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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 09:40:00 +0000
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-1:000000000000 0:f80ed73f9f9a
1 <tool id="parameters_maystro_workflow_2" name="Workflow-2 Parameters Maystro" version="@TOOL_VERSION@" profile="21.09">
2 <description>Store parameters of workflow-2 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 'DnaOptimizationProblemClass': '$DnaOptimizationProblemClass',
12 'methylation_protection': '$methylation_protection',
13 'allow_edits': '$allow_edits',
14 'avoid_patterns': '$avoid_patterns',
15 'hairpin_constraints': '$hairpin_constraints',
16 'gc_constraints': '$gc_constraints',
17 'kmer_size': '$kmer_size',
18 'assembly_plan_name': '$assembly_plan_name',
19 'topology': '$topology',
20 'enzyme': '$enzyme',
21 'execution': '$execution',
22 'db_uri': '$db_uri',
23 'table': '$table_name',
24 'fragment_column': '$fragment_column',
25 'sequence_column': '$sequence_column',
26 'annotation_column': '$annotation_column'
27 }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json'
28 #end if
29 && echo DEBG && cat '$output_json'
30 ]]></command>
31 <inputs>
32 <param name="DnaOptimizationProblemClass" type="select" label="DnaOptimizationProblem Calss" help="select the assambly class">
33 <option value="DnaOptimizationProblem" selected="True">DnaOptimizationProblem</option>
34 <option value="CircularDnaOptimizationProblem">CircularDnaOptimizationProblem</option>
35 </param>
36 <param name="avoid_patterns" type="text" area="true" optional="true" label="Avoid Patterns (one per line)" />
37 <param name="hairpin_constraints" type="text" area="true" label="Hairpins Constraints" optional="true" help="e.g. (you can add others Hairpins Constraints on a new line): stem_size=20, hairpin_window=200"/>
38 <param name="gc_constraints" type="text" area="true" label="Enforce GC Content Constraints" optional="true" help="e.g. (you can add others Enforce GC Content Constraints on a new line): mini=0.3, maxi=0.7, window=100"/>
39 <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/>
40 <param name="methylation_protection" type="boolean" checked="False" label="Enabel Methylation Protection"/>
41 <param name="allow_edits" type="boolean" checked="True" label="Allow Sequence Edits" help="If False, sequences cannot be edited by the domesticator, only extended
42 with flanks. If a sequence has for instance forbidden restriction sites,
43 the domesticaton will fail for this sequence (and this will be noted in
44 the report."/>
45 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
46 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
47 <option value="GibsonAssembly">Gibson_assembly</option>
48 <option value="BASICAssembly">BASIC_assembly</option>
49 <option value="BioBrickStandardAssembly">biobrick_assembly</option>
50 <option value="LigaseCyclingReactionAssembly">lcr_assembly</option>
51 </param>
52 <param name="topology" type="select" label="Assambly Topology" help="select circular or linear topology">
53 <option value="linear">linear</option>
54 <option value="circular" selected="True">circular</option>
55 </param>
56 <param name="enzyme" type="text" label="Enzyme" value="auto"/>
57 <section name="DB" title="DB conf" expanded='true'>
58 <param name="execution" type="boolean" label="Save To DB ?" checked ='false' optional="true" help="If True data will be saved in the DB" />
59 <param name="db_uri" type="text" optional="true" help='Only if Input Your Parameters As JSON is FALSE' />
60 <param name="table_name" type="text" optional="true" help='table name in DB' />
61 <param name="fragment_column" type="text" optional="true" help='Fragmnet column in DB' />
62 <param name="sequence_column" type="text" optional="true" help='Sequence column in DB' />
63 <param name="annotation_column" type="text" optional="true" help='Annotation column in DB' />
64 <param name="user_json" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' />
65 </section>
66 </inputs>
67 <outputs>
68 <data name="output_json" format="json" label="Workflow-2 Parameters"/>
69 </outputs>
70 <tests>
71 <!--manual parameters set-->
72 <test>
73 <param name="DnaOptimizationProblemClass" value="DnaOptimizationProblem"/>
74
75 <param name="avoid_patterns" value="BsaI_site
76 nNotI_site
77 nXbaI_site
78 nClaI_site
79 n8x1mer" />
80 <param name="hairpin_constraints" value='stem_size=20, hairpin_window=200'/>
81 <param name="gc_constraints" value="mini=0.3, maxi=0.7, window=100
82 mini=0.1, maxi=0.9, window=100"/>
83 <param name="kmer_size" value="15" />
84 <param name="methylation_protection" value="true"/>
85 <param name="assembly_plan_name" value="Type2sRestrictionAssembly" />
86 <param name="topology" value='circular'/>
87 <param name="enzyme" value="auto"/>
88 <param name="execution" value="true" />
89 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
90 <param name="table_name" value="sample" />
91 <param name="fragment_column" value="fragment" />
92 <param name="sequence_column" value="sequence" />
93 <param name="annotation_column" value="annotation" />
94 <output name="output_json">
95 <assert_contents>
96 <has_n_lines n="18" />
97 </assert_contents>
98 </output>
99 </test>
100 <!--JSON parameters set-->
101 <test>
102 <param name="user_json" value='test_json_workflow2.json'/>
103 <output name="output_json">
104 <assert_contents>
105 <has_n_lines n="18" />
106 </assert_contents>
107 </output>
108 </test>
109 </tests>
110 <help><![CDATA[
111 Parameters Maystro for workflow-2
112 =================================
113
114 Store and Generate a JSON file to be used as workflow-2 configuration. This JSON file can later be used as input to pass workflow-2 parameters
115
116 ]]></help>
117 <citations>
118 <citation type="bibtex">
119 @unpublished{parameters_maystro_workflow_2
120 author = {Ramiz Khaled},
121 title = {{parameters_maystro_workflow_2}},
122 url = {https://github.com/brsynth/},
123 }
124 </citation>
125 </citations>
126 </tool>