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comparison save_to_db.xml @ 5:f934215bdb78 draft default tip

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planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 02 Jun 2025 10:29:28 +0000
parents c7a7520afb4b
children
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4:c7a7520afb4b 5:f934215bdb78
37 <outputs> 37 <outputs>
38 <data name="output" format="txt" label="saving report" /> 38 <data name="output" format="txt" label="saving report" />
39 </outputs> 39 </outputs>
40 <tests> 40 <tests>
41 <!--Only 1 test can be execute because the fragment will be already saved for the second test and it will return error as the fragments are present in the DB (execut ../get_db_data/testMock.py to regenerate initial DB)--> 41 <!--Only 1 test can be execute because the fragment will be already saved for the second test and it will return error as the fragments are present in the DB (execut ../get_db_data/testMock.py to regenerate initial DB)-->
42 <!--test tool blocking from JSON -->
43 <test>
44 <param name="genbank_files">
45 <collection type="list">
46 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
47 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
48 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
49 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
50 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
51 </collection>
52 </param>
53 <param name="adv|json_conf" value="test-JSON_arg_block.json" />
54 <output name="output" file="test_raport.txt" ftype="txt" >
55 <assert_contents>
56 <has_n_lines n="5" />
57 <has_line_matching expression="p7_L7Ae-Weiss" />
58 <has_line_matching expression="p6_Nt-IgKLsequence" />
59 <has_line_matching expression="p6_Kozak-ATG" />
60 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
61 <has_line_matching expression="HC_Amp_ccdB" />
62 </assert_contents>
63 </output>
64 </test>
42 <!--test DB config in the tool --> 65 <!--test DB config in the tool -->
43 <test> 66 <test>
44 <param name="genbank_files"> 67 <param name="genbank_files">
45 <collection type="list"> 68 <collection type="list">
46 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" /> 69 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
88 <has_line_matching expression="HC_Amp_ccdB" /> 111 <has_line_matching expression="HC_Amp_ccdB" />
89 </assert_contents> 112 </assert_contents>
90 </output> 113 </output>
91 </test> 114 </test>
92 </tests> 115 </tests>
93 116
94 <help><![CDATA[ 117 <help><![CDATA[
95 Save Data To DB 118 Save Data To DB
96 =================== 119 ===================
97 120
98 Implemented a system to save GenBank (.gb) files in SQL DB, based on a connection via URI requests. 121 Implemented a system to save GenBank (.gb) files in SQL DB, based on a connection via URI requests.
104 * **DB Table Name**: Name of the target table in the PostgreSQL database. 127 * **DB Table Name**: Name of the target table in the PostgreSQL database.
105 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN". 128 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
106 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file. 129 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file.
107 * **DB IDs Column Name**: Column holding the unique fragment IDs. 130 * **DB IDs Column Name**: Column holding the unique fragment IDs.
108 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name). 131 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name).
132 * **DB config as a json file**: JSON file contains the DB configuration:
133 - "JSON_table": will be the key to the table name.
134 - "JSON_sequence_column": will be the key to the sequence column.
135 - "JSON_annotation_column": will be the key to the annotation column.
136 - "JSON_fragment_column": will be the key to the fragment column.
137 - "JSON_db_uri": will be the key to the URI.
138 - "execution": It is the key to execute or block the tool during a workflow ("True" or "False").
139 * NOTE: the JSON file can be generated using the json_db_config_generating tool.
109 ]]></help> 140 ]]></help>
110 <citations> 141 <citations>
111 <citation type="bibtex"> 142 <citation type="bibtex">
112 @unpublished{save_to_db 143 @unpublished{save_to_db
113 author = {Ramiz Khaled}, 144 author = {Ramiz Khaled},