Mercurial > repos > tduigou > cloning_simulation

annotate cloning_similation.xml @ 16:fbb241adf6c2 draft default tip

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
author tduigou
date Thu, 17 Jul 2025 10:17:24 +0000
parents 074a76e84b80
children
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dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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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>
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4 <token name="@VERSION_SUFFIX@">1</token>
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5 <token name="@TOOL_VERSION@">0.2.0</token>
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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])
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21 #set file_name_mapping_dom = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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22 #if $domesticated_input_paths != '' and $genbank_file_paths == ''
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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23 #set genbank_file_paths = ','.join([str(f) for f in $domesticated_input])
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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24 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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25 #set domesticated_input_paths = ''
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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26 #set file_name_mapping_dom = ''
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27 #end if
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28 mkdir 'outdir_zip' && mkdir 'outdir_gb' &&
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29 cp '$assembly_csv' 'assembly_csv.csv' &&
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30 python '$__tool_directory__/cloning_simulation.py'
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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31 --parts_files '$genbank_file_paths'
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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32 --domesticated_seq '$domesticated_input_paths'
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33 --assembly_csv 'assembly_csv.csv'
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34 --file_name_mapping '$file_name_mapping'
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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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 not $json_use.use_json_paramers:
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38 --enzyme '$json_use.enzyme'
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39 --topology '$json_use.topology'
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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40 --assembly_plan_name '$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'
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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"/>
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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="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" />
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56 <when value="false">
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57 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
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58 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
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59 <option value="GibsonAssembly">Gibson_assembly</option>
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60 <option value="BASICAssembly">BASIC_assembly</option>
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61 <option value="BioBrickStandardAssembly">biobrick_assembly</option>
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62 <option value="LigaseCyclingReactionAssembly">lcr_assembly</option>
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63 </param>
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64 <param name="topology" type="select" label="Assambly Topology" help="select circular or linear topology">
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65 <option value="linear">linear</option>
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66 <option value="circular" selected="True">circular</option>
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67 </param>
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68 <param name="enzyme" type="text" label="Enzyme" value="auto" optional="True"/>
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69 </when>
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70 <when value="true">
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71 <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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72 </when>
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73 </conditional>
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74 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" />
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75 </inputs>
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76 <outputs>
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77 <data format="zip" name="output_zip" label="simulation results (zip)"/>
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78 <collection name="construct_gb" type="list" label="simulation results (gb)">
2
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79 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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80 </collection>
0
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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81 </outputs>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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82 <tests>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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83 <!--test type2s_assembly class-->
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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84 <test>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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85 <param name="genbank_files">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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86 <collection type="list">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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87 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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88 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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89 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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90 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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91 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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92 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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93 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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94 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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95 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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96 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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97 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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98 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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99 </collection>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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100 </param>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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101 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
16
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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102 <conditional nam="json_use">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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103 <param name='use_json_paramers' value='false' />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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104 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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105 <param name="topology" value="circular"/>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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106 </conditional>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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107 <param name="use_file_names_as_ids" value="True" />
0
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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108 <output name="output_zip" ftype='zip'>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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109 <assert_contents>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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110 <has_archive_member path=".*" n="62"/>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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111 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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112 <has_size min="5"/>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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113 </has_archive_member>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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114 </assert_contents>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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115 </output>
3
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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116 <output_collection name="construct_gb" type="list" count="4">
2
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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117 <element name="construct_1">
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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118 <assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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119 <has_n_lines min="20" />
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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120 </assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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121 </element>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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122 <element name="construct_2">
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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123 <assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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124 <has_n_lines min="20" />
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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125 </assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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126 </element>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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127 <element name="construct_3">
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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128 <assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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129 <has_n_lines min="20" />
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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130 </assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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131 </element>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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132 <element name="construct_4">
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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133 <assert_contents>
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134 <has_n_lines min="20" />
