Mercurial > repos > tduigou > json_db_config_generating

comparison json_db_config_generating.xml @ 1:2909e53fac5b draft

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 02 Jun 2025 14:54:24 +0000
parents 95757ea6c333
children 33ebf3ea3eb6
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0:95757ea6c333 1:2909e53fac5b
10 'JSON_db_uri': '$db_uri', 10 'JSON_db_uri': '$db_uri',
11 'JSON_table': '$table_name', 11 'JSON_table': '$table_name',
12 'JSON_fragment_column': '$fragment_column', 12 'JSON_fragment_column': '$fragment_column',
13 'JSON_sequence_column': '$sequence_column', 13 'JSON_sequence_column': '$sequence_column',
14 'JSON_annotation_column': '$annotation_column' 14 'JSON_annotation_column': '$annotation_column'
15 }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" 15 }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json'
16 ]]></command> 16 ]]></command>
17 <inputs> 17 <inputs>
18 <param name="execution" type="boolean" label="execution key" checked="False" help="If True the execution key in the json file will be true" optional="true" /> 18 <conditional name="db_request">
19 <param name="db_uri" type="text" label="DB Connection URI" optional="true" /> 19 <param name="execution" type="select" label="Save To DB ?" help="If True the execution key in the json file will be true" optional="false">
20 <param name="table_name" type="text" label="DB Table Name" optional="true" /> 20 <option value="false" selected="True">NO</option>
21 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" /> 21 <option value="true">YES</option>
22 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" /> 22 </param>
23 <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" /> 23 <when value='true'>
24 <section name='db_config' title='DB config' expanded='true'>
25 <param name="db_uri" type="text" label="DB Connection URI" optional="true" />
26 <param name="table_name" type="text" label="DB Table Name" optional="true" />
27 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" />
28 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" />
29 <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" />
30 </section>
31 </when>
32 <when value='false'>
33 <section name='db_config' title='DB config' expanded='false'>
34 <param name="db_uri" type="text" label="DB Connection URI" optional="true" />
35 <param name="table_name" type="text" label="DB Table Name" optional="true" />
36 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" />
37 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" />
38 <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" />
39 </section>
40 </when>
41 </conditional>
24 </inputs> 42 </inputs>
25 <outputs> 43 <outputs>
26 <data name="output_json" format="json" label="JSON Conf" /> 44 <data name="output_json" format="json" label="JSON Conf" />
27 </outputs> 45 </outputs>
28 <tests> 46 <tests>
29 <!--test execution is true --> 47 <!--test execution is true -->
30 <test> 48 <test>
31 <param name="execution" value="True" /> 49 <conditional name="db_request">
32 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" /> 50 <param name="execution" value="true" />
33 <param name="table_name" value="sample" /> 51 <param name="db_config|db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
34 <param name="fragment_column" value="fragment" /> 52 <param name="db_config|table_name" value="sample" />
35 <param name="sequence_column" value="sequence" /> 53 <param name="db_config|fragment_column" value="fragment" />
36 <param name="annotation_column" value="annotation" /> 54 <param name="db_config|sequence_column" value="sequence" />
55 <param name="db_config|annotation_column" value="annotation" />
56 </conditional>
37 <output name="output_json"> 57 <output name="output_json">
38 <assert_contents> 58 <assert_contents>
39 <has_json_property_with_text property="execution" text="true" /> 59 <has_json_property_with_text property="execution" text="true" />
40 <has_json_property_with_text property="JSON_db_uri" text="postgresql://postgres:RK17__at__localhost:5432/test_fragments_db" /> 60 <has_json_property_with_text property="JSON_db_uri" text="postgresql://postgres:RK17__at__localhost:5432/test_fragments_db" />
41 <has_json_property_with_text property="JSON_table" text="sample" /> 61 <has_json_property_with_text property="JSON_table" text="sample" />
45 </assert_contents> 65 </assert_contents>
46 </output> 66 </output>
47 </test> 67 </test>
48 <!--test execution is false --> 68 <!--test execution is false -->
49 <test> 69 <test>
50 <param name="execution" value="False" /> 70 <conditional name="db_request">
51 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" /> 71 <param name="execution" value="false" />
52 <param name="table_name" value="sample" /> 72 </conditional>
53 <param name="fragment_column" value="fragment" />
54 <param name="sequence_column" value="sequence" />
55 <param name="annotation_column" value="annotation" />
56 <output name="output_json"> 73 <output name="output_json">
57 <assert_contents> 74 <assert_contents>
58 <has_json_property_with_text property="execution" text="false" /> 75 <has_json_property_with_text property="execution" text="false" />
59 <has_json_property_with_text property="JSON_db_uri" text="postgresql://postgres:RK17__at__localhost:5432/test_fragments_db" /> 76 <has_json_property_with_text property="JSON_db_uri" text="" />
60 <has_json_property_with_text property="JSON_table" text="sample" /> 77 <has_json_property_with_text property="JSON_table" text="" />
61 <has_json_property_with_text property="JSON_fragment_column" text="fragment" /> 78 <has_json_property_with_text property="JSON_fragment_column" text="" />
62 <has_json_property_with_text property="JSON_sequence_column" text="sequence" /> 79 <has_json_property_with_text property="JSON_sequence_column" text="" />
63 <has_json_property_with_text property="JSON_annotation_column" text="annotation" /> 80 <has_json_property_with_text property="JSON_annotation_column" text="" />
64 </assert_contents> 81 </assert_contents>
65 </output> 82 </output>
66 </test> 83 </test>
67 </tests> 84 </tests>
68 85