Mercurial > repos > tduigou > seq_from_db

annotate output.json @ 2:3bb9bbecae97 draft default tip

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
author tduigou
date Wed, 03 Sep 2025 14:07:14 +0000
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2
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-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": 3
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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 "input": {
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13 "id": "4a322b718ac1c0e2",
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14 "src": "hda"
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15 },
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16 "json_use|annotation_columns": "annotation",
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17 "json_use|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
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18 "json_use|fragment_column": "fragment",
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19 "json_use|sequence_column": "sequence",
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20 "json_use|table": "sample",
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21 "json_use|use_json_paramers": false
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22 },
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23 "job": {
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24 "command_line": "mkdir 'outdir' && python '/home/rkhaled/galaxytools/tools/seq_from_db/get_db_info.py' --input '/tmp/tmpk1dzvi78/files/c/1/9/dataset_c19fee65-2ddf-471a-97f2-745ff33b2e2b.dat' --use_json_paramers 'false' --sequence_column 'sequence' --annotation_columns 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output 'outdir' --report '/tmp/tmpk1dzvi78/job_working_directory/000/2/outputs/dataset_a220a67a-7465-433f-bf6b-8982cbe6f6c0.dat'",
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25 "command_version": "",
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26 "copied_from_job_id": null,
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27 "create_time": "2025-09-03T14:06:00.424294",
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28 "dependencies": [],
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29 "exit_code": 0,
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30 "external_id": "272095",
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31 "galaxy_version": "25.0",
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32 "handler": null,
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33 "history_id": "4a322b718ac1c0e2",
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34 "id": "1989000e072b2636",
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35 "inputs": {
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36 "input": {
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37 "id": "4a322b718ac1c0e2",
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38 "src": "hda",
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39 "uuid": "c19fee65-2ddf-471a-97f2-745ff33b2e2b"
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40 }
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41 },
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42 "job_messages": [],
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43 "job_metrics": [],
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44 "job_runner_name": null,
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45 "job_stderr": "",
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46 "job_stdout": "",
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47 "model_class": "Job",
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48 "output_collections": {
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49 "output_gb": {
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50 "id": "4a322b718ac1c0e2",
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51 "src": "hdca"
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52 }
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53 },
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54 "outputs": {
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55 "__new_primary_file_output_gb|part_A__": {
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56 "id": "692a3006cb4bc1fb",
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57 "src": "hda",
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58 "uuid": "9d1fe7c4-5dec-4419-b058-dc8b5ca2b484"
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59 },
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60 "__new_primary_file_output_gb|part_B__": {
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61 "id": "5bb9f161ccdcbe3d",
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62 "src": "hda",
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64 },
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65 "__new_primary_file_output_gb|part_C__": {
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66 "id": "c5357eb6f97cf3a5",
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69 },
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83 "uuid": "40e8c7bf-123b-474a-b428-b898dd08381c"
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89 },
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104 },
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109 },
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110 "__new_primary_file_output_gb|part_L__": {
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112 "src": "hda",
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114 },
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115 "report": {
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117 "src": "hda",
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118 "uuid": "a220a67a-7465-433f-bf6b-8982cbe6f6c0"
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119 }
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120 },
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121 "params": {
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122 "__input_ext": "\"input\"",
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123 "chromInfo": "\"/tmp/tmpk1dzvi78/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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124 "dbkey": "\"?\"",
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125 "json_use": "{\"__current_case__\": 0, \"annotation_columns\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table\": \"sample\", \"use_json_paramers\": false}"
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126 },
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127 "state": "ok",
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128 "stderr": "",
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129 "stdout": "Connected to database.\n",
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130 "tool_id": "seq_form_db",
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131 "tool_stderr": "",
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132 "tool_stdout": "Connected to database.\n",
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133 "update_time": "2025-09-03T14:06:07.610997",
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134 "user_email": "planemo@galaxyproject.org",
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135 "user_id": "4a322b718ac1c0e2"
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136 },
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137 "status": "success",
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138 "test_index": 0,
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139 "time_seconds": 17.504873752593994,
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140 "tool_id": "seq_form_db",
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141 "tool_version": "0.3.0+galaxy2"
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142 },
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143 "has_data": true,
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144 "id": "seq_form_db-0"
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145 },
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146 {
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147 "data": {
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148 "inputs": {
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149 "input": {
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150 "id": "7a3ba500dfe34f7d",
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151 "src": "hda"
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152 },
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153 "json_use|json_conf": {
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154 "id": "2342ce89d5e1ece0",
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155 "src": "hda"
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156 },
