Mercurial > repos > tduigou > seq_from_db

annotate seq_form_db.xml @ 3:46f629f79f55 draft default tip

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author tduigou
date Tue, 06 Jan 2026 11:48:06 +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 $json_use.use_json_paramers=='false':
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19 --sequence_column '$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="select" checked='false' label="Use parameters from JSON" help="extract parameters from json file">
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34 <option value="true">Get Parameters From JSON</option>
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35 <option value="false" selected="true">Set Parameters Manually</option>
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36 </param>
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37 <when value="false">
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38 <param name="table" type="text" label="DB Table Name" optional="false" />
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39 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="false" />
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40 <param name="annotation_columns" type="text" label="DB Column Contains Annotation For Ganbank File" optional="false" />
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41 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="false" />
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42 <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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43 </when>
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44 <when value="true">
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45 <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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46 </when>
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47 </conditional>
0
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48 </inputs>
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49 <outputs>
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50 <collection name="output_gb" type="list" label="GenBank Files collection" >
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51 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" />
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52 </collection>
2
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53 <data name='report' format='txt' label='missing fragments' />
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54 </outputs>
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55 <tests>
1
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56 <!--manual parameters-->
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57 <test>
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58 <param name="input" value="2-step-golden_gate_plan.csv" />
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59 <conditional name="json_use">
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60 <param name='use_json_paramers' value='false' />
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61 <param name="table" value="sample" />
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62 <param name="sequence_column" value="sequence" />
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63 <param name="annotation_columns" value="annotation" />
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64 <param name="fragment_column" value="fragment" />
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65 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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66 </conditional>
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67 <output_collection name="output_gb" type="list" count="12">
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68 <element name="part_A">
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69 <assert_contents>
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70 <has_n_lines min="10" />
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71 </assert_contents>
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72 </element>
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73 <element name="part_B">
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74 <assert_contents>
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75 <has_n_lines min="10" />
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76 </assert_contents>
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77 </element>
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78 <element name="part_C">
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79 <assert_contents>
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80 <has_n_lines min="10" />
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81 </assert_contents>
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82 </element>
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83 <element name="part_D">
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84 <assert_contents>
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85 <has_n_lines min="10" />
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86 </assert_contents>
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87 </element>
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88 <element name="part_E">
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89 <assert_contents>
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90 <has_n_lines min="10" />
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91 </assert_contents>
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92 </element>
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93 <element name="part_F">
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94 <assert_contents>
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95 <has_n_lines min="10" />
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96 </assert_contents>
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97 </element>
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98 <element name="part_G">
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99 <assert_contents>
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100 <has_n_lines min="10" />
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101 </assert_contents>
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102 </element>
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103 <element name="part_H">
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104 <assert_contents>
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105 <has_n_lines min="10" />
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106 </assert_contents>
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107 </element>
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108 <element name="part_I">
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109 <assert_contents>
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110 <has_n_lines min="10" />
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111 </assert_contents>
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112 </element>
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113 <element name="part_J">
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114 <assert_contents>
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115 <has_n_lines min="10" />
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116 </assert_contents>
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117 </element>
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118 <element name="part_K">
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119 <assert_contents>
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120 <has_n_lines min="10" />
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121 </assert_contents>
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122 </element>
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123 <element name="part_L">
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124 <assert_contents>
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125 <has_n_lines min="10" />
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126 </assert_contents>
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127 </element>
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128 </output_collection>
2
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129 <output name='report'>
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130 <assert_contents>
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131 <has_n_lines n="0" />
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132 </assert_contents>
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133 </output>
1
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134 </test>
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135 <!--JSON parameters-->
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136 <test>
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137 <param name="input" value="2-step-golden_gate_plan.csv" />
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138 <conditional name="json_use">
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139 <param name="use_json_paramers" value='true'/>
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140 <param name="json_conf" value="test-JSON.json" />
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141 </conditional>
0
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142 <output_collection name="output_gb" type="list" count="12">
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143 <element name="part_A">
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144 <assert_contents>
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145 <has_n_lines min="10" />
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146 </assert_contents>
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147 </element>
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148 <element name="part_B">
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149 <assert_contents>
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150 <has_n_lines min="10" />
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151 </assert_contents>
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152 </element>
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153 <element name="part_C">
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154 <assert_contents>
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155 <has_n_lines min="10" />
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156 </assert_contents>
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157 </element>
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158 <element name="part_D">
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159 <assert_contents>
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160 <has_n_lines min="10" />
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161 </assert_contents>
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162 </element>
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163 <element name="part_E">
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164 <assert_contents>
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165 <has_n_lines min="10" />
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166 </assert_contents>
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167 </element>
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168 <element name="part_F">
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169 <assert_contents>
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170 <has_n_lines min="10" />
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171 </assert_contents>
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172 </element>
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173 <element name="part_G">
