846605ee4",
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95 "src": "hda"
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96 }
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97 },
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98 "job": {
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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'",
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100 "command_version": "",
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101 "copied_from_job_id": null,
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102 "create_time": "2025-07-17T12:08:43.857384",
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103 "dependencies": [],
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104 "exit_code": 0,
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105 "external_id": "135995",
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106 "galaxy_version": "25.0",
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107 "handler": null,
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108 "history_id": "b08444d846605ee4",
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109 "id": "e67c2cbedbcb0da1",
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110 "inputs": {
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111 "DB|user_json": {
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112 "id": "b08444d846605ee4",
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113 "src": "hda",
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114 "uuid": "bbd9a440-a787-439e-9b36-2c1c45dae0a3"
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115 }
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116 },
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117 "job_messages": [],
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118 "job_metrics": [],
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119 "job_runner_name": null,
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120 "job_stderr": "",
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121 "job_stdout": "",
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122 "model_class": "Job",
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123 "output_collections": {},
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124 "outputs": {
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125 "output_json": {
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126 "id": "e67c2cbedbcb0da1",
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127 "src": "hda",
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128 "uuid": "6eed7c7c-77ce-4d77-b2ef-0a367df7e250"
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129 }
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130 },
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131 "params": {
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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\"}]}}",
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133 "DnaOptimizationProblemClass": "\"DnaOptimizationProblem\"",
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134 "__input_ext": "\"input\"",
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135 "allow_edits": "true",
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136 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
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137 "avoid_patterns": null,
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138 "chromInfo": "\"/tmp/tmpnxavcgf5/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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139 "dbkey": "\"?\"",
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140 "enzyme": "\"auto\"",
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141 "gc_constraints": null,
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142 "hairpin_constraints": null,
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143 "kmer_size": "\"\"",
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144 "methylation_protection": "false",
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145 "topology": "\"circular\""
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146 },
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147 "state": "ok",
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148 "stderr": "",
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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",
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150 "tool_id": "parameters_maystro_workflow_2",
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151 "tool_stderr": "",
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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",
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153 "update_time": "2025-07-17T12:08:49.096516",
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154 "user_email": "planemo@galaxyproject.org",
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155 "user_id": "d952758136b0c83c"
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156 },
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157 "status": "success",
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158 "test_index": 1,
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159 "time_seconds": 15.298557996749878,
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160 "tool_id": "parameters_maystro_workflow_2",
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161 "tool_version": "0.1.0"
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162 },
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163 "has_data": true,
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164 "id": "parameters_maystro_workflow_2-1"
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165 }
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166 ],
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167 "version": "0.1"
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168 }