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157 "json_use|use_json_paramers": true
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158 },
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159 "job": {
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160 "command_line": "mkdir 'outdir' && python '/home/rkhaled/galaxytools/tools/seq_from_db/get_db_info.py' --input '/tmp/tmpk1dzvi78/files/4/2/c/dataset_42c93e52-005a-4165-b3c9-ad6a994555b6.dat' --use_json_paramers 'true' --json_conf '/tmp/tmpk1dzvi78/files/b/f/8/dataset_bf8fdbb1-ad99-4618-95c0-95a8c77b0b33.dat' --output 'outdir' --report '/tmp/tmpk1dzvi78/job_working_directory/000/5/outputs/dataset_e887b8ce-78bc-411c-9e9a-2473e4f5c094.dat'",
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161 "command_version": "",
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162 "copied_from_job_id": null,
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163 "create_time": "2025-09-03T14:06:18.140280",
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164 "dependencies": [
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165 {
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166 "cacheable": false,
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167 "dependency_resolver": {
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168 "auto_init": true,
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169 "auto_install": true,
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170 "can_uninstall_dependencies": true,
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171 "ensure_channels": "conda-forge,bioconda",
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172 "model_class": "CondaDependencyResolver",
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173 "prefix": "/home/rkhaled/miniconda3",
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174 "read_only": false,
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175 "resolver_type": "conda",
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176 "resolves_simple_dependencies": true,
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177 "use_local": false,
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178 "versionless": false
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179 },
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180 "dependency_type": "conda",
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181 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ceb490c4aa844ebbe7d57435fac907dbf01ddab1023bddca4355753f079716f1",
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182 "exact": true,
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183 "model_class": "MergedCondaDependency",
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184 "name": "pandas",
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185 "version": "2.2.3"
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186 },
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187 {
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188 "cacheable": false,
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189 "dependency_resolver": {
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190 "auto_init": true,
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191 "auto_install": true,
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192 "can_uninstall_dependencies": true,
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193 "ensure_channels": "conda-forge,bioconda",
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194 "model_class": "CondaDependencyResolver",
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195 "prefix": "/home/rkhaled/miniconda3",
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196 "read_only": false,
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197 "resolver_type": "conda",
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198 "resolves_simple_dependencies": true,
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199 "use_local": false,
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200 "versionless": false
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201 },
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202 "dependency_type": "conda",
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203 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ceb490c4aa844ebbe7d57435fac907dbf01ddab1023bddca4355753f079716f1",
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204 "exact": true,
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205 "model_class": "MergedCondaDependency",
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206 "name": "sqlalchemy",
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207 "version": "2.0.40"
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208 },
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209 {
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210 "cacheable": false,
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211 "dependency_resolver": {
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212 "auto_init": true,
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213 "auto_install": true,
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214 "can_uninstall_dependencies": true,
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215 "ensure_channels": "conda-forge,bioconda",
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216 "model_class": "CondaDependencyResolver",
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217 "prefix": "/home/rkhaled/miniconda3",
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218 "read_only": false,
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219 "resolver_type": "conda",
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220 "resolves_simple_dependencies": true,
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221 "use_local": false,
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222 "versionless": false
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223 },
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224 "dependency_type": "conda",
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225 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ceb490c4aa844ebbe7d57435fac907dbf01ddab1023bddca4355753f079716f1",
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226 "exact": true,
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227 "model_class": "MergedCondaDependency",
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228 "name": "psycopg2",
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229 "version": "2.9.9"
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230 },
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231 {
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232 "cacheable": false,
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233 "dependency_resolver": {
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234 "auto_init": true,
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235 "auto_install": true,
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236 "can_uninstall_dependencies": true,
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237 "ensure_channels": "conda-forge,bioconda",
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238 "model_class": "CondaDependencyResolver",
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239 "prefix": "/home/rkhaled/miniconda3",
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240 "read_only": false,
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241 "resolver_type": "conda",
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242 "resolves_simple_dependencies": true,
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243 "use_local": false,
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244 "versionless": false
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245 },
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246 "dependency_type": "conda",
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247 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ceb490c4aa844ebbe7d57435fac907dbf01ddab1023bddca4355753f079716f1",
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248 "exact": true,
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249 "model_class": "MergedCondaDependency",
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250 "name": "biopython",
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251 "version": "1.85"
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252 }
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253 ],
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254 "exit_code": 0,
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255 "external_id": "272369",
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256 "galaxy_version": "25.0",
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257 "handler": null,
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258 "history_id": "1989000e072b2636",
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259 "id": "c5357eb6f97cf3a5",