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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135 </assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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136 </element>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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137 </output_collection>
0
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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138 </test>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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139 <!--test gibson_assembly class-->
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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140 <test>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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141 <param name="genbank_files">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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142 <collection type="list">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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143 <element name="gibson_sequences" value="Gibson_assembly_dataset/gibson_sequences.fa" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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144 </collection>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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145 </param>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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146 <param name="assembly_csv" value="Gibson_assembly_dataset/gibson_assembly.csv" />
16
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
147 <conditional nam="json_use">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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148 <param name='use_json_paramers' value='false' />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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149 <param name='assembly_plan_name' value='GibsonAssembly' />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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150 <param name="topology" value="circular"/>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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151 </conditional>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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152 <param name="use_file_names_as_ids" value="True" />
0
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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153 <output name="output_zip" ftype='zip'>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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154 <assert_contents>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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155 <has_archive_member path=".*" n="78"/>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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156 <has_archive_member path="assambly_simulation/Report.pdf">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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157 <has_size min="5"/>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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158 </has_archive_member>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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159 </assert_contents>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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160 </output>
3
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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161 <output_collection name="construct_gb" type="list" count="3">
2
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diff changeset
162 <element name="construct_1">
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163 <assert_contents>
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164 <has_n_lines min="20" />
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165 </assert_contents>
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166 </element>
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167 <element name="construct_2">
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168 <assert_contents>
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169 <has_n_lines min="20" />
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170 </assert_contents>
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171 </element>
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172 <element name="construct_3">
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173 <assert_contents>
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174 <has_n_lines min="20" />
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175 </assert_contents>
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176 </element>
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177 </output_collection>
0
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178 </test>
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179 <!--test lcr_assembly class-->
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180 <test>
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181 <param name="genbank_files">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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182 <collection type="list">
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183 <element name="RFP_GFP_plasmid_BOs" value="lcr_assembly_dataset/RFP_GFP_plasmid_BOs.fa" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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184 <element name="RFP_GFP_plasmid_parts" value="lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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185 </collection>
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186 </param>
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187 <param name="assembly_csv" value="lcr_assembly_dataset/assembly_plan.csv" />
16
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188 <conditional nam="json_use">
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189 <param name='use_json_paramers' value='false' />
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190 <param name='assembly_plan_name' value='LigaseCyclingReactionAssembly' />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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191 <param name="topology" value="circular"/>
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192 </conditional>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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193 <param name="use_file_names_as_ids" value="True" />
0
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194 <output name="output_zip" ftype='zip'>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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195 <assert_contents>
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196 <has_archive_member path=".*" n="68"/>
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197 <has_archive_member path="assambly_simulation/Report.pdf">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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198 <has_size min="5"/>
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199 </has_archive_member>
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200 </assert_contents>
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201 </output>
3
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202 <output_collection name="construct_gb" type="list" count="0">
2
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203 </output_collection>
0
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204 </test>
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205 <!--test BASIC_assembly class-->
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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206 <test>
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207 <param name="genbank_files">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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208 <collection type="list">
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209 <element name="GFP" value="BASIC_assembly_dataset/GFP.gb" />
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210 <element name="p15A_kan" value="BASIC_assembly_dataset/p15A_kan.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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211 <element name="promoter" value="BASIC_assembly_dataset/promoter.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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212 <element name="RFP" value="BASIC_assembly_dataset/RFP.gb" />
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213 <element name="oligos" value="BASIC_assembly_dataset/oligos.fa" />
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214 </collection>
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215 </param>
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216 <param name="assembly_csv" value="BASIC_assembly_dataset/basic_assembly.csv" />
16
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217 <conditional nam="json_use">
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218 <param name='use_json_paramers' value='false' />
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219 <param name='assembly_plan_name' value='BASICAssembly' />
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220 <param name="topology" value="circular"/>
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221 </conditional>
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222 <param name="use_file_names_as_ids" value="True" />
0
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223 <output name="output_zip" ftype='zip'>
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224 <assert_contents>
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225 <has_archive_member path=".*" n="47"/>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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226 <has_archive_member path="assambly_simulation/Report.pdf">
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227 <has_size min="5"/>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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228 </has_archive_member>
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229 </assert_contents>
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230 </output>
3
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231 <output_collection name="construct_gb" type="list" count="0">
2
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232 </output_collection>
0
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233 </test>
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234 <!--test biobrick_assembly class-->
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235 <test>
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236 <param name="genbank_files">
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237 <collection type="list">
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238 <element name="BBa_E0040_GFP" value="BioBrick_assembly_dataset/BBa_E0040_GFP.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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239 <element name="BBa_J23119_prom" value="BioBrick_assembly_dataset/BBa_J23119_prom.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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240 <element name="BBa_J23119_prom_flawed" value="BioBrick_assembly_dataset/BBa_J23119_prom_flawed.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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241 <element name="BBa_J61048_term" value="BioBrick_assembly_dataset/BBa_J61048_term.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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242 <element name="BBa_K611094_bar" value="BioBrick_assembly_dataset/BBa_K611094_bar.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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243 </collection>
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244 </param>
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245 <param name="assembly_csv" value="BioBrick_assembly_dataset/hierarchical_biobrick.csv" />
16
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diff changeset
246 <conditional nam="json_use">
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247 <param name='use_json_paramers' value='false' />
