Mercurial > repos > tduigou > cloning_simulation

annotate cloning_similation.xml @ 2:e7ecf6e21b49 draft default tip

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit e8c8f102cab10531ed588be4ecb8a0d01e797f09
author tduigou
date Tue, 06 Jan 2026 11:34:13 +0000
parents 2655e08cd61a
children
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3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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1 <tool id="cloning_simulation" name="Cloning Simulation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>A cloning simulator for synthetic biology</description>
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3 <macros>
2
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4 <token name="@VERSION_SUFFIX@">2</token>
1
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5 <token name="@TOOL_VERSION@">0.2.0</token>
0
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="0.1.11">flametree</requirement>
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9 <requirement type="package" version="1.85"> biopython </requirement>
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10 <requirement type="package" version="0.1.10">proglog</requirement>
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11 <requirement type="package" version="2.2.3">pandas</requirement>
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12 <requirement type="package" version="2.0.12">dnacauldron</requirement>
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13 <requirement type="package" version="0.3.9">pdf-reports</requirement>
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14 <requirement type="package" version="0.1.8">sequenticon</requirement>
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15 <requirement type="package" version="3.1.5">dna_features_viewer</requirement>
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16 </requirements>
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17 <command detect_errors="exit_code"><![CDATA[
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18 #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
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19 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
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20 #set domesticated_input_paths = ','.join([str(f) for f in $domesticated_input])
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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21 #set file_name_mapping_dom = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
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22 #if $domesticated_input_paths != '' and $genbank_file_paths == ''
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23 #set genbank_file_paths = ','.join([str(f) for f in $domesticated_input])
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24 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
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25 #set domesticated_input_paths = ''
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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26 #set file_name_mapping_dom = ''
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27 #end if
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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28 mkdir 'outdir_zip' && mkdir 'outdir_gb' &&
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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29 cp '$assembly_csv' 'assembly_csv.csv' &&
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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30 python '$__tool_directory__/cloning_simulation.py'
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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31 --parts_files '$genbank_file_paths'
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32 --domesticated_seq '$domesticated_input_paths'
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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33 --assembly_csv 'assembly_csv.csv'
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34 --file_name_mapping '$file_name_mapping'
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35 --file_name_mapping_dom '$file_name_mapping_dom'
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36 --use_json_paramers '$json_use.use_json_paramers'
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37 #if $json_use.use_json_paramers=='false':
1
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38 --enzyme '$json_use.enzyme'
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39 --topology '$json_use.topology'
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40 --assembly_plan_name '$json_use.assembly_plan_name'
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41 #else:
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42 --json_conf '$json_use.json_conf'
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43 #end if
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44 --use_file_names_as_id '$use_file_names_as_ids'
0
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45 --outdir_simulation 'outdir_zip'
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46 --outdir_gb 'outdir_gb'
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47 --output_simulation 'output_zip.zip' &&
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48 cp 'output_zip.zip' '$output_zip'
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49 ]]></command>
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50 <inputs>
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51 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" optional="True"/>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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52 <param name="assembly_csv" type="data" format="csv" label="Assemby csv"/>
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53 <param name="domesticated_input" type="data_collection" collection_type="list" format="genbank" label="Domesticated GenBank" optional="True"/>
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54 <conditional name="json_use">
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55 <param name="use_json_paramers" type="select" label="Use parameters from JSON" help="extract parameters from json file">
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56 <option value="true">Get Parameters From JSON</option>
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57 <option value="false" selected="true">Set Parameters Manually</option>
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58 </param>
1
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59 <when value="false">
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60 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
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61 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
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62 <option value="GibsonAssembly">Gibson_assembly</option>
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63 <option value="BASICAssembly">BASIC_assembly</option>
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64 <option value="BioBrickStandardAssembly">biobrick_assembly</option>
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65 <option value="LigaseCyclingReactionAssembly">lcr_assembly</option>
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66 </param>
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67 <param name="topology" type="select" label="Assambly Topology" help="select circular or linear topology">
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68 <option value="linear">linear</option>
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69 <option value="circular" selected="True">circular</option>
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70 </param>
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71 <param name="enzyme" type="text" label="Enzyme" value="auto" optional="True"/>
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72 </when>
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73 <when value="true">
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74 <param name="json_conf" type="data" format='json' label="DB config as a json file" help="JSON file specifying the database URI, table name and the column names for annotation and sequence data" optional="false" />
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75 </when>
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76 </conditional>
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77 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" />
0
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78 </inputs>
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79 <outputs>
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80 <data format="zip" name="output_zip" label="simulation results (zip)"/>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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81 <collection name="construct_gb" type="list" label="simulation results (gb)">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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82 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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83 </collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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84 </outputs>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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85 <tests>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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86 <!--test type2s_assembly class-->
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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87 <test>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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88 <param name="genbank_files">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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89 <collection type="list">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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90 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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91 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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92 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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93 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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94 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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95 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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96 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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97 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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98 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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99 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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100 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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101 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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102 </collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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103 </param>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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104 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
2
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105 <conditional name="json_use">
1
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106 <param name='use_json_paramers' value='false' />
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107 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
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108 <param name="topology" value="circular"/>
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109 </conditional>
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110 <param name="use_file_names_as_ids" value="True" />
0
