Mercurial > repos > tduigou > parameters_maystro_workflow_2

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author tduigou
date Wed, 23 Jul 2025 09:40:00 +0000
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1 <tool id="parameters_maystro_workflow_2" name="Workflow-2 Parameters Maystro" version="@TOOL_VERSION@" profile="21.09">
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2 <description>Store parameters of workflow-2 to be used again</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.1.0</token>
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5 </macros>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #if $user_json and str($user_json) != 'None':
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8 cp '$user_json' '$output_json'
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9 #else
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10 python3 -c "import json; params = {
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11 'DnaOptimizationProblemClass': '$DnaOptimizationProblemClass',
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12 'methylation_protection': '$methylation_protection',
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13 'allow_edits': '$allow_edits',
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14 'avoid_patterns': '$avoid_patterns',
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15 'hairpin_constraints': '$hairpin_constraints',
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16 'gc_constraints': '$gc_constraints',
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17 'kmer_size': '$kmer_size',
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18 'assembly_plan_name': '$assembly_plan_name',
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19 'topology': '$topology',
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20 'enzyme': '$enzyme',
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21 'execution': '$execution',
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22 'db_uri': '$db_uri',
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23 'table': '$table_name',
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24 'fragment_column': '$fragment_column',
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25 'sequence_column': '$sequence_column',
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26 'annotation_column': '$annotation_column'
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27 }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json'
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28 #end if
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29 && echo DEBG && cat '$output_json'
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30 ]]></command>
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31 <inputs>
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32 <param name="DnaOptimizationProblemClass" type="select" label="DnaOptimizationProblem Calss" help="select the assambly class">
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33 <option value="DnaOptimizationProblem" selected="True">DnaOptimizationProblem</option>
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34 <option value="CircularDnaOptimizationProblem">CircularDnaOptimizationProblem</option>
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35 </param>
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36 <param name="avoid_patterns" type="text" area="true" optional="true" label="Avoid Patterns (one per line)" />
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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"/>
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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"/>
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39 <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/>
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40 <param name="methylation_protection" type="boolean" checked="False" label="Enabel Methylation Protection"/>
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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
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42 with flanks. If a sequence has for instance forbidden restriction sites,
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43 the domesticaton will fail for this sequence (and this will be noted in
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44 the report."/>
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45 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
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46 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
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47 <option value="GibsonAssembly">Gibson_assembly</option>
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48 <option value="BASICAssembly">BASIC_assembly</option>
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49 <option value="BioBrickStandardAssembly">biobrick_assembly</option>
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50 <option value="LigaseCyclingReactionAssembly">lcr_assembly</option>
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51 </param>
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52 <param name="topology" type="select" label="Assambly Topology" help="select circular or linear topology">
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53 <option value="linear">linear</option>
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54 <option value="circular" selected="True">circular</option>
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55 </param>
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56 <param name="enzyme" type="text" label="Enzyme" value="auto"/>
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57 <section name="DB" title="DB conf" expanded='true'>
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58 <param name="execution" type="boolean" label="Save To DB ?" checked ='false' optional="true" help="If True data will be saved in the DB" />
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59 <param name="db_uri" type="text" optional="true" help='Only if Input Your Parameters As JSON is FALSE' />
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60 <param name="table_name" type="text" optional="true" help='table name in DB' />
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61 <param name="fragment_column" type="text" optional="true" help='Fragmnet column in DB' />
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62 <param name="sequence_column" type="text" optional="true" help='Sequence column in DB' />
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63 <param name="annotation_column" type="text" optional="true" help='Annotation column in DB' />
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64 <param name="user_json" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' />
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65 </section>
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66 </inputs>
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67 <outputs>
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68 <data name="output_json" format="json" label="Workflow-2 Parameters"/>
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69 </outputs>
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70 <tests>
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71 <!--manual parameters set-->
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72 <test>
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73 <param name="DnaOptimizationProblemClass" value="DnaOptimizationProblem"/>
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74
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75 <param name="avoid_patterns" value="BsaI_site
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76 nNotI_site
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77 nXbaI_site
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78 nClaI_site
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79 n8x1mer" />
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80 <param name="hairpin_constraints" value='stem_size=20, hairpin_window=200'/>
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81 <param name="gc_constraints" value="mini=0.3, maxi=0.7, window=100
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82 mini=0.1, maxi=0.9, window=100"/>
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83 <param name="kmer_size" value="15" />
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84 <param name="methylation_protection" value="true"/>
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85 <param name="assembly_plan_name" value="Type2sRestrictionAssembly" />
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86 <param name="topology" value='circular'/>
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87 <param name="enzyme" value="auto"/>
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88 <param name="execution" value="true" />
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89 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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90 <param name="table_name" value="sample" />
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91 <param name="fragment_column" value="fragment" />
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92 <param name="sequence_column" value="sequence" />
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93 <param name="annotation_column" value="annotation" />
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94 <output name="output_json">
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95 <assert_contents>
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96 <has_n_lines n="18" />
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97 </assert_contents>
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98 </output>
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99 </test>
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100 <!--JSON parameters set-->
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101 <test>
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102 <param name="user_json" value='test_json_workflow2.json'/>
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103 <output name="output_json">
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104 <assert_contents>
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105 <has_n_lines n="18" />
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106 </assert_contents>
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107 </output>
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108 </test>
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109 </tests>
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110 <help><![CDATA[
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111 Parameters Maystro for workflow-2
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112 =================================
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113
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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
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115
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116 ]]></help>
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117 <citations>
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118 <citation type="bibtex">
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119 @unpublished{parameters_maystro_workflow_2
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120 author = {Ramiz Khaled},
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121 title = {{parameters_maystro_workflow_2}},
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122 url = {https://github.com/brsynth/},
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123 }
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124 </citation>
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125 </citations>
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126 </tool>