Mercurial > repos > tduigou > parameters_maystro_workflow_0

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author tduigou
date Wed, 23 Jul 2025 09:39:39 +0000
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1 <tool id="parameters_maystro_workflow_0" name="Workflow-0 Parameters Maystro" version="@TOOL_VERSION@" profile="21.09">
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2 <description>Store parameters of workflow-0 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 'avoid_patterns': '$avoid_patterns',
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12 'hairpin_constraints': '$hairpin_constraints',
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13 'gc_constraints': '$gc_constraints',
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14 'kmer_size': '$kmer_size',
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15 'execution': '$execution',
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16 'db_uri': '$db_uri',
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17 'table': '$table_name',
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18 'fragment_column': '$fragment_column',
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19 'sequence_column': '$sequence_column',
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20 'annotation_column': '$annotation_column'
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21 }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json'
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22 #end if
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23 && echo DEBG && cat '$output_json'
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24 ]]></command>
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25 <inputs>
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26 <param name="avoid_patterns" type="text" area="true" optional="true" label="Avoid Patterns (one per line)" />
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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"/>
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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"/>
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29 <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/>
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30 <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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31 <param name="db_uri" type="text" optional="true" help='Only if Input Your Parameters As JSON is FALSE' />
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32 <param name="table_name" type="text" optional="true" help='table name in DB' />
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33 <param name="fragment_column" type="text" optional="true" help='Fragmnet column in DB' />
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34 <param name="sequence_column" type="text" optional="true" help='Sequence column in DB' />
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35 <param name="annotation_column" type="text" optional="true" help='Annotation column in DB' />
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36 <param name="user_json" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' />
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37 </inputs>
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38 <outputs>
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39 <data name="output_json" format="json" label="Workflow-0 Parameters"/>
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40 </outputs>
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41 <tests>
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42 <!--manual parameters set-->
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43 <test>
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44 <param name="avoid_patterns" value="BsaI_site
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45 BsmBI_site
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46 BbsI_site
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47 SapI_site
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48 8x1mer
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49 5x3mer
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50 9x2mer" />
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51 <param name="hairpin_constraints" value='stem_size=20, hairpin_window=200'/>
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52 <param name="gc_constraints" value="mini=0.3, maxi=0.7, window=100
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53 mini=0.1, maxi=0.9, window=100"/>
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54 <param name="kmer_size" value="15" />
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55 <param name="execution" value="true" />
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56 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
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57 <param name="table_name" value="sample" />
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58 <param name="fragment_column" value="fragment" />
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59 <param name="sequence_column" value="sequence" />
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60 <param name="annotation_column" value="annotation" />
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61 <output name="output_json">
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62 <assert_contents>
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63 <has_n_lines n="12" />
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64 </assert_contents>
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65 </output>
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66 </test>
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67 <!--JSON parameters set-->
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68 <test>
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69 <param name="user_json" value='test_json.json'/>
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70 <output name="output_json">
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71 <assert_contents>
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72 <has_n_lines n="12" />
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73 </assert_contents>
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74 </output>
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78 Parameters Maystro for workflow-0
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79 =================================
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80
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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
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82
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83 ]]></help>
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84 <citations>
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85 <citation type="bibtex">
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86 @unpublished{parameters_maystro_workflow_0
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87 author = {Ramiz Khaled},
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88 title = {{parameters_maystro_workflow_0}},
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89 url = {https://github.com/brsynth/},
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90 }
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91 </citation>
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92 </citations>
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93 </tool>