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260 "inputs": {
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261 "input": {
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262 "id": "7a3ba500dfe34f7d",
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263 "src": "hda",
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264 "uuid": "42c93e52-005a-4165-b3c9-ad6a994555b6"
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265 },
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266 "json_use|json_conf": {
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267 "id": "2342ce89d5e1ece0",
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268 "src": "hda",
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269 "uuid": "bf8fdbb1-ad99-4618-95c0-95a8c77b0b33"
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270 }
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271 },
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272 "job_messages": [],
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273 "job_metrics": [],
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274 "job_runner_name": null,
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275 "job_stderr": "",
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339 },
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340 "__new_primary_file_output_gb|part_L__": {
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344 },
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345 "report": {
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347 "src": "hda",
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348 "uuid": "e887b8ce-78bc-411c-9e9a-2473e4f5c094"
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349 }
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350 },
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351 "params": {
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352 "__input_ext": "\"input\"",
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353 "chromInfo": "\"/tmp/tmpk1dzvi78/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
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354 "dbkey": "\"?\"",
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355 "json_use": "{\"__current_case__\": 1, \"json_conf\": {\"values\": [{\"id\": 16, \"src\": \"hda\"}]}, \"use_json_paramers\": true}"
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356 },
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357 "state": "ok",
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358 "stderr": "",
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359 "stdout": "Connected to database.\n",
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360 "tool_id": "seq_form_db",
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361 "tool_stderr": "",
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362 "tool_stdout": "Connected to database.\n",
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363 "update_time": "2025-09-03T14:06:25.140121",
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364 "user_email": "planemo@galaxyproject.org",
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365 "user_id": "4a322b718ac1c0e2"
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366 },
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367 "status": "success",
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368 "test_index": 1,
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369 "time_seconds": 17.440069437026978,
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370 "tool_id": "seq_form_db",
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371 "tool_version": "0.3.0+galaxy2"
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372 },
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373 "has_data": true,
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374 "id": "seq_form_db-1"
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375 },
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376 {
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377 "data": {
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378 "inputs": {
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379 "input": {
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380 "id": "4c3f7df96ce49d27",
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381 "src": "hda"
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382 },
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383 "json_use|annotation_columns": "annotation",
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384 "json_use|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",
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385 "json_use|fragment_column": "fragment",
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386 "json_use|sequence_column": "sequence",
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387 "json_use|table": "sample",
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388 "json_use|use_json_paramers": false
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389 },
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390 "job": {
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391 "command_line": "mkdir 'outdir' && python '/home/rkhaled/galaxytools/tools/seq_from_db/get_db_info.py' --input '/tmp/tmpk1dzvi78/files/9/b/a/dataset_9ba7c27f-7f63-48f9-82df-f0ffa32fe875.dat' --use_json_paramers 'false' --sequence_column 'sequence' --annotation_columns 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output 'outdir' --report '/tmp/tmpk1dzvi78/job_working_directory/000/7/outputs/dataset_2099de02-84b6-464f-a603-26ec7fd84555.dat'",
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392 "command_version": "",
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393 "copied_from_job_id": null,
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394 "create_time": "2025-09-03T14:06:35.187563",
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395 "dependencies": [
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396 {
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397 "cacheable": false,
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398 "dependency_resolver": {
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399 "auto_init": true,
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400 "auto_install": true,
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401 "can_uninstall_dependencies": true,
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402 "ensure_channels": "conda-forge,bioconda",
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403 "model_class": "CondaDependencyResolver",
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404 "prefix": "/home/rkhaled/miniconda3",
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405 "read_only": false,
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diff changeset
406 "resolver_type": "conda",
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407 "resolves_simple_dependencies": true,
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diff changeset
408 "use_local": false,
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diff changeset
409 "versionless": false
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410 },
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411 "dependency_type": "conda",
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412 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ceb490c4aa844ebbe7d57435fac907dbf01ddab1023bddca4355753f079716f1",
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413 "exact": true,
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414 "model_class": "MergedCondaDependency",
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415 "name": "pandas",
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416 "version": "2.2.3"
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417 },
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418 {
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419 "cacheable": false,
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420 "dependency_resolver": {
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421 "auto_init": true,
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422 "auto_install": true,
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423 "can_uninstall_dependencies": true,
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424 "ensure_channels": "conda-forge,bioconda",
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425 "model_class": "CondaDependencyResolver",
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426 "prefix": "/home/rkhaled/miniconda3",
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427 "read_only": false,
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428 "resolver_type": "conda",
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429 "resolves_simple_dependencies": true,
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430 "use_local": false,
