Mercurial > repos > tduigou > parameters_maystro_workflow_2

annotate output.json @ 1:813aec57e9fd draft default tip

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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 08:58:02 +0000
parents 4e2ae28020f7
children
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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 "annotation_column": "annotation",
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13 "assembly_plan_name": "Type2sRestrictionAssembly",
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14 "avoid_patterns": "BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer",
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15 "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
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16 "enzyme": "auto",
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17 "execution": true,
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18 "fragment_column": "fragment",
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19 "gc_constraints": "mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100",
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20 "hairpin_constraints": "stem_size=20, hairpin_window=200",
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21 "kmer_size": "15",
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22 "sequence_column": "sequence",
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23 "table_name": "sample",
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24 "topology": "circular"
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25 },
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26 "job": {
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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'",
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28 "command_version": "",
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29 "copied_from_job_id": null,
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30 "create_time": "2025-07-31T08:57:00.548068",
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31 "dependencies": [],
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32 "exit_code": 0,
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33 "external_id": "205407",
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34 "galaxy_version": "25.0",
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35 "handler": null,
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36 "history_id": "57c9e3825b6e5989",
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37 "id": "57c9e3825b6e5989",
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38 "inputs": {},
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39 "job_messages": [],
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40 "job_metrics": [],
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41 "job_runner_name": null,
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42 "job_stderr": "",
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43 "job_stdout": "",
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44 "model_class": "Job",
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45 "output_collections": {},
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46 "outputs": {
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47 "output_json": {
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48 "id": "57c9e3825b6e5989",
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49 "src": "hda",
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50 "uuid": "1bfb5292-6b8f-4b66-9d74-cedaf9200451"
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51 }
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52 },
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53 "params": {
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54 "__input_ext": "\"input\"",
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55 "annotation_column": "\"annotation\"",
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56 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
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57 "avoid_patterns": "\"BsaI_site BsmBI_site BbsI_site SapI_site 8x1mer 5x3mer 9x2mer\"",
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58 "chromInfo": "\"/tmp/tmpt0l5fyog/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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59 "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"",
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60 "dbkey": "\"?\"",
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61 "enzyme": "\"auto\"",
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62 "execution": "true",
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63 "fragment_column": "\"fragment\"",
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64 "gc_constraints": "\"mini=0.3, maxi=0.7, window=100 mini=0.1, maxi=0.9, window=100\"",
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65 "hairpin_constraints": "\"stem_size=20, hairpin_window=200\"",
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66 "kmer_size": "\"15\"",
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67 "sequence_column": "\"sequence\"",
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68 "table_name": "\"sample\"",
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69 "topology": "\"circular\"",
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70 "user_json": null
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71 },
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72 "state": "ok",
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73 "stderr": "",
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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}",
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75 "tool_id": "parameters_maystro_workflow_1",
0
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76 "tool_stderr": "",
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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}",
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78 "update_time": "2025-07-31T08:57:06.352395",
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79 "user_email": "planemo@galaxyproject.org",
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80 "user_id": "57c9e3825b6e5989"
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81 },
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82 "status": "success",
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83 "test_index": 0,
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84 "time_seconds": 6.245003700256348,
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85 "tool_id": "parameters_maystro_workflow_1",
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86 "tool_version": "0.1.0"
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87 },
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88 "has_data": true,
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89 "id": "parameters_maystro_workflow_1-0"
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90 },
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91 {
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92 "data": {
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93 "inputs": {
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94 "user_json": {
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95 "id": "b8cd89e8131d3fe7",
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96 "src": "hda"
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97 }
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98 },
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99 "job": {
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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'",
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101 "command_version": "",
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102 "copied_from_job_id": null,
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103 "create_time": "2025-07-31T08:57:16.707828",
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104 "dependencies": [],
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105 "exit_code": 0,
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106 "external_id": "205636",
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107 "galaxy_version": "25.0",
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108 "handler": null,
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109 "history_id": "b8cd89e8131d3fe7",
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110 "id": "abe44dd8383948e0",
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111 "inputs": {
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112 "user_json": {
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113 "id": "b8cd89e8131d3fe7",
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114 "src": "hda",
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115 "uuid": "d79830ca-f30e-4f82-8b67-150bf816c265"
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116 }
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117 },
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118 "job_messages": [],
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119 "job_metrics": [],
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120 "job_runner_name": null,
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121 "job_stderr": "",
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122 "job_stdout": "",
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123 "model_class": "Job",
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124 "output_collections": {},
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125 "outputs": {
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126 "output_json": {
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127 "id": "abe44dd8383948e0",
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128 "src": "hda",
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129 "uuid": "cd60237f-3d8d-4a7e-ac4c-b10728db646e"
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130 }
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131 },
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132 "params": {
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133 "__input_ext": "\"input\"",
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134 "annotation_column": null,
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135 "assembly_plan_name": "\"Type2sRestrictionAssembly\"",
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136 "avoid_patterns": null,
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137 "chromInfo": "\"/tmp/tmpt0l5fyog/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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138 "db_uri": null,
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139 "dbkey": "\"?\"",
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140 "enzyme": "\"auto\"",
1
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141 "execution": "false",
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142 "fragment_column": null,
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143 "gc_constraints": null,
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144 "hairpin_constraints": null,
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145 "kmer_size": "\"\"",
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146 "sequence_column": null,
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147 "table_name": null,
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148 "topology": "\"circular\""
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149 },
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150 "state": "ok",
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151 "stderr": "",
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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",
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153 "tool_id": "parameters_maystro_workflow_1",
0
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154 "tool_stderr": "",
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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",
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156 "update_time": "2025-07-31T08:57:22.628561",
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157 "user_email": "planemo@galaxyproject.org",
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158 "user_id": "57c9e3825b6e5989"
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159 },
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160 "status": "success",
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161 "test_index": 1,
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162 "time_seconds": 15.919075965881348,
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163 "tool_id": "parameters_maystro_workflow_1",
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164 "tool_version": "0.1.0"
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165 },
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166 "has_data": true,
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167 "id": "parameters_maystro_workflow_1-1"
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168 }
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169 ],
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170 "version": "0.1"
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171 }