Mercurial > repos > tduigou > seq_to_db

annotate seq_to_db.xml @ 0:178d068648f4 draft

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
author tduigou
date Thu, 12 Jun 2025 08:27:18 +0000
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children 5db1c2b9edb8
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178d068648f4 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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1 <tool id="seq_to_db" name="Save Sequence Data In DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Save fragment's sequence in an accessible database and import it from .gb files</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">1</token>
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5 <token name="@TOOL_VERSION@">0.2.0</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 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
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14 #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
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15 python '$__tool_directory__/save_to_db.py'
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16 --input '$genbank_file_paths'
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17 --sequence_column '$sequence_column'
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18 --annotation_column '$annotation_column'
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19 --db_uri '$db_uri'
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20 --table '$table'
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21 --fragment_column '$fragment_column'
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22 --output '$output'
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23 --file_name_mapping '$file_name_mapping'
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24 --json_conf '$json_conf'
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25 --execution_enable '$execution_enable'
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26 ]]></command>
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27 <inputs>
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28 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
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29 <param name="table" type="text" label="DB Table Name" optional="true" help="It can be extracted from JSON file -key:'JSON_table'-" />
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30 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" help="It can be extracted from JSON file -key:'JSON_sequence_column'-" />
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31 <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" help="It can be extracted from JSON file -key:'JSON_annotation_column'-" />
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32 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" help="It can be extracted from JSON file -key:'JSON_fragment_column'-" />
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33 <param name="db_uri" type="text" label="DB Connection URI" help="postgresql://(user_name or container_name):password@host:port/path/to/database (It can be extracted from JSON file -key:'JSON_db_uri'-)" optional="true" />
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34 <section name='adv' title='Advance' expanded='false'>
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35 <param name="execution_enable" type="boolean" checked='true' label="Send Requenst to DB" help="enable or desable the interaction with the DB (can be usefull in workflows)" />
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36 <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="true" />
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37 </section>
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38 </inputs>
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39 <outputs>
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40 <data name="output" format="txt" label="saving report" />
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41 </outputs>
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42 <tests>
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43 <!--test tool blocking from galaxy. It is commented because it should faild as it is a test to validate that the tool can be blocked from json file -->
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44 <test>
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45 <param name="genbank_files">
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46 <collection type="list">
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47 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
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48 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
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49 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
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50 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
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51 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
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52 </collection>
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53 </param>
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54 <param name="table" value="sample" />
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55 <param name="sequence_column" value="sequence" />
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56 <param name="annotation_column" value="annotation" />
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57 <param name="fragment_column" value="fragment" />
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58 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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59 <param name="adv|execution_enable" value="false" />
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60 <output name="output" file="test_raport.txt" ftype="txt" >
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61 <assert_contents>
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62 <has_n_lines n="5" />
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63 <has_line_matching expression="p7_L7Ae-Weiss" />
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64 <has_line_matching expression="p6_Nt-IgKLsequence" />
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65 <has_line_matching expression="p6_Kozak-ATG" />
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66 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
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67 <has_line_matching expression="HC_Amp_ccdB" />
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68 </assert_contents>
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69 </output>
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70 </test>
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71 <!--test tool blocking from JSON. It is commented because it should faild as it is a test to validate that the tool can be blocked from json file -->
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72 <test>
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73 <param name="genbank_files">
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74 <collection type="list">
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75 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
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76 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
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77 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
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78 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
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79 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
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80 </collection>
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81 </param>
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82 <param name="adv|json_conf" value="test-JSON_arg_block.json" />
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83 <output name="output" file="test_raport.txt" ftype="txt" >
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84 <assert_contents>
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85 <has_n_lines n="5" />
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86 <has_line_matching expression="p7_L7Ae-Weiss" />
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87 <has_line_matching expression="p6_Nt-IgKLsequence" />
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88 <has_line_matching expression="p6_Kozak-ATG" />
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89 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
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90 <has_line_matching expression="HC_Amp_ccdB" />
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91 </assert_contents>
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92 </output>
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93 </test>
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94 <!--Only 1 test can be execute because the fragment will be already saved for the second test and it will return error as the fragments are present in the DB (execut ../get_db_data/testMock.py to regenerate initial DB)-->
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95 <!--test DB config in the tool -->
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96 <test>
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97 <param name="genbank_files">
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98 <collection type="list">
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99 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
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100 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
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101 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
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102 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
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103 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
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104 </collection>
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105 </param>
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106 <param name="table" value="sample" />
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107 <param name="sequence_column" value="sequence" />
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108 <param name="annotation_column" value="annotation" />
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109 <param name="fragment_column" value="fragment" />
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110 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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111 <output name="output" file="test_raport.txt" ftype="txt" >
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112 <assert_contents>
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113 <has_n_lines n="5" />
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114 <has_line_matching expression="p7_L7Ae-Weiss" />
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115 <has_line_matching expression="p6_Nt-IgKLsequence" />
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116 <has_line_matching expression="p6_Kozak-ATG" />
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117 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
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118 <has_line_matching expression="HC_Amp_ccdB" />
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119 </assert_contents>
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120 </output>
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121 </test>
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122 <!--test DB config from JSON. It is commented because the save can be done only on time then the fragment willl be in the DB and it will return a failure. to run the test comment the test above (one saving test in the run)-->
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123 <test>
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124 <param name="genbank_files">
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125 <collection type="list">
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126 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
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127 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
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128 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
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129 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
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130 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
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131 </collection>
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132 </param>
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133 <param name="adv|json_conf" value="test-JSON_arg.json" />
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134 <output name="output" file="test_raport.txt" ftype="txt" >
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135 <assert_contents>
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136 <has_n_lines n="5" />
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137 <has_line_matching expression="p7_L7Ae-Weiss" />
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138 <has_line_matching expression="p6_Nt-IgKLsequence" />
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139 <has_line_matching expression="p6_Kozak-ATG" />
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140 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
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141 <has_line_matching expression="HC_Amp_ccdB" />
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142 </assert_contents>
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143 </output>
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144 </test>
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145 </tests>
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146
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147 <help><![CDATA[
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148 Save Sequence Data In DB
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149 ========================
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150
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151 Implemented a system to save GenBank (.gb) files in an accessible DB, based on a connection via URI requests.
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152
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153 **Parameters**:
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154 ---------------
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155 * **GenBank File(s)**: List of GenBaks files.
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156 * **DB Table Name**: Name of the target table in the PostgreSQL database.
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157 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
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158 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file.
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159 * **DB IDs Column Name**: Column holding the unique fragment IDs.
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160 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://postgres:pass@localhost:5432/test_fragments_db).
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161 * **Send Requenst to DB**: Enable or Desable the interaction with the DB (can be usefull in workflows).
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162 * **DB config as a json file**: JSON file contains the DB configuration:
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163 - "JSON_table": will be the key to the table name.
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164 - "JSON_sequence_column": will be the key to the sequence column.
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165 - "JSON_annotation_column": will be the key to the annotation column.
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166 - "JSON_fragment_column": will be the key to the fragment column.
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167 - "JSON_db_uri": will be the key to the URI.
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168 - "execution": It is the key to execute or block the tool during a workflow ("True" or "False").
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169 ]]></help>
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170 <citations>
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171 <citation type="bibtex">
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172 @unpublished{seq_to_db
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173 author = {Ramiz Khaled},
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174 title = {{seq_to_db}},
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175 url = {https://github.com/brsynth/},
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176 }
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177 </citation>
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178 </citations>
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179 </tool>