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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit e8c8f102cab10531ed588be4ecb8a0d01e797f09
author tduigou
date Tue, 06 Jan 2026 11:34:13 +0000
parents 2655e08cd61a
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1:2655e08cd61a 2:e7ecf6e21b49
1 <tool id="cloning_simulation" name="Cloning Simulation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="cloning_simulation" name="Cloning Simulation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>A cloning simulator for synthetic biology</description> 2 <description>A cloning simulator for synthetic biology</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">1</token> 4 <token name="@VERSION_SUFFIX@">2</token>
5 <token name="@TOOL_VERSION@">0.2.0</token> 5 <token name="@TOOL_VERSION@">0.2.0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="0.1.11">flametree</requirement> 8 <requirement type="package" version="0.1.11">flametree</requirement>
9 <requirement type="package" version="1.85"> biopython </requirement> 9 <requirement type="package" version="1.85"> biopython </requirement>
32 --domesticated_seq '$domesticated_input_paths' 32 --domesticated_seq '$domesticated_input_paths'
33 --assembly_csv 'assembly_csv.csv' 33 --assembly_csv 'assembly_csv.csv'
34 --file_name_mapping '$file_name_mapping' 34 --file_name_mapping '$file_name_mapping'
35 --file_name_mapping_dom '$file_name_mapping_dom' 35 --file_name_mapping_dom '$file_name_mapping_dom'
36 --use_json_paramers '$json_use.use_json_paramers' 36 --use_json_paramers '$json_use.use_json_paramers'
37 #if not $json_use.use_json_paramers: 37 #if $json_use.use_json_paramers=='false':
38 --enzyme '$json_use.enzyme' 38 --enzyme '$json_use.enzyme'
39 --topology '$json_use.topology' 39 --topology '$json_use.topology'
40 --assembly_plan_name '$json_use.assembly_plan_name' 40 --assembly_plan_name '$json_use.assembly_plan_name'
41 #else: 41 #else:
42 --json_conf '$json_use.json_conf' 42 --json_conf '$json_use.json_conf'
50 <inputs> 50 <inputs>
51 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" optional="True"/> 51 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" optional="True"/>
52 <param name="assembly_csv" type="data" format="csv" label="Assemby csv"/> 52 <param name="assembly_csv" type="data" format="csv" label="Assemby csv"/>
53 <param name="domesticated_input" type="data_collection" collection_type="list" format="genbank" label="Domesticated GenBank" optional="True"/> 53 <param name="domesticated_input" type="data_collection" collection_type="list" format="genbank" label="Domesticated GenBank" optional="True"/>
54 <conditional name="json_use"> 54 <conditional name="json_use">
55 <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" /> 55 <param name="use_json_paramers" type="select" label="Use parameters from JSON" help="extract parameters from json file">
56 <option value="true">Get Parameters From JSON</option>
57 <option value="false" selected="true">Set Parameters Manually</option>
58 </param>
56 <when value="false"> 59 <when value="false">
57 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class"> 60 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
58 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option> 61 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
59 <option value="GibsonAssembly">Gibson_assembly</option> 62 <option value="GibsonAssembly">Gibson_assembly</option>
60 <option value="BASICAssembly">BASIC_assembly</option> 63 <option value="BASICAssembly">BASIC_assembly</option>
97 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" /> 100 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
98 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" /> 101 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
99 </collection> 102 </collection>
100 </param> 103 </param>
101 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" /> 104 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
