Mercurial > repos > tduigou > seq_from_db

annotate seq_form_db.xml @ 2:11a3752feb0a draft default tip

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author tduigou
date Wed, 15 Oct 2025 12:33:41 +0000
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1 <tool id="seq_form_db" name="Get sequences Data From DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Import fragment's data from an accessible DB and export it as .gb files</description>
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3 <macros>
2
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4 <token name="@VERSION_SUFFIX@">2</token>
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5 <token name="@TOOL_VERSION@">0.3.0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="2.2.3">pandas</requirement>
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9 <requirement type="package" version="2.0.40">sqlalchemy</requirement>
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10 <requirement type="package" version="2.9.9">psycopg2</requirement>
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11 <requirement type="package" version="1.85">biopython</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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14 mkdir 'outdir' &&
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15 python '$__tool_directory__/get_db_info.py'
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16 --input '$input'
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17 --use_json_paramers '$json_use.use_json_paramers'
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18 #if not $json_use.use_json_paramers:
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19 --sequence_column '$json_use.sequence_column'
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20 --annotation_columns '$json_use.annotation_columns'
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21 --db_uri '$json_use.db_uri'
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22 --table '$json_use.table'
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23 --fragment_column '$json_use.fragment_column'
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24 #else:
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25 --json_conf '$json_use.json_conf'
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26 #end if
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27 --output 'outdir'
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28 --report '$report'
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29 ]]></command>
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30 <inputs>
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31 <param name="input" type="data" format="csv" label="Input CSV File" />
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32 <conditional name="json_use">
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33 <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" />
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34 <when value="false">
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35 <param name="table" type="text" label="DB Table Name" optional="false" />
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36 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="false" />
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37 <param name="annotation_columns" type="text" label="DB Column Contains Annotation For Ganbank File" optional="false" />
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38 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="false" />
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39 <param name="db_uri" type="text" label="DB Connection URI" help="postgresql://user_name:password@host:port/path/to/database" optional="false" />
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40 </when>
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41 <when value="true">
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42 <param name="json_conf" type="data" format='json' label="DB config as a json file" help="JSON file specifying the database URI, table name and the column names for annotation and sequence data" optional="false" />
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43 </when>
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44 </conditional>
0
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45 </inputs>
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46 <outputs>
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47 <collection name="output_gb" type="list" label="GenBank Files collection" >
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48 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" />
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49 </collection>
2
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50 <data name='report' format='txt' label='missing fragments' />
0
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51 </outputs>
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52 <tests>
1
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53 <!--manual parameters-->
0
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54 <test>
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55 <param name="input" value="2-step-golden_gate_plan.csv" />
1
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56 <conditional name="json_use">
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57 <param name='use_json_paramers' value='false' />
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58 <param name="table" value="sample" />
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59 <param name="sequence_column" value="sequence" />
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60 <param name="annotation_columns" value="annotation" />
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61 <param name="fragment_column" value="fragment" />
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62 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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63 </conditional>
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64 <output_collection name="output_gb" type="list" count="12">
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65 <element name="part_A">
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66 <assert_contents>
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67 <has_n_lines min="10" />
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68 </assert_contents>
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69 </element>
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70 <element name="part_B">
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71 <assert_contents>
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72 <has_n_lines min="10" />
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73 </assert_contents>
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74 </element>
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75 <element name="part_C">
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76 <assert_contents>
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77 <has_n_lines min="10" />
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78 </assert_contents>
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79 </element>
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80 <element name="part_D">
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81 <assert_contents>
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82 <has_n_lines min="10" />
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83 </assert_contents>
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84 </element>
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85 <element name="part_E">
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86 <assert_contents>
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87 <has_n_lines min="10" />
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88 </assert_contents>
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89 </element>
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90 <element name="part_F">
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91 <assert_contents>
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92 <has_n_lines min="10" />
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93 </assert_contents>
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94 </element>
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95 <element name="part_G">
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96 <assert_contents>
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97 <has_n_lines min="10" />
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98 </assert_contents>
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99 </element>
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100 <element name="part_H">
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101 <assert_contents>
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102 <has_n_lines min="10" />
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103 </assert_contents>
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104 </element>
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105 <element name="part_I">
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106 <assert_contents>
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107 <has_n_lines min="10" />
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108 </assert_contents>
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109 </element>
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110 <element name="part_J">
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111 <assert_contents>
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112 <has_n_lines min="10" />
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113 </assert_contents>
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114 </element>
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115 <element name="part_K">
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116 <assert_contents>
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117 <has_n_lines min="10" />
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118 </assert_contents>
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119 </element>
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120 <element name="part_L">
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121 <assert_contents>
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122 <has_n_lines min="10" />
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123 </assert_contents>
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124 </element>
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125 </output_collection>
2
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126 <output name='report'>
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127 <assert_contents>
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128 <has_n_lines n="0" />
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129 </assert_contents>
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130 </output>
1
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131 </test>
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132 <!--JSON parameters-->
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133 <test>
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134 <param name="input" value="2-step-golden_gate_plan.csv" />
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135 <conditional name="json_use">
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136 <param name="use_json_paramers" value='true'/>
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137 <param name="json_conf" value="test-JSON.json" />
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138 </conditional>
0
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139 <output_collection name="output_gb" type="list" count="12">
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140 <element name="part_A">
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141 <assert_contents>
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142 <has_n_lines min="10" />
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143 </assert_contents>
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144 </element>
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145 <element name="part_B">
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146 <assert_contents>
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147 <has_n_lines min="10" />
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148 </assert_contents>
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149 </element>
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150 <element name="part_C">
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151 <assert_contents>
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152 <has_n_lines min="10" />
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153 </assert_contents>
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154 </element>
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155 <element name="part_D">
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156 <assert_contents>
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157 <has_n_lines min="10" />