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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111 <output name="output_zip" ftype='zip'>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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112 <assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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113 <has_archive_member path=".*" n="62"/>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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114 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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115 <has_size min="5"/>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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116 </has_archive_member>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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117 </assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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118 </output>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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119 <output_collection name="construct_gb" type="list" count="4">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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120 <element name="construct_1">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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121 <assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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122 <has_n_lines min="20" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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123 </assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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124 </element>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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125 <element name="construct_2">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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126 <assert_contents>
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127 <has_n_lines min="20" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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128 </assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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129 </element>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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130 <element name="construct_3">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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131 <assert_contents>
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132 <has_n_lines min="20" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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133 </assert_contents>
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134 </element>
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135 <element name="construct_4">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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136 <assert_contents>
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137 <has_n_lines min="20" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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138 </assert_contents>
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139 </element>
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140 </output_collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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141 </test>
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142 <!--test gibson_assembly class-->
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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143 <test>
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144 <param name="genbank_files">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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145 <collection type="list">
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146 <element name="gibson_sequences" value="Gibson_assembly_dataset/gibson_sequences.fa" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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147 </collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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148 </param>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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149 <param name="assembly_csv" value="Gibson_assembly_dataset/gibson_assembly.csv" />
2
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150 <conditional name="json_use">
1
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151 <param name='use_json_paramers' value='false' />
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152 <param name='assembly_plan_name' value='GibsonAssembly' />
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153 <param name="topology" value="circular"/>
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154 </conditional>
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155 <param name="use_file_names_as_ids" value="True" />
0
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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156 <output name="output_zip" ftype='zip'>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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157 <assert_contents>
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158 <has_archive_member path=".*" n="78"/>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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159 <has_archive_member path="assambly_simulation/Report.pdf">
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160 <has_size min="5"/>
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161 </has_archive_member>
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162 </assert_contents>
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163 </output>
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164 <output_collection name="construct_gb" type="list" count="3">
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165 <element name="construct_1">
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166 <assert_contents>
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167 <has_n_lines min="20" />
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168 </assert_contents>
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169 </element>
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170 <element name="construct_2">
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171 <assert_contents>
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172 <has_n_lines min="20" />
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173 </assert_contents>
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174 </element>
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175 <element name="construct_3">
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176 <assert_contents>
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177 <has_n_lines min="20" />
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178 </assert_contents>
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179 </element>
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180 </output_collection>
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181 </test>
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182 <!--test lcr_assembly class-->
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183 <test>
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184 <param name="genbank_files">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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185 <collection type="list">
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186 <element name="RFP_GFP_plasmid_BOs" value="lcr_assembly_dataset/RFP_GFP_plasmid_BOs.fa" />
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187 <element name="RFP_GFP_plasmid_parts" value="lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa" />
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188 </collection>
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189 </param>
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190 <param name="assembly_csv" value="lcr_assembly_dataset/assembly_plan.csv" />
2
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191 <conditional name="json_use">
1
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192 <param name='use_json_paramers' value='false' />
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193 <param name='assembly_plan_name' value='LigaseCyclingReactionAssembly' />
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194 <param name="topology" value="circular"/>
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195 </conditional>
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196 <param name="use_file_names_as_ids" value="True" />
0
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197 <output name="output_zip" ftype='zip'>
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198 <assert_contents>
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199 <has_archive_member path=".*" n="68"/>
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200 <has_archive_member path="assambly_simulation/Report.pdf">
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201 <has_size min="5"/>
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202 </has_archive_member>
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203 </assert_contents>
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204 </output>
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205 <output_collection name="construct_gb" type="list" count="0">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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206 </output_collection>
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207 </test>
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208 <!--test BASIC_assembly class-->
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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209 <test>
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210 <param name="genbank_files">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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211 <collection type="list">
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212 <element name="GFP" value="BASIC_assembly_dataset/GFP.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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213 <element name="p15A_kan" value="BASIC_assembly_dataset/p15A_kan.gb" />
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214 <element name="promoter" value="BASIC_assembly_dataset/promoter.gb" />
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215 <element name="RFP" value="BASIC_assembly_dataset/RFP.gb" />
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216 <element name="oligos" value="BASIC_assembly_dataset/oligos.fa" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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217 </collection>
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218 </param>
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219 <param name="assembly_csv" value="BASIC_assembly_dataset/basic_assembly.csv" />
2
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220 <conditional name="json_use">
1
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221 <param name='use_json_paramers' value='false' />
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222 <param name='assembly_plan_name' value='BASICAssembly' />
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223 <param name="topology" value="circular"/>
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224 </conditional>
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225 <param name="use_file_names_as_ids" value="True" />
0
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226 <output name="output_zip" ftype='zip'>
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227 <assert_contents>
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228 <has_archive_member path=".*" n="47"/>
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229 <has_archive_member path="assambly_simulation/Report.pdf">
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230 <has_size min="5"/>
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231 </has_archive_member>
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232 </assert_contents>
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233 </output>
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234 <output_collection name="construct_gb" type="list" count="0">
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235 </output_collection>
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236 </test>
