Mercurial > repos > tduigou > seq_from_db

annotate seq_form_db.xml @ 1:54e716c11b71 draft

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author tduigou
date Tue, 29 Jul 2025 12:01:32 +0000
parents 934050a8037e
children 3bb9bbecae97
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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>
1
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4 <token name="@VERSION_SUFFIX@">2</token>
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5 <token name="@TOOL_VERSION@">0.3.0</token>
0
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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 '$json_use.json_conf'
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26 #end if
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27 --output 'outdir'
1
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28 --report '$report'
0
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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>
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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>
1
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50 <data name='report' format='txt' label='text report' />
0
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51 </outputs>
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52 <tests>
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53 <!--manual parameters-->
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54 <test>
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55 <param name="input" value="2-step-golden_gate_plan.csv" />
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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>
1
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126 <output name='report'>
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127 <assert_contents>
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128 <has_n_lines n="1" />
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129 <has_line_matching expression="NO missing fragments in DB" />
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130 </assert_contents>
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131 </output>
0
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132 </test>
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133 <!--JSON parameters-->
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134 <test>
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135 <param name="input" value="2-step-golden_gate_plan.csv" />
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136 <conditional name="json_use">
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137 <param name="use_json_paramers" value='true'/>
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138 <param name="json_conf" value="test-JSON.json" />
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139 </conditional>
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140 <output_collection name="output_gb" type="list" count="12">
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141 <element name="part_A">
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142 <assert_contents>
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143 <has_n_lines min="10" />
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144 </assert_contents>
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145 </element>
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146 <element name="part_B">
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147 <assert_contents>
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148 <has_n_lines min="10" />
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149 </assert_contents>
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150 </element>
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151 <element name="part_C">
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152 <assert_contents>
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153 <has_n_lines min="10" />
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154 </assert_contents>
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155 </element>
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156 <element name="part_D">
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157 <assert_contents>
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158 <has_n_lines min="10" />
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159 </assert_contents>
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160 </element>
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161 <element name="part_E">
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162 <assert_contents>
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163 <has_n_lines min="10" />
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164 </assert_contents>
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165 </element>
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166 <element name="part_F">
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167 <assert_contents>
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168 <has_n_lines min="10" />
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169 </assert_contents>
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170 </element>
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171 <element name="part_G">
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172 <assert_contents>
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173 <has_n_lines min="10" />
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174 </assert_contents>
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175 </element>
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176 <element name="part_H">
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177 <assert_contents>
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178 <has_n_lines min="10" />
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179 </assert_contents>
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180 </element>
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181 <element name="part_I">
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182 <assert_contents>
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183 <has_n_lines min="10" />
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184 </assert_contents>
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185 </element>
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186 <element name="part_J">
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187 <assert_contents>
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188 <has_n_lines min="10" />
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189 </assert_contents>
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190 </element>
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191 <element name="part_K">
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192 <assert_contents>
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193 <has_n_lines min="10" />
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194 </assert_contents>
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195 </element>
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196 <element name="part_L">
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197 <assert_contents>
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198 <has_n_lines min="10" />
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199 </assert_contents>
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200 </element>
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201 </output_collection>
1
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202 <output name='report'>
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203 <assert_contents>
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204 <has_n_lines n="1" />
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205 <has_line_matching expression="NO missing fragments in DB" />
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206 </assert_contents>
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207 </output>
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208 </test>
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209 <!--test missing fragments-->
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210 <test>
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211 <param name="input" value="test_missing_input.csv" />
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212 <conditional name="json_use">
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213 <param name='use_json_paramers' value='false' />
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214 <param name="table" value="sample" />
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215 <param name="sequence_column" value="sequence" />
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216 <param name="annotation_columns" value="annotation" />
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217 <param name="fragment_column" value="fragment" />
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218 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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219 </conditional>
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220 <output_collection name="output_gb" type="list" count="12">
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221 <element name="part_A">
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222 <assert_contents>
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223 <has_n_lines min="10" />
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224 </assert_contents>
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225 </element>
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226 <element name="part_B">
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227 <assert_contents>
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228 <has_n_lines min="10" />
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229 </assert_contents>
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230 </element>
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231 <element name="part_C">
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232 <assert_contents>
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233 <has_n_lines min="10" />
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234 </assert_contents>
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235 </element>
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236 <element name="part_D">
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237 <assert_contents>
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238 <has_n_lines min="10" />
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239 </assert_contents>
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240 </element>
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241 <element name="part_E">
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242 <assert_contents>
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243 <has_n_lines min="10" />
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244 </assert_contents>
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245 </element>
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246 <element name="part_F">
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247 <assert_contents>
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248 <has_n_lines min="10" />
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249 </assert_contents>
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250 </element>
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251 <element name="part_G">
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252 <assert_contents>
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253 <has_n_lines min="10" />
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254 </assert_contents>
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255 </element>
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256 <element name="part_H">
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257 <assert_contents>
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258 <has_n_lines min="10" />
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259 </assert_contents>
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260 </element>
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261 <element name="part_I">
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262 <assert_contents>
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263 <has_n_lines min="10" />
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264 </assert_contents>
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265 </element>
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266 <element name="part_J">
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267 <assert_contents>
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268 <has_n_lines min="10" />
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269 </assert_contents>
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270 </element>
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271 <element name="part_K">
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272 <assert_contents>
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273 <has_n_lines min="10" />
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274 </assert_contents>
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275 </element>
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276 <element name="part_L">
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277 <assert_contents>
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278 <has_n_lines min="10" />
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279 </assert_contents>
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280 </element>
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281 </output_collection>
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282 <output name='report'>
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283 <assert_contents>
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284 <has_n_lines n="7" />
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285 <has_line_matching expression="Missing fragment in DB:" />
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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 ---------------
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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)
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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.
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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).
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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>