Mercurial > repos > tduigou > cloning_simulation

annotate cloning_similation.xml @ 1:2655e08cd61a draft default tip

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
author tduigou
date Wed, 23 Jul 2025 09:46:59 +0000
parents 3a3b0f7cb5c2
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>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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3 <macros>
1
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4 <token name="@VERSION_SUFFIX@">1</token>
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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[
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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18 #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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19 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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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 == ''
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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23 #set genbank_file_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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24 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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25 #set domesticated_input_paths = ''
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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26 #set file_name_mapping_dom = ''
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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27 #end if
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28 mkdir 'outdir_zip' && mkdir 'outdir_gb' &&
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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29 cp '$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'
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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32 --domesticated_seq '$domesticated_input_paths'
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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33 --assembly_csv 'assembly_csv.csv'
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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34 --file_name_mapping '$file_name_mapping'
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35 --file_name_mapping_dom '$file_name_mapping_dom'
1
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36 --use_json_paramers '$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 '$json_use.topology'
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40 --assembly_plan_name '$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'
1
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47 --output_simulation 'output_zip.zip' &&
0
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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"/>
1
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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" />
0
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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)">
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79 <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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80 </collection>
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81 </outputs>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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82 <tests>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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83 <!--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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84 <test>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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85 <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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86 <collection type="list">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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87 <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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88 <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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89 <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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90 <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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91 <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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92 <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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93 <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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94 <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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95 <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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96 <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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97 <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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98 <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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99 </collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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100 </param>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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101 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
1
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102 <conditional nam="json_use">
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103 <param name='use_json_paramers' value='false' />
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104 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
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105 <param name="topology" value="circular"/>
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106 </conditional>
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107 <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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108 <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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109 <assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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110 <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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111 <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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112 <has_size min="5"/>
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113 </has_archive_member>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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114 </assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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115 </output>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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116 <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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117 <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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118 <assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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119 <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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120 </assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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121 </element>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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122 <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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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 <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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125 </assert_contents>
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126 </element>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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127 <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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128 <assert_contents>
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129 <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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130 </assert_contents>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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131 </element>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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132 <element name="construct_4">
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133 <assert_contents>
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134 <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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135 </assert_contents>
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136 </element>
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137 </output_collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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138 </test>
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139 <!--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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140 <test>
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141 <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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142 <collection type="list">
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143 <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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144 </collection>
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145 </param>
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146 <param name="assembly_csv" value="Gibson_assembly_dataset/gibson_assembly.csv" />
1
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147 <conditional nam="json_use">
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148 <param name='use_json_paramers' value='false' />
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149 <param name='assembly_plan_name' value='GibsonAssembly' />
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150 <param name="topology" value="circular"/>
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151 </conditional>
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152 <param name="use_file_names_as_ids" value="True" />
0
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153 <output name="output_zip" ftype='zip'>
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154 <assert_contents>
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155 <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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156 <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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157 <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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158 </has_archive_member>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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159 </assert_contents>
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160 </output>
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161 <output_collection name="construct_gb" type="list" count="3">
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162 <element name="construct_1">
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163 <assert_contents>
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164 <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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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>
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178 </test>
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179 <!--test lcr_assembly class-->
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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180 <test>
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181 <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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182 <collection type="list">
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183 <element name="RFP_GFP_plasmid_BOs" value="lcr_assembly_dataset/RFP_GFP_plasmid_BOs.fa" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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184 <element name="RFP_GFP_plasmid_parts" value="lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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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" />
1
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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' />
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191 <param name="topology" value="circular"/>
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192 </conditional>
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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'>
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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">
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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>
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202 <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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203 </output_collection>
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204 </test>
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205 <!--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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206 <test>
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207 <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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208 <collection type="list">
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209 <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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210 <element name="p15A_kan" value="BASIC_assembly_dataset/p15A_kan.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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211 <element name="promoter" value="BASIC_assembly_dataset/promoter.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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212 <element name="RFP" value="BASIC_assembly_dataset/RFP.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="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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214 </collection>
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215 </param>
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216 <param name="assembly_csv" value="BASIC_assembly_dataset/basic_assembly.csv" />
1
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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"/>
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226 <has_archive_member path="assambly_simulation/Report.pdf">
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227 <has_size min="5"/>
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228 </has_archive_member>
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229 </assert_contents>
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230 </output>
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231 <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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232 </output_collection>
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233 </test>
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234 <!--test biobrick_assembly class-->
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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235 <test>
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236 <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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237 <collection type="list">
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238 <element name="BBa_E0040_GFP" value="BioBrick_assembly_dataset/BBa_E0040_GFP.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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239 <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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240 <element name="BBa_J23119_prom_flawed" value="BioBrick_assembly_dataset/BBa_J23119_prom_flawed.gb" />