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237 <!--test biobrick_assembly class-->
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238 <test>
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239 <param name="genbank_files">
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240 <collection type="list">
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241 <element name="BBa_E0040_GFP" value="BioBrick_assembly_dataset/BBa_E0040_GFP.gb" />
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242 <element name="BBa_J23119_prom" value="BioBrick_assembly_dataset/BBa_J23119_prom.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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243 <element name="BBa_J23119_prom_flawed" value="BioBrick_assembly_dataset/BBa_J23119_prom_flawed.gb" />
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244 <element name="BBa_J61048_term" value="BioBrick_assembly_dataset/BBa_J61048_term.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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245 <element name="BBa_K611094_bar" value="BioBrick_assembly_dataset/BBa_K611094_bar.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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246 </collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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247 </param>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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248 <param name="assembly_csv" value="BioBrick_assembly_dataset/hierarchical_biobrick.csv" />
2
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249 <conditional name="json_use">
1
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250 <param name='use_json_paramers' value='false' />
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251 <param name='assembly_plan_name' value='BioBrickStandardAssembly' />
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252 <param name="topology" value="circular"/>
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253 </conditional>
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254 <param name="use_file_names_as_ids" value="True" />
0
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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255 <output name="output_zip" ftype='zip'>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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256 <assert_contents>
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257 <has_archive_member path=".*" n="47"/>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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258 <has_archive_member path="assambly_simulation/Report.pdf">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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259 <has_size min="5"/>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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260 </has_archive_member>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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261 </assert_contents>
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262 </output>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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263 <output_collection name="construct_gb" type="list" count="3">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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264 <element name="C1_prom_barcode">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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265 <assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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266 <has_n_lines min="20" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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267 </assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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268 </element>
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269 <element name="C2_gfp_term">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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270 <assert_contents>
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271 <has_n_lines min="20" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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272 </assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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273 </element>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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274 <element name="C3_final">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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275 <assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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276 <has_n_lines min="20" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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277 </assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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278 </element>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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279 </output_collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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280 </test>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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281 <!--test type2s_assembly with domesticated files-->
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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282 <test>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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283 <param name="genbank_files">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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284 <collection type="list">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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285 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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286 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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287 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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288 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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289 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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290 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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291 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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292 </collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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293 </param>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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294 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
2
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295 <conditional name="json_use">
1
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296 <param name='use_json_paramers' value='false' />
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297 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
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298 <param name="topology" value="circular"/>
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299 </conditional>
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300 <param name="use_file_names_as_ids" value="True" />
0
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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301 <param name="domesticated_input">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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302 <collection type="list">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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303 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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304 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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305 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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306 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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307 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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308 </collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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309 </param>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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310 <output name="output_zip" ftype='zip'>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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311 <assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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312 <has_archive_member path=".*" n="62"/>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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313 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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314 <has_size min="5"/>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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315 </has_archive_member>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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316 </assert_contents>
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317 </output>
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318 <output_collection name="construct_gb" type="list" count="4">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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319 <element name="construct_1">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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320 <assert_contents>
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321 <has_n_lines min="20" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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322 </assert_contents>
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323 </element>
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324 <element name="construct_2">
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325 <assert_contents>
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326 <has_n_lines min="20" />
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327 </assert_contents>
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328 </element>
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329 <element name="construct_3">
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330 <assert_contents>
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331 <has_n_lines min="20" />
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332 </assert_contents>
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333 </element>
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334 <element name="construct_4">
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335 <assert_contents>
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336 <has_n_lines min="20" />
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337 </assert_contents>
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338 </element>
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339 </output_collection>
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340 </test>
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341 <!--test only domestication input-->
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342 <test>
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343 <param name="domesticated_input">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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344 <collection type="list">
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345 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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346 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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347 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
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348 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
