Mercurial > repos > tduigou > json_db_config_generating
changeset 4:f103f5253a93 draft
planemo upload for repository https://github.com/brsynth commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
| author | tduigou |
|---|---|
| date | Wed, 11 Jun 2025 15:25:55 +0000 |
| parents | 8eb6c417d4f5 |
| children | 40aa268ce07f |
| files | json_db_config_generating.xml json_db_config_generating_boolean.xml |
| diffstat | 2 files changed, 109 insertions(+), 109 deletions(-) [+] |
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--- a/json_db_config_generating.xml Mon Jun 02 15:10:45 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,109 +0,0 @@ -<tool id="json_db_config_generating" name="JSON DB_Config Generating" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> - <description>Genarate a JSON file used as DB config</description> - <macros> - <token name="@VERSION_SUFFIX@">2</token> - <token name="@TOOL_VERSION@">0.1.0</token> - </macros> - <command detect_errors="exit_code"><![CDATA[ - python3 -c "import json; params = { - 'execution': '$execution', - 'JSON_db_uri': '$db_uri', - 'JSON_table': '$table_name', - 'JSON_fragment_column': '$fragment_column', - 'JSON_sequence_column': '$sequence_column', - 'JSON_annotation_column': '$annotation_column' - }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json' - ]]></command> - <inputs> - <conditional name="db_request"> - <param name="execution" type="boolean" label="Save To DB ?" checked ='false' help="If True the execution key in the json file will be true" optional="false"/> - <when value='true'> - <section name='db_config' title='DB config' expanded='true'> - <param name="db_uri" type="text" label="DB Connection URI" optional="true" /> - <param name="table_name" type="text" label="DB Table Name" optional="true" /> - <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" /> - <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" /> - <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" /> - </section> - </when> - <when value='false'> - <section name='db_config' title='DB config' expanded='false'> - <param name="db_uri" type="text" label="DB Connection URI" optional="true" /> - <param name="table_name" type="text" label="DB Table Name" optional="true" /> - <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" /> - <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" /> - <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" /> - </section> - </when> - </conditional> - </inputs> - <outputs> - <data name="output_json" format="json" label="JSON Conf" /> - </outputs> - <tests> - <!--test execution is true --> - <test> - <conditional name="db_request"> - <param name="execution" value="true" /> - <param name="db_config|db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" /> - <param name="db_config|table_name" value="sample" /> - <param name="db_config|fragment_column" value="fragment" /> - <param name="db_config|sequence_column" value="sequence" /> - <param name="db_config|annotation_column" value="annotation" /> - </conditional> - <output name="output_json"> - <assert_contents> - <has_json_property_with_text property="execution" text="true" /> - <has_json_property_with_text property="JSON_db_uri" text="postgresql://postgres:RK17__at__localhost:5432/test_fragments_db" /> - <has_json_property_with_text property="JSON_table" text="sample" /> - <has_json_property_with_text property="JSON_fragment_column" text="fragment" /> - <has_json_property_with_text property="JSON_sequence_column" text="sequence" /> - <has_json_property_with_text property="JSON_annotation_column" text="annotation" /> - </assert_contents> - </output> - </test> - <!--test execution is false --> - <test> - <conditional name="db_request"> - <param name="execution" value="false" /> - </conditional> - <output name="output_json"> - <assert_contents> - <has_json_property_with_text property="execution" text="false" /> - <has_json_property_with_text property="JSON_db_uri" text="" /> - <has_json_property_with_text property="JSON_table" text="" /> - <has_json_property_with_text property="JSON_fragment_column" text="" /> - <has_json_property_with_text property="JSON_sequence_column" text="" /> - <has_json_property_with_text property="JSON_annotation_column" text="" /> - </assert_contents> - </output> - </test> - </tests> - - <help><![CDATA[ -JSON DB_Config Generating -========================= - -Generate a JSON file to be used as a DB configuration. This JSON file can later be used to access the database via the specified URI, as well as the defined table and column names. -This tool is primarily designed to control the execution of the save_to_db tool by enabling or disabling its execution and by providing the database configuration through a JSON file. - -**Parameters**: ---------------- -* **execution key**: The value of execution key in the JSON (true or false) -* **DB Table Name**: Name of the target table in the PostgreSQL database. -* **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN". -* **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file. -* **DB IDs Column Name**: Column holding the unique fragment IDs. -* **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name). -* NOTE: This tool is designed to manage the execution of save_to_db within a workflow. If parameters are set directly in save_to_db via the user interface, the