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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241 <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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242 <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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243 </collection>
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244 </param>
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245 <param name="assembly_csv" value="BioBrick_assembly_dataset/hierarchical_biobrick.csv" />
1
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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' />
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249 <param name="topology" value="circular"/>
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250 </conditional>
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251 <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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252 <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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253 <assert_contents>
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254 <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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255 <has_archive_member path="assambly_simulation/Report.pdf">
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256 <has_size min="5"/>
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257 </has_archive_member>
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258 </assert_contents>
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259 </output>
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260 <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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261 <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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262 <assert_contents>
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263 <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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264 </assert_contents>
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265 </element>
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266 <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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267 <assert_contents>
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268 <has_n_lines min="20" />
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269 </assert_contents>
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270 </element>
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271 <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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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 <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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274 </assert_contents>
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275 </element>
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276 </output_collection>
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277 </test>
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278 <!--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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279 <test>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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280 <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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281 <collection type="list">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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282 <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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283 <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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284 <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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285 <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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286 <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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287 <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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288 <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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289 </collection>
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290 </param>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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291 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
1
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292 <conditional nam="json_use">
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293 <param name='use_json_paramers' value='false' />
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294 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
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295 <param name="topology" value="circular"/>
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296 </conditional>
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297 <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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298 <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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299 <collection type="list">
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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300 <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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301 <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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302 <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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303 <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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304 <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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305 </collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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306 </param>
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307 <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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308 <assert_contents>
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309 <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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310 <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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311 <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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312 </has_archive_member>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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313 </assert_contents>
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314 </output>
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315 <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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316 <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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317 <assert_contents>
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318 <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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319 </assert_contents>
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320 </element>
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321 <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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322 <assert_contents>
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323 <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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324 </assert_contents>
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325 </element>
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326 <element name="construct_3">
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327 <assert_contents>
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328 <has_n_lines min="20" />
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329 </assert_contents>
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330 </element>
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331 <element name="construct_4">
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332 <assert_contents>
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333 <has_n_lines min="20" />
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334 </assert_contents>
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335 </element>
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336 </output_collection>
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337 </test>
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338 <!--test only domestication input-->
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339 <test>
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340 <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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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" />
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343 <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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344 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
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345 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
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346 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
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347 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
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348 <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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349 <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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350 <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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351 <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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352 <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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353 <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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354 </collection>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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355 </param>
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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356 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
1
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357 <conditional nam="json_use">
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358 <param name='use_json_paramers' value='false' />
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359 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
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360 <param name="topology" value="circular"/>
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361 </conditional>
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362 <param name="use_file_names_as_ids" value="True" />
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363 <output name="output_zip" ftype='zip'>
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364 <assert_contents>
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365 <has_archive_member path=".*" n="62"/>
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366 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
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367 <has_size min="5"/>
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368 </has_archive_member>
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369 </assert_contents>
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370 </output>
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371 <output_collection name="construct_gb" type="list" count="4">
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372 <element name="construct_1">
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373 <assert_contents>
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374 <has_n_lines min="20" />
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375 </assert_contents>
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376 </element>
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377 <element name="construct_2">
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378 <assert_contents>
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379 <has_n_lines min="20" />
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380 </assert_contents>
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381 </element>
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382 <element name="construct_3">
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383 <assert_contents>
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384 <has_n_lines min="20" />
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385 </assert_contents>
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386 </element>
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387 <element name="construct_4">
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388 <assert_contents>
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389 <has_n_lines min="20" />
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390 </assert_contents>
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391 </element>
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392 </output_collection>
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393 </test>
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394 <!--test JSON param-->
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395 <test>
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396 <param name="genbank_files">
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397 <collection type="list">
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398 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
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399 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
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400 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
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401 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
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402 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
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403 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
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404 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
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405 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
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406 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
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407 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
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408 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
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409 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
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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" />
0
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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>
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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
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453 ====================
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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 ---------------
1
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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.
0
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460 * **Assemby csv**: csv file containes the construct names with their parts. (Without Header)
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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**:
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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>