Mercurial > repos > tduigou > get_db_info

annotate get_DB_data.xml @ 12:ee28ec28140d draft

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author tduigou
date Fri, 23 May 2025 12:45:20 +0000
parents 6c1e564bb278
children 5b16f2911491
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1 <tool id="get_DB_data" name="Get Data From DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Import GenBank data from a PostgreSQL database running in a Docker container and export it as .gb files</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@TOOL_VERSION@">0.1.0</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 --sequence_column '$sequence_column'
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18 --annotation_columns '$annotation_columns'
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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 'outdir'
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23 ]]></command>
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24 <inputs>
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25 <param name="input" type="data" format="csv" label="Input CSV File" />
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26 <param name="table" type="text" label="DB Table Name" optional="false" />
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27 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="false" />
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28 <param name="annotation_columns" type="text" label="DB Column Contains Annotation For Ganbank File" optional="false" />
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29 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="false" />
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30 <param name="db_uri" type="text" label="DB Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
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31 </inputs>
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32 <outputs>
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33 <collection name="output_gb" type="list" label="GenBank Files collection" >
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34 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" />
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35 </collection>
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36 </outputs>
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37 <tests>
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38 <!--python get_db_info.py -input 'test-data/test_input.csv' -sequence_column 'sequence' -annotation_column 'annotation' -db_uri 'postgresql://postgres:RK17@localhost:5432/test_fragments_db' -table 'sample' -fragment_column 'fragment' -output 'test-data/output'-->
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39 <test>
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40 <param name="input" value="test_input.csv" />
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41 <param name="table" value="sample" />
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42 <param name="sequence_column" value="sequence" />
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43 <param name="annotation_columns" value="annotation" />
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44 <param name="fragment_column" value="fragment" />
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45 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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46 <output_collection name="output_gb" type="list" count="4">
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47 <element name="ACP10001AaCbbBS">
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48 <assert_contents>
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49 <has_n_lines min="3" />
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50 </assert_contents>
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51 </element>
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52 <element name="CFP10002AaCbbBS">
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53 <assert_contents>
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54 <has_n_lines min="3" />
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55 </assert_contents>
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56 </element>
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57 <element name="QWE10004AaCbbBS">
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58 <assert_contents>
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59 <has_n_lines min="3" />
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60 </assert_contents>
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61 </element>
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62 <element name="XYZ10003AaCbbBS">
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63 <assert_contents>
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64 <has_n_lines min="3" />
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65 </assert_contents>
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66 </element>
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67 </output_collection>
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68 </test>
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69 </tests>
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70
0
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71 <help><![CDATA[
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72 Get Data From DB
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73 ===================
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74
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75 Implemented a system to generate GenBank (.gb) files from CSV input, based on data retrieved from a PostgreSQL database via URI requests.
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76 The tool is tested on a locally hosted PostgreSQL database running in a Docker container.
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77
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78 **Parameters**:
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79 ---------------
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80 * **Input CSV File**: Contains construct IDs in the first column and their corresponding fragments in the following columns. (Without Header)
10
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81 * **DB Table Name**: Name of the target table in the PostgreSQL database.
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82 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
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83 * **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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84 * **DB IDs Column Name**: Column holding the unique fragment IDs.
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85 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name).
0
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86 ]]></help>
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87 <citations>
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88 <citation type="bibtex">
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89 @unpublished{get_DB_data
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90 author = {Ramiz Khaled},
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91 title = {{get_DB_data}},
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92 url = {https://github.com/brsynth/},
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93 }
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94 </citation>
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95 </citations>
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96 </tool>