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comparison seq_form_db.xml @ 1:7680420caf9f draft

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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
author tduigou
date Wed, 23 Jul 2025 09:44:50 +0000
parents 3dfba58f44f1
children 11a3752feb0a
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0:3dfba58f44f1 1:7680420caf9f
1 <tool id="seq_form_db" name="Get sequences Data From DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="seq_form_db" name="Get sequences Data From DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Import fragment's data from an accessible DB and export it as .gb files</description> 2 <description>Import fragment's data from an accessible DB and export it as .gb files</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">1</token>
5 <token name="@TOOL_VERSION@">0.1.0</token> 5 <token name="@TOOL_VERSION@">0.2.0</token>
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 <requirement type="package" version="1.85">biopython</requirement>
12 </requirements> 12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 mkdir 'outdir' && 14 mkdir 'outdir' &&
15 python '$__tool_directory__/get_db_info.py' 15 python '$__tool_directory__/get_db_info.py'
16 --input '$input' 16 --input '$input'
17 --sequence_column '$sequence_column' 17 --use_json_paramers '$json_use.use_json_paramers'
18 --annotation_columns '$annotation_columns' 18 #if not $json_use.use_json_paramers:
19 --db_uri '$db_uri' 19 --sequence_column '$json_use.sequence_column'
20 --table '$table' 20 --annotation_columns '$json_use.annotation_columns'
21 --fragment_column '$fragment_column' 21 --db_uri '$json_use.db_uri'
22 --table '$json_use.table'
23 --fragment_column '$json_use.fragment_column'
24 #else:
25 --json_conf '$json_use.json_conf'
26 #end if
22 --output 'outdir' 27 --output 'outdir'
23 ]]></command> 28 ]]></command>
24 <inputs> 29 <inputs>
25 <param name="input" type="data" format="csv" label="Input CSV File" /> 30 <param name="input" type="data" format="csv" label="Input CSV File" />
26 <param name="table" type="text" label="DB Table Name" optional="false" /> 31 <conditional name="json_use">
27 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="false" /> 32 <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" />
28 <param name="annotation_columns" type="text" label="DB Column Contains Annotation For Ganbank File" optional="false" /> 33 <when value="false">
29 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="false" /> 34 <param name="table" type="text" label="DB Table Name" optional="false" />
30 <param name="db_uri" type="text" label="DB Connection URI" help="postgresql://container_name:password@host:port/path/to/database" optional="false" /> 35 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="false" />
36 <param name="annotation_columns" type="text" label="DB Column Contains Annotation For Ganbank File" optional="false" />
37 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="false" />
38 <param name="db_uri" type="text" label="DB Connection URI" help="postgresql://user_name:password@host:port/path/to/database" optional="false" />
39 </when>
40 <when value="true">
41 <param name="json_conf" type="data" format='json' label="DB config as a json file" help="JSON file specifying the database URI, table name and the column names for annotation and sequence data" optional="false" />
42 </when>
43 </conditional>
31 </inputs> 44 </inputs>
32 <outputs> 45 <outputs>
33 <collection name="output_gb" type="list" label="GenBank Files collection" > 46 <collection name="output_gb" type="list" label="GenBank Files collection" >
34 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" /> 47 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir" />
35 </collection> 48 </collection>
36 </outputs> 49 </outputs>
37 <tests> 50 <tests>
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'--> 51 <!--manual parameters-->
39 <test> 52 <test>
40 <param name="input" value="2-step-golden_gate_plan.csv" /> 53 <param name="input" value="2-step-golden_gate_plan.csv" />
41 <param name="table" value="sample" /> 54 <conditional name="json_use">
42 <param name="sequence_column" value="sequence" /> 55 <param name='use_json_paramers' value='false' />
43 <param name="annotation_columns" value="annotation" /> 56 <param name="table" value="sample" />
