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planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
author tduigou
date Wed, 23 Jul 2025 09:40:14 +0000
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-1:000000000000 0:c4f98010d9ac
1 <tool id="parameters_maystro_workflow_1" name="Workflow-1 Parameters Maystro" version="@TOOL_VERSION@" profile="21.09">
2 <description>Store parameters of workflow-1 to be used again</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.1.0</token>
5 </macros>
6 <command detect_errors="exit_code"><![CDATA[
7 #if $user_json and str($user_json) != 'None':
8 cp '$user_json' '$output_json'
9 #else
10 python3 -c "import json; params = {
11 'assembly_plan_name': '$assembly_plan_name',
12 'topology': '$topology',
13 'enzyme': '$enzyme',
14 'execution': '$execution',
15 'db_uri': '$db_uri',
16 'table': '$table_name',
17 'fragment_column': '$fragment_column',
18 'sequence_column': '$sequence_column',
19 'annotation_column': '$annotation_column'
20 }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json'
21 #end if
22 && echo DEBG && cat '$output_json'
23 ]]></command>
24 <inputs>
25 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
26 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
27 <option value="GibsonAssembly">Gibson_assembly</option>
28 <option value="BASICAssembly">BASIC_assembly</option>
29 <option value="BioBrickStandardAssembly">biobrick_assembly</option>
30 <option value="LigaseCyclingReactionAssembly">lcr_assembly</option>
31 </param>
32 <param name="topology" type="select" label="Assambly Topology" help="select circular or linear topology">
33 <option value="linear">linear</option>
34 <option value="circular" selected="True">circular</option>
35 </param>
36 <param name="enzyme" type="text" label="Enzyme" value="auto"/>
37 <param name="execution" type="boolean" label="Save To DB ?" checked ='false' optional="true" help="If True data will be saved in the DB" />
38 <param name="db_uri" type="text" optional="true" help='Only if Input Your Parameters As JSON is FALSE' />
39 <param name="table_name" type="text" optional="true" help='table name in DB' />
40 <param name="fragment_column" type="text" optional="true" help='Fragmnet column in DB' />
41 <param name="sequence_column" type="text" optional="true" help='Sequence column in DB' />
42 <param name="annotation_column" type="text" optional="true" help='Annotation column in DB' />
43 <param name="user_json" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' />
44 </inputs>
45 <outputs>
46 <data name="output_json" format="json" label="Workflow-1 Parameters"/>
47 </outputs>
48 <tests>
49 <!--manual parameters set-->
50 <test>
51 <param name="assembly_plan_name" value="Type2sRestrictionAssembly" />
52 <param name="topology" value='circular'/>
53 <param name="enzyme" value="auto"/>
54 <param name="execution" value="true" />
55 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
56 <param name="table_name" value="sample" />
57 <param name="fragment_column" value="fragment" />
58 <param name="sequence_column" value="sequence" />
59 <param name="annotation_column" value="annotation" />
60 <output name="output_json">
61 <assert_contents>
62 <has_n_lines n="11" />
63 </assert_contents>
64 </output>
65 </test>
66 <!--JSON parameters set-->
67 <test>
68 <param name="user_json" value='test-JSON_workflow1.json'/>
69 <output name="output_json">
70 <assert_contents>
71 <has_n_lines n="11" />
72 </assert_contents>
73 </output>
74 </test>
75 </tests>
76 <help><![CDATA[
77 Parameters Maystro for workflow-1
78 =================================
79
80 Store and Generate a JSON file to be used as workflow-1 configuration. This JSON file can later be used as input to pass workflow-1 parameters
81
82 ]]></help>
83 <citations>
84 <citation type="bibtex">
85 @unpublished{parameters_maystro_workflow_1
86 author = {Ramiz Khaled},
87 title = {{parameters_maystro_workflow_1}},
88 url = {https://github.com/brsynth/},
89 }
90 </citation>
91 </citations>
92 </tool>