Mercurial > repos > tduigou > get_db_info

comparison get_DB_data.xml @ 6:56a0938d534d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 18 Apr 2025 12:52:49 +0000
parents a52626182172
children 8984fabea52c
comparison
equal deleted inserted replaced
5:a52626182172 6:56a0938d534d
18 --annotation_columns '$annotation_columns' 18 --annotation_columns '$annotation_columns'
19 --db_uri '$db_uri' 19 --db_uri '$db_uri'
20 --table '$table' 20 --table '$table'
21 --fragment_column '$fragment_column' 21 --fragment_column '$fragment_column'
22 --output 'outdir' 22 --output 'outdir'
23 --output_missing '$output_missing'
24 ]]></command> 23 ]]></command>
25 <inputs> 24 <inputs>
26 <param name="input" type="data" format="csv" label="Input CSV file" /> 25 <param name="input" type="data" format="csv" label="Input CSV file" />
27 <param name="table" type="text" label="Database Table Name" optional="false" /> 26 <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" optional="false" /> 27 <param name="sequence_column" type="text" label="DB column contains sequence for ganbank file" optional="false" />
32 </inputs> 31 </inputs>
33 <outputs> 32 <outputs>
34 <collection name="output_gb" type="list" label="GenBank Files collection" > 33 <collection name="output_gb" type="list" label="GenBank Files collection" >
35 <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" />
36 </collection> 35 </collection>
37 <data name="output_missing" format="txt" label="DB Missing Fragments (txt)">
38 </data>
39 </outputs> 36 </outputs>
40 <tests> 37 <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'--> 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'-->
42 <test> 39 <test>
43 <param name="input" value="test_input.csv" /> 40 <param name="input" value="test_input.csv" />
44 <param name="table" value="sample" /> 41 <param name="table" value="sample" />
45 <param name="sequence_column" value="sequence" /> 42 <param name="sequence_column" value="sequence" />
46 <param name="annotation_columns" value="annotation" /> 43 <param name="annotation_columns" value="annotation" />
67 <has_n_lines min="3" /> 64 <has_n_lines min="3" />
68 </assert_contents> 65 </assert_contents>
69 </element> 66 </element>
70 </output_collection> 67 </output_collection>
71 </test> 68 </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" />
81 </test>
82 </tests> 69 </tests>
83 70
84 <help><![CDATA[ 71 <help><![CDATA[
85 Pick Data From DB 72 Pick Data From DB
86 =================== 73 ===================
87 74
88 DBget data from SQL DB in docker container. 75 generate GanDank files from csv file based on SQL DB.
89 ]]></help> 76 ]]></help>
90 <citations> 77 <citations>
91 <citation type="bibtex"> 78 <citation type="bibtex">
92 @unpublished{get_DB_data 79 @unpublished{get_DB_data
93 author = {Ramiz Khaled}, 80 author = {Ramiz Khaled},