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comparison maystro_workflow_0.xml @ 0:9ab8b3673816 draft default tip

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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 09:39:39 +0000
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-1:000000000000 0:9ab8b3673816
1 <tool id="parameters_maystro_workflow_0" name="Workflow-0 Parameters Maystro" version="@TOOL_VERSION@" profile="21.09">
2 <description>Store parameters of workflow-0 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 'avoid_patterns': '$avoid_patterns',
12 'hairpin_constraints': '$hairpin_constraints',
13 'gc_constraints': '$gc_constraints',
14 'kmer_size': '$kmer_size',
15 'execution': '$execution',
16 'db_uri': '$db_uri',
17 'table': '$table_name',
18 'fragment_column': '$fragment_column',
19 'sequence_column': '$sequence_column',
20 'annotation_column': '$annotation_column'
21 }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json'
22 #end if
23 && echo DEBG && cat '$output_json'
24 ]]></command>
25 <inputs>
26 <param name="avoid_patterns" type="text" area="true" optional="true" label="Avoid Patterns (one per line)" />
27 <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"/>
28 <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"/>
29 <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/>
30 <param name="execution" type="boolean" label="Save To DB ?" checked ='false' optional="true" help="If True data will be saved in the DB" />
31 <param name="db_uri" type="text" optional="true" help='Only if Input Your Parameters As JSON is FALSE' />
32 <param name="table_name" type="text" optional="true" help='table name in DB' />
33 <param name="fragment_column" type="text" optional="true" help='Fragmnet column in DB' />
34 <param name="sequence_column" type="text" optional="true" help='Sequence column in DB' />
35 <param name="annotation_column" type="text" optional="true" help='Annotation column in DB' />
36 <param name="user_json" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' />
37 </inputs>
38 <outputs>
39 <data name="output_json" format="json" label="Workflow-0 Parameters"/>
40 </outputs>
41 <tests>
42 <!--manual parameters set-->
43 <test>
44 <param name="avoid_patterns" value="BsaI_site
45 BsmBI_site
46 BbsI_site
47 SapI_site
48 8x1mer
49 5x3mer
50 9x2mer" />
51 <param name="hairpin_constraints" value='stem_size=20, hairpin_window=200'/>
52 <param name="gc_constraints" value="mini=0.3, maxi=0.7, window=100
53 mini=0.1, maxi=0.9, window=100"/>
54 <param name="kmer_size" value="15" />
55 <param name="execution" value="true" />
56 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
57 <param name="table_name" value="sample" />
58 <param name="fragment_column" value="fragment" />
59 <param name="sequence_column" value="sequence" />
60 <param name="annotation_column" value="annotation" />
61 <output name="output_json">
62 <assert_contents>
63 <has_n_lines n="12" />
64 </assert_contents>
65 </output>
66 </test>
67 <!--JSON parameters set-->
68 <test>
69 <param name="user_json" value='test_json.json'/>
70 <output name="output_json">
71 <assert_contents>
72 <has_n_lines n="12" />
73 </assert_contents>
74 </output>
75 </test>
76 </tests>
77 <help><![CDATA[
78 Parameters Maystro for workflow-0
79 =================================
80
81 Store and Generate a JSON file to be used as workflow-0 configuration. This JSON file can later be used as input to pass workflow-0 parameters
82
83 ]]></help>
84 <citations>
85 <citation type="bibtex">
86 @unpublished{parameters_maystro_workflow_0
87 author = {Ramiz Khaled},
88 title = {{parameters_maystro_workflow_0}},
89 url = {https://github.com/brsynth/},
90 }
91 </citation>
92 </citations>
93 </tool>