Mercurial > repos > tduigou > get_db_info

comparison get_DB_data.xml @ 4:61158f32e5c3 draft

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 18 Apr 2025 09:56:13 +0000
parents 72e99f02308e
children a52626182172
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3:72e99f02308e 4:61158f32e5c3
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="2.2.3">pandas</requirement> 8 <requirement type="package" version="2.2.3">pandas</requirement>
9 <requirement type="package" version="2.0.40">sqlalchemy</requirement> 9 <requirement type="package" version="2.0.40">sqlalchemy</requirement>
10 <requirement type="package" version="2.9.9">psycopg2</requirement> 10 <requirement type="package" version="2.9.9">psycopg2</requirement>
11 <requirement type="package" version="1.85">biopython</requirement>
11 </requirements> 12 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
13 python '$__tool_directory__/get_db_info.py' 14 mkdir 'outdir' &&
15 python '$__tool_directory__/get_db_info.py'
14 --input '$input' 16 --input '$input'
17 --sequence_column '$sequence_column'
18 --annotation_columns '$annotation_columns'
15 --db_uri '$db_uri' 19 --db_uri '$db_uri'
16 --table '$table' 20 --table '$table'
17 --fragment_column '$fragment_column' 21 --fragment_column '$fragment_column'
18 --output '$output' 22 --output 'outdir'
23 --output_missing '$output_missing'
19 ]]></command> 24 ]]></command>
20 <inputs> 25 <inputs>
21 <param name="input" type="data" format="csv" label="Input CSV file" /> 26 <param name="input" type="data" format="csv" label="Input CSV file" />
22 <param name="table" type="text" label="Database Table Name" optional="false" /> 27 <param name="table" type="text" label="Database Table Name" optional="false" />
28 <param name="sequence_column" type="text" label="DB column contains sequence for ganbank file" />
29 <param name="annotation_columns" type="text" label="DB column contains annotation for ganbank file" />
23 <param name="fragment_column" type="text" label="Database Fragments Column Name" optional="false" /> 30 <param name="fragment_column" type="text" label="Database Fragments Column Name" optional="false" />
24 <param name="db_uri" type="text" label="Database Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" /> 31 <param name="db_uri" type="text" label="Database Connection URI" help="postgresql+psycopg2://username:password@db_container_name:port/database" optional="false" />
25 </inputs> 32 </inputs>
26 <outputs> 33 <outputs>
27 <data name="output" format="json" label="DB Annotated Fragments (json)"> 34 <collection name="output_gb" type="list" label="GenBank Files collection" >
35 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" />
36 </collection>
37 <data name="output_missing" format="txt" label="DB Missing Fragments (txt)">
28 </data> 38 </data>
29 </outputs> 39 </outputs>
30 <!--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'-->
31 <tests> 40 <tests>
41 <!--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' -output_missing 'test-data/output.txt'-->
32 <test> 42 <test>
33 <param name="input" value="test_input.csv" /> 43 <param name="input" value="test_input.csv" />
34 <param name="table" value="sample" /> 44 <param name="table" value="sample" />
45 <param name="sequence_column" value="sequence" />
46 <param name="annotation_columns" value="annotation" />
35 <param name="fragment_column" value="fragment" /> 47 <param name="fragment_column" value="fragment" />
36 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" /> 48 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
37 <output name="output" file="output_annotations.json" ftype="json" /> 49 <output_collection name="output_gb" type="list" count="4">
50 <element name="ACP10001AaCbbBS">
51 <assert_contents>
52 <has_n_lines min="3" />
53 </assert_contents>
54 </element>
55 <element name="CFP10002AaCbbBS">
56 <assert_contents>
57 <has_n_lines min="3" />
58 </assert_contents>
59 </element>
60 <element name="QWE10004AaCbbBS">
61 <assert_contents>
62 <has_n_lines min="3" />
63 </assert_contents>
64 </element>
65 <element name="XYZ10003AaCbbBS">
66 <assert_contents>
67 <has_n_lines min="3" />
68 </assert_contents>
69 </element>
70 </output_collection>
71 </test>
72 <!--python get_db_info.py -input 'test-data/test_missing_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' -output_missing 'test-data/output.txt'-->
73 <test>
74 <param name="input" value="test_missing_input.csv" />
75 <param name="table" value="sample" />
76 <param name="sequence_column" value="sequence" />
77 <param name="annotation_columns" value="annotation" />
78 <param name="fragment_column" value="fragment" />
79 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
80 <output name="output_missing" file="output_annotations.txt" ftype="txt" />
38 </test> 81 </test>
39 </tests> 82 </tests>
83
40 <help><![CDATA[ 84 <help><![CDATA[
41 Pick Data From DB 85 Pick Data From DB
42 =================== 86 ===================
43 87
44 DBget data from SQL DB in docker container. 88 DBget data from SQL DB in docker container.