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158 </assert_contents>
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159 </element>
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160 <element name="part_E">
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161 <assert_contents>
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162 <has_n_lines min="10" />
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163 </assert_contents>
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164 </element>
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165 <element name="part_F">
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166 <assert_contents>
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167 <has_n_lines min="10" />
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168 </assert_contents>
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169 </element>
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170 <element name="part_G">
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171 <assert_contents>
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172 <has_n_lines min="10" />
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173 </assert_contents>
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174 </element>
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175 <element name="part_H">
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176 <assert_contents>
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177 <has_n_lines min="10" />
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178 </assert_contents>
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179 </element>
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180 <element name="part_I">
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181 <assert_contents>
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182 <has_n_lines min="10" />
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183 </assert_contents>
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184 </element>
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185 <element name="part_J">
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186 <assert_contents>
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187 <has_n_lines min="10" />
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188 </assert_contents>
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189 </element>
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190 <element name="part_K">
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191 <assert_contents>
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192 <has_n_lines min="10" />
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193 </assert_contents>
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194 </element>
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195 <element name="part_L">
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196 <assert_contents>
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197 <has_n_lines min="10" />
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198 </assert_contents>
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199 </element>
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200 </output_collection>
2
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201 <output name='report'>
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202 <assert_contents>
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203 <has_n_lines n="0" />
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204 </assert_contents>
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205 </output>
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206 </test>
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207 <!--test missing fragments-->
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208 <test>
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209 <param name="input" value="test_missing_input.csv" />
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210 <conditional name="json_use">
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211 <param name='use_json_paramers' value='false' />
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212 <param name="table" value="sample" />
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213 <param name="sequence_column" value="sequence" />
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214 <param name="annotation_columns" value="annotation" />
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215 <param name="fragment_column" value="fragment" />
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216 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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217 </conditional>
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218 <output_collection name="output_gb" type="list" count="12">
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219 <element name="part_A">
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220 <assert_contents>
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221 <has_n_lines min="10" />
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222 </assert_contents>
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223 </element>
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224 <element name="part_B">
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225 <assert_contents>
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226 <has_n_lines min="10" />
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227 </assert_contents>
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228 </element>
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229 <element name="part_C">
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230 <assert_contents>
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231 <has_n_lines min="10" />
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232 </assert_contents>
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233 </element>
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234 <element name="part_D">
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235 <assert_contents>
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236 <has_n_lines min="10" />
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237 </assert_contents>
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238 </element>
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239 <element name="part_E">
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240 <assert_contents>
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241 <has_n_lines min="10" />
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242 </assert_contents>
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243 </element>
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244 <element name="part_F">
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245 <assert_contents>
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246 <has_n_lines min="10" />
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247 </assert_contents>
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248 </element>
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249 <element name="part_G">
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250 <assert_contents>
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251 <has_n_lines min="10" />
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252 </assert_contents>
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253 </element>
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254 <element name="part_H">
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255 <assert_contents>
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256 <has_n_lines min="10" />
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257 </assert_contents>
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258 </element>
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259 <element name="part_I">
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260 <assert_contents>
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261 <has_n_lines min="10" />
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262 </assert_contents>
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263 </element>
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264 <element name="part_J">
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265 <assert_contents>
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266 <has_n_lines min="10" />
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267 </assert_contents>
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268 </element>
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269 <element name="part_K">
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270 <assert_contents>
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271 <has_n_lines min="10" />
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272 </assert_contents>
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273 </element>
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274 <element name="part_L">
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275 <assert_contents>
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276 <has_n_lines min="10" />
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277 </assert_contents>
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278 </element>
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279 </output_collection>
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280 <output name='report'>
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281 <assert_contents>
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282 <has_n_lines n="6" />
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283 <has_line_matching expression="ACP10001AaCbbBS" />
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284 <has_line_matching expression="NEW20001BbDccKT" />
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285 <has_line_matching expression="XYZ10003AaCbbBS" />
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286 <has_line_matching expression="CFP10002AaCbbBS" />
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287 <has_line_matching expression="ALT30005CcEddLM" />
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288 <has_line_matching expression="QWE10004AaCbbBS" />
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289 </assert_contents>
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290 </output>
0
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291 </test>
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292 </tests>
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293
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294 <help><![CDATA[
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295 Get sequences Data From DB
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296 ==========================
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297
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298 Implemented a system to generate GenBank (.gb) files for ADN fragments in CSV input, based on data retrieved from an accessible database via URI requests.
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299
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300 **Parameters**:
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301 ---------------
1
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302 * **Use parameters from JSON**: Yes/No parameter to ask user if he wants to set parameters manually or using JSON file.
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303 * **Input CSV File**: Assembly CSV contains construct IDs in the first column and their corresponding fragments in the following columns. (Without Header)
0
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304 * **DB Table Name**: Name of the target table in the database.
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305 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
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306 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, starting with "FEATURES" and including "LOCUS" information. Other metadata is optional.
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307 * **DB IDs Column Name**: Column holding the unique fragment IDs.
1
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308 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user_name:pass@localhost:5432/test_fragments_db).
0
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309 ]]></help>
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310 <citations>
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311 <citation type="bibtex">
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312 @unpublished{seq_form_db
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313 author = {Ramiz Khaled},
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314 title = {{seq_form_db}},
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315 url = {https://github.com/brsynth/},
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316 }
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317 </citation>
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318 </citations>
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319 </tool>