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349 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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350 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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351 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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352 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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353 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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354 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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355 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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356 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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357 </collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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358 </param>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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359 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
2
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360 <conditional name="json_use">
1
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361 <param name='use_json_paramers' value='false' />
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362 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
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363 <param name="topology" value="circular"/>
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364 </conditional>
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365 <param name="use_file_names_as_ids" value="True" />
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366 <output name="output_zip" ftype='zip'>
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367 <assert_contents>
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368 <has_archive_member path=".*" n="62"/>
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369 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
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370 <has_size min="5"/>
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371 </has_archive_member>
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372 </assert_contents>
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373 </output>
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374 <output_collection name="construct_gb" type="list" count="4">
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375 <element name="construct_1">
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376 <assert_contents>
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377 <has_n_lines min="20" />
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378 </assert_contents>
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379 </element>
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380 <element name="construct_2">
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381 <assert_contents>
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382 <has_n_lines min="20" />
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383 </assert_contents>
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384 </element>
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385 <element name="construct_3">
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386 <assert_contents>
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387 <has_n_lines min="20" />
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388 </assert_contents>
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389 </element>
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390 <element name="construct_4">
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391 <assert_contents>
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392 <has_n_lines min="20" />
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393 </assert_contents>
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394 </element>
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395 </output_collection>
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396 </test>
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397 <!--test JSON param-->
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398 <test>
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399 <param name="genbank_files">
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400 <collection type="list">
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401 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
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diff changeset
402 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
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403 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
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404 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
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405 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
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406 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
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407 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
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408 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
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409 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
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410 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
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411 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
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412 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
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413 </collection>
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414 </param>
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415 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
2
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416 <conditional name="json_use">
1
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417 <param name="use_json_paramers" value='true'/>
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418 <param name="json_conf" value="test-JSON.json" />
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419 </conditional>
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420 <param name="use_file_names_as_ids" value="True" />
0
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421 <output name="output_zip" ftype='zip'>
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422 <assert_contents>
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423 <has_archive_member path=".*" n="62"/>
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424 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
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425 <has_size min="5"/>
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426 </has_archive_member>
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427 </assert_contents>
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428 </output>
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429 <output_collection name="construct_gb" type="list" count="4">
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430 <element name="construct_1">
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431 <assert_contents>
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432 <has_n_lines min="20" />
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433 </assert_contents>
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434 </element>
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435 <element name="construct_2">
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436 <assert_contents>
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437 <has_n_lines min="20" />
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438 </assert_contents>
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439 </element>
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440 <element name="construct_3">
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441 <assert_contents>
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442 <has_n_lines min="20" />
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443 </assert_contents>
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444 </element>
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445 <element name="construct_4">
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446 <assert_contents>
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447 <has_n_lines min="20" />
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448 </assert_contents>
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449 </element>
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450 </output_collection>
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451 </test>
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452 </tests>
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453
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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454 <help><![CDATA[
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455 Cloning_Simulation
2
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456 ====================
0
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457
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458 The Cloning Simulation tool is based on the DnaCauldron package developed by the EGF Biofoundry. It enables rapid and accurate assembly simulation of DNA parts for modular cloning systems, such as Golden Gate Assembly (complete documentation `here <https://edinburgh-genome-foundry.github.io/DnaCauldron/>`_).
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459
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460 **Parameters**:
2
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461 ----------------
1
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462 * **Use parameters from JSON**: Yes/No parameter to ask user if he wants to set parameters manually or using JSON file.
0
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463 * **Assemby csv**: csv file containes the construct names with their parts. (Without Header)
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464 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s).
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465 * **Domesticated GenBank**: Dimesticated GenBank list (Optional)
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466 * **Topology**: Can be "circular", "linear".
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467 * **Enzyme**: It will be selected automatically, or you can set one from this dictionnary : `dict <https://github.com/biopython/biopython/blob/master/Bio/Restriction/Restriction_Dictionary.py>`_
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468 * **Assembly Class**:
2
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469 - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `Golden Gate dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_golden_gate>`_
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470 - "gibson_assembly": GibsonAssembly `Gibson dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/gibson_assembly>`_
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471 - "BASIC_assembly": BASICAssembly `BASIC dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/BASIC_assembly>`_
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472 - "biobrick_assembly": BioBrickStandardAssembly, `biobrick dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_biobrick>`_
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473 - "lcr_assembly": LigaseCyclingReactionAssembly `lcr dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/lcr_assembly>`_
0
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474 ]]></help>
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475 <citations>
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476 <citation type="bibtex">
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477 @unpublished{cloning_simulation
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478 author = {Ramiz Khaled},
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479 title = {{cloning_simulation}},
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480 url = {https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb},
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481 }
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482 </citation>
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483 </citations>
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484 </tool>