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248 <param name='assembly_plan_name' value='BioBrickStandardAssembly' />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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249 <param name="topology" value="circular"/>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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250 </conditional>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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251 <param name="use_file_names_as_ids" value="True" />
0
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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252 <output name="output_zip" ftype='zip'>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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253 <assert_contents>
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254 <has_archive_member path=".*" n="47"/>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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255 <has_archive_member path="assambly_simulation/Report.pdf">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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256 <has_size min="5"/>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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257 </has_archive_member>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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258 </assert_contents>
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259 </output>
3
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260 <output_collection name="construct_gb" type="list" count="3">
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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261 <element name="C1_prom_barcode">
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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262 <assert_contents>
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263 <has_n_lines min="20" />
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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264 </assert_contents>
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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265 </element>
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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266 <element name="C2_gfp_term">
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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267 <assert_contents>
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268 <has_n_lines min="20" />
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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269 </assert_contents>
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270 </element>
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271 <element name="C3_final">
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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272 <assert_contents>
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273 <has_n_lines min="20" />
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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274 </assert_contents>
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275 </element>
2
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276 </output_collection>
0
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277 </test>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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278 <!--test type2s_assembly with domesticated files-->
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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279 <test>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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280 <param name="genbank_files">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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281 <collection type="list">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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282 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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283 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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284 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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285 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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286 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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287 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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288 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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289 </collection>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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290 </param>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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291 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
16
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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292 <conditional nam="json_use">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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293 <param name='use_json_paramers' value='false' />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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294 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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295 <param name="topology" value="circular"/>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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296 </conditional>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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297 <param name="use_file_names_as_ids" value="True" />
0
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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298 <param name="domesticated_input">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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299 <collection type="list">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
300 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
301 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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302 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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303 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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304 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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305 </collection>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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306 </param>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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307 <output name="output_zip" ftype='zip'>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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308 <assert_contents>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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309 <has_archive_member path=".*" n="62"/>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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310 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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311 <has_size min="5"/>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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312 </has_archive_member>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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313 </assert_contents>
dc450979fcd4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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314 </output>
3
044d36066cb3 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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315 <output_collection name="construct_gb" type="list" count="4">
2
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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316 <element name="construct_1">
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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317 <assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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318 <has_n_lines min="20" />
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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319 </assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
320 </element>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
321 <element name="construct_2">
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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322 <assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
323 <has_n_lines min="20" />
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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324 </assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
325 </element>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
326 <element name="construct_3">
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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327 <assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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328 <has_n_lines min="20" />
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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329 </assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
330 </element>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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diff changeset
331 <element name="construct_4">
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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diff changeset
332 <assert_contents>
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
tduigou
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diff changeset
333 <has_n_lines min="20" />
3171db614963 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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334 </assert_contents>
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335 </element>
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336 </output_collection>
0
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337 </test>
6
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338 <!--test only domestication input-->
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339 <test>
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340 <param name="domesticated_input">
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341 <collection type="list">
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342 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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343 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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344 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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345 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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346 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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347 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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348 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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349 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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350 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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351 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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352 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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353 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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354 </collection>
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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355 </param>
e1e985913204 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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356 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
16
