Mercurial > repos > tduigou > get_db_info

comparison get_DB_data.xml @ 7:8984fabea52c draft

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 18 Apr 2025 13:04:32 +0000
parents 56a0938d534d
children 87585c392228
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6:56a0938d534d 7:8984fabea52c
20 --table '$table' 20 --table '$table'
21 --fragment_column '$fragment_column' 21 --fragment_column '$fragment_column'
22 --output 'outdir' 22 --output 'outdir'
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param name="input" type="data" format="csv" label="Input CSV file" /> 25 <param name="input" type="data" format="tsv" label="Input TSV file" />
26 <param name="table" type="text" label="Database Table Name" optional="false" /> 26 <param name="table" type="text" label="Database Table Name" optional="false" />
27 <param name="sequence_column" type="text" label="DB column contains sequence for ganbank file" optional="false" /> 27 <param name="sequence_column" type="text" label="DB column contains sequence for ganbank file" optional="false" />
28 <param name="annotation_columns" type="text" label="DB column contains annotation for ganbank file" optional="false" /> 28 <param name="annotation_columns" type="text" label="DB column contains annotation for ganbank file" optional="false" />
29 <param name="fragment_column" type="text" label="Database Fragments Column Name" optional="false" /> 29 <param name="fragment_column" type="text" label="Database Fragments Column Name" optional="false" />
30 <param name="db_uri" type="text" label="Database Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" /> 30 <param name="db_uri" type="text" label="Database Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
33 <collection name="output_gb" type="list" label="GenBank Files collection" > 33 <collection name="output_gb" type="list" label="GenBank Files collection" >
34 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" /> 34 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" />
35 </collection> 35 </collection>
36 </outputs> 36 </outputs>
37 <tests> 37 <tests>
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'--> 38 <!--python get_db_info.py -input 'test-data/test_input.tsv' -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'-->
39 <test> 39 <test>
40 <param name="input" value="test_input.csv" /> 40 <param name="input" value="test_input.tsv" />
41 <param name="table" value="sample" /> 41 <param name="table" value="sample" />
42 <param name="sequence_column" value="sequence" /> 42 <param name="sequence_column" value="sequence" />
43 <param name="annotation_columns" value="annotation" /> 43 <param name="annotation_columns" value="annotation" />
44 <param name="fragment_column" value="fragment" /> 44 <param name="fragment_column" value="fragment" />
45 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" /> 45 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
70 70
71 <help><![CDATA[ 71 <help><![CDATA[
72 Pick Data From DB 72 Pick Data From DB
73 =================== 73 ===================
74 74
75 generate GanDank files from csv file based on SQL DB. 75 generate GanDank files from tsv file based on SQL DB.
76 ]]></help> 76 ]]></help>
77 <citations> 77 <citations>
78 <citation type="bibtex"> 78 <citation type="bibtex">
79 @unpublished{get_DB_data 79 @unpublished{get_DB_data
80 author = {Ramiz Khaled}, 80 author = {Ramiz Khaled},