44 <param name="fragment_column" value="fragment" /> 57 <param name="sequence_column" value="sequence" />
45 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" /> 58 <param name="annotation_columns" value="annotation" />
59 <param name="fragment_column" value="fragment" />
60 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
61 </conditional>
62 <output_collection name="output_gb" type="list" count="12">
63 <element name="part_A">
64 <assert_contents>
65 <has_n_lines min="10" />
66 </assert_contents>
67 </element>
68 <element name="part_B">
69 <assert_contents>
70 <has_n_lines min="10" />
71 </assert_contents>
72 </element>
73 <element name="part_C">
74 <assert_contents>
75 <has_n_lines min="10" />
76 </assert_contents>
77 </element>
78 <element name="part_D">
79 <assert_contents>
80 <has_n_lines min="10" />
81 </assert_contents>
82 </element>
83 <element name="part_E">
84 <assert_contents>
85 <has_n_lines min="10" />
86 </assert_contents>
87 </element>
88 <element name="part_F">
89 <assert_contents>
90 <has_n_lines min="10" />
91 </assert_contents>
92 </element>
93 <element name="part_G">
94 <assert_contents>
95 <has_n_lines min="10" />
96 </assert_contents>
97 </element>
98 <element name="part_H">
99 <assert_contents>
100 <has_n_lines min="10" />
101 </assert_contents>
102 </element>
103 <element name="part_I">
104 <assert_contents>
105 <has_n_lines min="10" />
106 </assert_contents>
107 </element>
108 <element name="part_J">
109 <assert_contents>
110 <has_n_lines min="10" />
111 </assert_contents>
112 </element>
113 <element name="part_K">
114 <assert_contents>
115 <has_n_lines min="10" />
116 </assert_contents>
117 </element>
118 <element name="part_L">
119 <assert_contents>
120 <has_n_lines min="10" />
121 </assert_contents>
122 </element>
123 </output_collection>
124 </test>
125 <!--JSON parameters-->
126 <test>
127 <param name="input" value="2-step-golden_gate_plan.csv" />
128 <conditional name="json_use">
129 <param name="use_json_paramers" value='true'/>
130 <param name="json_conf" value="test-JSON.json" />
131 </conditional>
46 <output_collection name="output_gb" type="list" count="12"> 132 <output_collection name="output_gb" type="list" count="12">
47 <element name="part_A"> 133 <element name="part_A">
48 <assert_contents> 134 <assert_contents>
49 <has_n_lines min="10" /> 135 <has_n_lines min="10" />
50 </assert_contents> 136 </assert_contents>
114 200
115 Implemented a system to generate GenBank (.gb) files for ADN fragments in CSV input, based on data retrieved from an accessible database via URI requests. 201 Implemented a system to generate GenBank (.gb) files for ADN fragments in CSV input, based on data retrieved from an accessible database via URI requests.
116 202
117 **Parameters**: 203 **Parameters**:
118 --------------- 204 ---------------
119 * **Input CSV File**: Assembly csv contains construct IDs in the first column and their corresponding fragments in the following columns. (Without Header) 205 * **Use parameters from JSON**: Yes/No parameter to ask user if he wants to set parameters manually or using JSON file.
206 * **Input CSV File**: Assembly CSV contains construct IDs in the first column and their corresponding fragments in the following columns. (Without Header)
120 * **DB Table Name**: Name of the target table in the database. 207 * **DB Table Name**: Name of the target table in the database.
121 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN". 208 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
122 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, starting with "FEATURES" and including "LOCUS" information. Other metadata is optional. 209 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, starting with "FEATURES" and including "LOCUS" information. Other metadata is optional.
123 * **DB IDs Column Name**: Column holding the unique fragment IDs. 210 * **DB IDs Column Name**: Column holding the unique fragment IDs.
124 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://postgres:pass@localhost:5432/test_fragments_db). 211 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://user_name:pass@localhost:5432/test_fragments_db).
125 ]]></help> 212 ]]></help>
126 <citations> 213 <citations>
127 <citation type="bibtex"> 214 <citation type="bibtex">
128 @unpublished{seq_form_db 215 @unpublished{seq_form_db
129 author = {Ramiz Khaled}, 216 author = {Ramiz Khaled},