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431 "versionless": false
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432 },
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433 "dependency_type": "conda",
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434 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ceb490c4aa844ebbe7d57435fac907dbf01ddab1023bddca4355753f079716f1",
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435 "exact": true,
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436 "model_class": "MergedCondaDependency",
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437 "name": "sqlalchemy",
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438 "version": "2.0.40"
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439 },
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440 {
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441 "cacheable": false,
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442 "dependency_resolver": {
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443 "auto_init": true,
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diff changeset
444 "auto_install": true,
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diff changeset
445 "can_uninstall_dependencies": true,
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446 "ensure_channels": "conda-forge,bioconda",
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447 "model_class": "CondaDependencyResolver",
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448 "prefix": "/home/rkhaled/miniconda3",
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449 "read_only": false,
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diff changeset
450 "resolver_type": "conda",
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451 "resolves_simple_dependencies": true,
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diff changeset
452 "use_local": false,
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453 "versionless": false
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454 },
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455 "dependency_type": "conda",
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456 "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-ceb490c4aa844ebbe7d57435fac907dbf01ddab1023bddca4355753f079716f1",
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457 "exact": true,
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458 "model_class": "MergedCondaDependency",
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459 "name": "psycopg2",
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476 },
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483 }
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484 ],
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486 "external_id": "272614",
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494 "src": "hda",
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496 }
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497 },
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498 "job_messages": [],
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499 "job_metrics": [],
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501 "job_stderr": "",
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502 "job_stdout": "",
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505 "output_gb": {
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506 "id": "692a3006cb4bc1fb",
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507 "src": "hdca"
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508 }
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509 },
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510 "outputs": {
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511 "__new_primary_file_output_gb|part_A__": {
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515 },
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520 },
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525 },
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540 },
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541 "__new_primary_file_output_gb|part_G__": {
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553 "src": "hda",
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555 },
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556 "__new_primary_file_output_gb|part_J__": {
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557 "id": "0ba9e9781a802f97",
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558 "src": "hda",
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560 },
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561 "__new_primary_file_output_gb|part_K__": {
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562 "id": "1cd3d77f4e0bb87b",
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563 "src": "hda",
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565 },
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566 "__new_primary_file_output_gb|part_L__": {
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567 "id": "fc7f2bf0d5edf8ad",
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568 "src": "hda",
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569 "uuid": "cb4b9a89-166d-4d35-9b20-6e06c71ff3fc"
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570 },
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571 "report": {
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572 "id": "cc9ee5a2b3669654",
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573 "src": "hda",
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574 "uuid": "2099de02-84b6-464f-a603-26ec7fd84555"
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diff changeset
575 }
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576 },
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577 "params": {
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578 "__input_ext": "\"input\"",
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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579 "chromInfo": "\"/tmp/tmpk1dzvi78/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"",
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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580 "dbkey": "\"?\"",
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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581 "json_use": "{\"__current_case__\": 0, \"annotation_columns\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table\": \"sample\", \"use_json_paramers\": false}"
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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582 },
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583 "state": "ok",
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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584 "stderr": "",
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585 "stdout": "Connected to database.\n",
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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586 "tool_id": "seq_form_db",
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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587 "tool_stderr": "",
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588 "tool_stdout": "Connected to database.\n",
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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589 "update_time": "2025-09-03T14:06:41.527586",
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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590 "user_email": "planemo@galaxyproject.org",
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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591 "user_id": "4a322b718ac1c0e2"
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592 },
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593 "status": "success",
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594 "test_index": 2,
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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595 "time_seconds": 16.304288148880005,
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596 "tool_id": "seq_form_db",
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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597 "tool_version": "0.3.0+galaxy2"
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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598 },
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599 "has_data": true,
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600 "id": "seq_form_db-2"
3bb9bbecae97 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 767392e3136912fa30d1e0786eba789dd77d722c-dirty
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601 }
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602 ],
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603 "version": "0.1"
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604 }