JSON file data will be ignored. - ]]></help> - <citations> - <citation type="bibtex"> - @unpublished{json_db_config_generating - author = {Ramiz Khaled}, - title = {{json_db_config_generating}}, - url = {https://github.com/brsynth/}, - } - </citation> - </citations> -</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/json_db_config_generating_boolean.xml Wed Jun 11 15:25:55 2025 +0000 @@ -0,0 +1,109 @@ +<tool id="json_db_config_generating" name="JSON DB_Config Generating" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> + <description>Genarate a JSON file used as DB config</description> + <macros> + <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">0.1.0</token> + </macros> + <command detect_errors="exit_code"><![CDATA[ + python3 -c "import json; params = { + 'execution': '$execution', + 'JSON_db_uri': '$db_uri', + 'JSON_table': '$table_name', + 'JSON_fragment_column': '$fragment_column', + 'JSON_sequence_column': '$sequence_column', + 'JSON_annotation_column': '$annotation_column' + }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" + ]]></command> + <inputs> + <conditional name="db_request"> + <param name="execution" type="boolean" label="Save To DB ?" checked ='false' help="If True the execution key in the json file will be true" /> + <when value='true'> + <section name='db_config' title='DB config' expanded='true'> + <param name="db_uri" type="text" label="DB Connection URI" optional="true" /> + <param name="table_name" type="text" label="DB Table Name" optional="true" /> + <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" /> + <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" /> + <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" /> + </section> + </when> + <when value='false'> + <section name='db_config' title='DB config' expanded='false'> + <param name="db_uri" type="text" label="DB Connection URI" optional="true" /> + <param name="table_name" type="text" label="DB Table Name" optional="true" /> + <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" /> + <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" /> + <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" /> + </section> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_json" format="json" label="JSON Conf" /> + </outputs> + <tests> + <!--test execution is true --> + <test> + <conditional name="db_request"> + <param name="execution" value="true" /> + <param name="db_config|db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" /> + <param name="db_config|table_name" value="sample" /> + <param name="db_config|fragment_column" value="fragment" /> + <param name="db_config|sequence_column" value="sequence" /> + <param name="db_config|annotation_column" value="annotation" /> + </conditional> + <output name="output_json"> + <assert_contents> + <has_json_property_with_text property="execution" text="true" /> + <has_json_property_with_text property="JSON_db_uri" text="postgresql://postgres:RK17__at__localhost:5432/test_fragments_db" /> + <has_json_property_with_text property="JSON_table" text="sample" /> + <has_json_property_with_text property="JSON_fragment_column" text="fragment" /> + <has_json_property_with_text property="JSON_sequence_column" text="sequence" /> + <has_json_property_with_text property="JSON_annotation_column" text="annotation" /> + </assert_contents> + </output> + </test> + <!--test execution is false --> + <test> + <conditional name="db_request"> + <param name="execution" value="false" /> + </conditional> + <output name="output_json"> + <assert_contents> + <has_json_property_with_text property="execution" text="false" /> + <has_json_property_with_text property="JSON_db_uri" text="" /> + <has_json_property_with_text property="JSON_table" text="" /> + <has_json_property_with_text property="JSON_fragment_column" text="" /> + <has_json_property_with_text property="JSON_sequence_column" text="" /> + <has_json_property_with_text property="JSON_annotation_column" text="" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +JSON DB_Config Generating +========================= + +Generate a JSON file to be used as a DB configuration. This JSON file can later be used to access the database via the specified URI, as well as the defined table and column names. +This tool is primarily designed to control the execution of the save_to_db tool by enabling or disabling its execution and by providing the database configuration through a JSON file. + +**Parameters**: +--------------- +* **execution key**: The value of execution key in the JSON (true or false) +* **DB Table Name**: Name of the target table in the PostgreSQL database. +* **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN". +* **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file. +* **DB IDs Column Name**: Column holding the unique fragment IDs. +* **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user:password@host:port/DB_name). +* NOTE: This tool is designed to manage the execution of save_to_db within a workflow. If parameters are set directly in save_to_db via the user interface, the JSON file data will be ignored. + ]]></help> + <citations> + <citation type="bibtex"> + @unpublished{json_db_config_generating + author = {Ramiz Khaled}, + title = {{json_db_config_generating}}, + url = {https://github.com/brsynth/}, + } + </citation> + </citations> +</tool> \ No newline at end of file