Mercurial > repos > tduigou > get_db_info

annotate get_DB_data.xml @ 0:41ac63b5d221 draft

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author tduigou
date Thu, 10 Apr 2025 08:45:18 +0000
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41ac63b5d221 planemo upload for repository https://github.com/brsynth commit 15dbdd1f0a222a8e1b0fb5c16b36885520a3d005
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1 <tool id="get_DB_data" name="get data from DB" version="0.1.0" profile="21.09">
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2 <description>Import data from Sorbonne Biofondry DB</description>
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3 <requirements>
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4 <requirement type="package" version="2.2.3">pandas</requirement>
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5 <requirement type="package" version="2.0.40">sqlalchemy</requirement>
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6 <requirement type="package" version="2.9.9">psycopg2</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 python '$__tool_directory__/get_db_info.py'
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10 --input '$input'
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11 --db_uri '$db_uri'
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12 --table '$table'
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13 --fragment_column '$fragment_column'
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14 --output '$output'
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15 ]]></command>
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16 <inputs>
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17 <param name="input" type="data" format="csv" label="Input CSV file" />
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18 <param name="table" type="text" label="Database Table Name" optional="false" />
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19 <param name="fragment_column" type="text" label="Database Fragments Column Name" optional="false" />
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20 <param name="db_uri" type="text" label="Database Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
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21 </inputs>
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22 <outputs>
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23 <data name="output" format="json" label="DB Annotated Fragments (json)">
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24 </data>
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25 </outputs>
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26 <!--python get_DB_info.py -input 'test-data/test_input.csv' -db_uri 'postgresql://postgres:RK17@localhost:5432/test_fragments_db' -table 'sample' -fragment_column 'fragment' -output 'test-data/output.json'-->
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27 <tests>
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28 <test>
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29 <param name="input" value="test_input.csv" />
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30 <param name="table" value="sample" />
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31 <param name="fragment_column" value="fragment" />
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32 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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33 <output name="output" file="output_annotations.json" ftype="json" />
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 Pick Data From DB
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38 ===================
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39
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40 DBget data from SQL DB in docker container.
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41 ]]></help>
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42 <citations>
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43 <citation type="bibtex">
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44 @unpublished{get_DB_data
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45 author = {Ramiz Khaled},
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46 title = {{get_DB_data}},
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47 url = {https://github.com/brsynth/},
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48 }
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49 </citation>
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50 </citations>
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51 </tool>