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174 <assert_contents>
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175 <has_n_lines min="10" />
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176 </assert_contents>
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177 </element>
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178 <element name="part_H">
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179 <assert_contents>
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180 <has_n_lines min="10" />
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181 </assert_contents>
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182 </element>
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183 <element name="part_I">
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184 <assert_contents>
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185 <has_n_lines min="10" />
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186 </assert_contents>
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187 </element>
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188 <element name="part_J">
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189 <assert_contents>
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190 <has_n_lines min="10" />
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191 </assert_contents>
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192 </element>
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193 <element name="part_K">
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194 <assert_contents>
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195 <has_n_lines min="10" />
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196 </assert_contents>
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197 </element>
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198 <element name="part_L">
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199 <assert_contents>
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200 <has_n_lines min="10" />
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201 </assert_contents>
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202 </element>
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203 </output_collection>
2
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204 <output name='report'>
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205 <assert_contents>
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206 <has_n_lines n="0" />
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207 </assert_contents>
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208 </output>
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209 </test>
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210 <!--test missing fragments-->
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211 <test>
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212 <param name="input" value="test_missing_input.csv" />
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213 <conditional name="json_use">
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214 <param name='use_json_paramers' value='false' />
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215 <param name="table" value="sample" />
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216 <param name="sequence_column" value="sequence" />
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217 <param name="annotation_columns" value="annotation" />
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218 <param name="fragment_column" value="fragment" />
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219 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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220 </conditional>
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221 <output_collection name="output_gb" type="list" count="12">
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222 <element name="part_A">
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223 <assert_contents>
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224 <has_n_lines min="10" />
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225 </assert_contents>
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226 </element>
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227 <element name="part_B">
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228 <assert_contents>
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229 <has_n_lines min="10" />
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230 </assert_contents>
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231 </element>
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232 <element name="part_C">
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233 <assert_contents>
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234 <has_n_lines min="10" />
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235 </assert_contents>
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236 </element>
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237 <element name="part_D">
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238 <assert_contents>
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239 <has_n_lines min="10" />
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240 </assert_contents>
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241 </element>
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242 <element name="part_E">
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243 <assert_contents>
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244 <has_n_lines min="10" />
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245 </assert_contents>
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246 </element>
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247 <element name="part_F">
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248 <assert_contents>
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249 <has_n_lines min="10" />
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250 </assert_contents>
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251 </element>
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252 <element name="part_G">
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253 <assert_contents>
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254 <has_n_lines min="10" />
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255 </assert_contents>
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256 </element>
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257 <element name="part_H">
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258 <assert_contents>
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259 <has_n_lines min="10" />
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260 </assert_contents>
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261 </element>
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262 <element name="part_I">
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263 <assert_contents>
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264 <has_n_lines min="10" />
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265 </assert_contents>
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266 </element>
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267 <element name="part_J">
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268 <assert_contents>
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269 <has_n_lines min="10" />
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270 </assert_contents>
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271 </element>
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272 <element name="part_K">
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273 <assert_contents>
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274 <has_n_lines min="10" />
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275 </assert_contents>
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276 </element>
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277 <element name="part_L">
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278 <assert_contents>
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279 <has_n_lines min="10" />
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280 </assert_contents>
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281 </element>
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282 </output_collection>
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283 <output name='report'>
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284 <assert_contents>
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285 <has_n_lines n="6" />
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286 <has_line_matching expression="ACP10001AaCbbBS" />
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287 <has_line_matching expression="NEW20001BbDccKT" />
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288 <has_line_matching expression="XYZ10003AaCbbBS" />
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289 <has_line_matching expression="CFP10002AaCbbBS" />
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290 <has_line_matching expression="ALT30005CcEddLM" />
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291 <has_line_matching expression="QWE10004AaCbbBS" />
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292 </assert_contents>
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293 </output>
0
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294 </test>
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295 </tests>
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296
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297 <help><![CDATA[
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298 Get sequences Data From DB
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299 ==========================
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300
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301 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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302
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303 **Parameters**:
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304 ---------------
1
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305 * **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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306 * **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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307 * **DB Table Name**: Name of the target table in the database.
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308 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
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309 * **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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310 * **DB IDs Column Name**: Column holding the unique fragment IDs.
1
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311 * **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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312 ]]></help>
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313 <citations>
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314 <citation type="bibtex">
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315 @unpublished{seq_form_db
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316 author = {Ramiz Khaled},
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317 title = {{seq_form_db}},
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318 url = {https://github.com/brsynth/},
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319 }
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320 </citation>
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321 </citations>
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322 </tool>