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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357 <conditional nam="json_use">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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358 <param name='use_json_paramers' value='false' />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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359 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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360 <param name="topology" value="circular"/>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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361 </conditional>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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362 <param name="use_file_names_as_ids" value="True" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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363 <output name="output_zip" ftype='zip'>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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364 <assert_contents>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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365 <has_archive_member path=".*" n="62"/>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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366 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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367 <has_size min="5"/>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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368 </has_archive_member>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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369 </assert_contents>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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370 </output>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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371 <output_collection name="construct_gb" type="list" count="4">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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372 <element name="construct_1">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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373 <assert_contents>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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374 <has_n_lines min="20" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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375 </assert_contents>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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376 </element>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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377 <element name="construct_2">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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378 <assert_contents>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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379 <has_n_lines min="20" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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380 </assert_contents>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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381 </element>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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382 <element name="construct_3">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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383 <assert_contents>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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384 <has_n_lines min="20" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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385 </assert_contents>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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386 </element>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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387 <element name="construct_4">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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388 <assert_contents>
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389 <has_n_lines min="20" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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390 </assert_contents>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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391 </element>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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392 </output_collection>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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393 </test>
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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394 <!--test JSON param-->
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395 <test>
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396 <param name="genbank_files">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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397 <collection type="list">
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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398 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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399 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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400 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
401 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
402 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
403 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
404 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
405 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
406 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
407 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
408 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
409 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
fbb241adf6c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit af45e5e0e81535ab0423b0bcff8b5b220bb9b4d0-dirty
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diff changeset
410 </collection>
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411 </param>
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412 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
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413 <conditional nam="json_use">
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414 <param name="use_json_paramers" value='true'/>
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415 <param name="json_conf" value="test-JSON.json" />
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416 </conditional>
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417 <param name="use_file_names_as_ids" value="True" />
6
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418 <output name="output_zip" ftype='zip'>
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419 <assert_contents>
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420 <has_archive_member path=".*" n="62"/>
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421 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
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422 <has_size min="5"/>
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423 </has_archive_member>
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424 </assert_contents>
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425 </output>
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426 <output_collection name="construct_gb" type="list" count="4">
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427 <element name="construct_1">
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428 <assert_contents>
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429 <has_n_lines min="20" />
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430 </assert_contents>
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431 </element>
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432 <element name="construct_2">
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433 <assert_contents>
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434 <has_n_lines min="20" />
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435 </assert_contents>
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436 </element>
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437 <element name="construct_3">
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438 <assert_contents>
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439 <has_n_lines min="20" />
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440 </assert_contents>
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441 </element>
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442 <element name="construct_4">
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443 <assert_contents>
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444 <has_n_lines min="20" />
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445 </assert_contents>
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446 </element>
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447 </output_collection>
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448 </test>
0
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449 </tests>
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450
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451 <help><![CDATA[
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452 Cloning_Simulation
6
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453 ====================
0
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454
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455 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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456
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457 **Parameters**:
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458 ---------------
16
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459 * **Use parameters from JSON**: Yes/No parameter to ask user if he wants to set parameters manually or using JSON file.
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460 * **Assemby csv**: csv file containes the construct names with their parts. (Without Header)
0
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461 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s).
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462 * **Domesticated GenBank**: Dimesticated GenBank list (Optional)
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463 * **Topology**: Can be "circular", "linear".
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464 * **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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465 * **Assembly Class**:
0
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466 - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_golden_gate>`_
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467 - "gibson_assembly": GibsonAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/gibson_assembly>`_
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468 - "BASIC_assembly": BASICAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/BASIC_assembly>`_
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469 - "biobrick_assembly": BioBrickStandardAssembly, `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_biobrick>`_
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470 - "lcr_assembly": LigaseCyclingReactionAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/lcr_assembly>`_
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471 ]]></help>
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472 <citations>
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473 <citation type="bibtex">
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474 @unpublished{cloning_simulation
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475 author = {Ramiz Khaled},
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476 title = {{cloning_simulation}},
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477 url = {https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb},
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478 }
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479 </citation>
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480 </citations>
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481 </tool>