102 <conditional nam="json_use"> 105 <conditional name="json_use">
103 <param name='use_json_paramers' value='false' /> 106 <param name='use_json_paramers' value='false' />
104 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' /> 107 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
105 <param name="topology" value="circular"/> 108 <param name="topology" value="circular"/>
106 </conditional> 109 </conditional>
107 <param name="use_file_names_as_ids" value="True" /> 110 <param name="use_file_names_as_ids" value="True" />
142 <collection type="list"> 145 <collection type="list">
143 <element name="gibson_sequences" value="Gibson_assembly_dataset/gibson_sequences.fa" /> 146 <element name="gibson_sequences" value="Gibson_assembly_dataset/gibson_sequences.fa" />
144 </collection> 147 </collection>
145 </param> 148 </param>
146 <param name="assembly_csv" value="Gibson_assembly_dataset/gibson_assembly.csv" /> 149 <param name="assembly_csv" value="Gibson_assembly_dataset/gibson_assembly.csv" />
147 <conditional nam="json_use"> 150 <conditional name="json_use">
148 <param name='use_json_paramers' value='false' /> 151 <param name='use_json_paramers' value='false' />
149 <param name='assembly_plan_name' value='GibsonAssembly' /> 152 <param name='assembly_plan_name' value='GibsonAssembly' />
150 <param name="topology" value="circular"/> 153 <param name="topology" value="circular"/>
151 </conditional> 154 </conditional>
152 <param name="use_file_names_as_ids" value="True" /> 155 <param name="use_file_names_as_ids" value="True" />
183 <element name="RFP_GFP_plasmid_BOs" value="lcr_assembly_dataset/RFP_GFP_plasmid_BOs.fa" /> 186 <element name="RFP_GFP_plasmid_BOs" value="lcr_assembly_dataset/RFP_GFP_plasmid_BOs.fa" />
184 <element name="RFP_GFP_plasmid_parts" value="lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa" /> 187 <element name="RFP_GFP_plasmid_parts" value="lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa" />
185 </collection> 188 </collection>
186 </param> 189 </param>
187 <param name="assembly_csv" value="lcr_assembly_dataset/assembly_plan.csv" /> 190 <param name="assembly_csv" value="lcr_assembly_dataset/assembly_plan.csv" />
188 <conditional nam="json_use"> 191 <conditional name="json_use">
189 <param name='use_json_paramers' value='false' /> 192 <param name='use_json_paramers' value='false' />
190 <param name='assembly_plan_name' value='LigaseCyclingReactionAssembly' /> 193 <param name='assembly_plan_name' value='LigaseCyclingReactionAssembly' />
191 <param name="topology" value="circular"/> 194 <param name="topology" value="circular"/>
192 </conditional> 195 </conditional>
193 <param name="use_file_names_as_ids" value="True" /> 196 <param name="use_file_names_as_ids" value="True" />
212 <element name="RFP" value="BASIC_assembly_dataset/RFP.gb" /> 215 <element name="RFP" value="BASIC_assembly_dataset/RFP.gb" />
213 <element name="oligos" value="BASIC_assembly_dataset/oligos.fa" /> 216 <element name="oligos" value="BASIC_assembly_dataset/oligos.fa" />
214 </collection> 217 </collection>
215 </param> 218 </param>
216 <param name="assembly_csv" value="BASIC_assembly_dataset/basic_assembly.csv" /> 219 <param name="assembly_csv" value="BASIC_assembly_dataset/basic_assembly.csv" />
217 <conditional nam="json_use"> 220 <conditional name="json_use">
218 <param name='use_json_paramers' value='false' /> 221 <param name='use_json_paramers' value='false' />
219 <param name='assembly_plan_name' value='BASICAssembly' /> 222 <param name='assembly_plan_name' value='BASICAssembly' />
220 <param name="topology" value="circular"/> 223 <param name="topology" value="circular"/>
221 </conditional> 224 </conditional>
222 <param name="use_file_names_as_ids" value="True" /> 225 <param name="use_file_names_as_ids" value="True" />
241 <element name="BBa_J61048_term" value="BioBrick_assembly_dataset/BBa_J61048_term.gb" /> 244 <element name="BBa_J61048_term" value="BioBrick_assembly_dataset/BBa_J61048_term.gb" />
242 <element name="BBa_K611094_bar" value="BioBrick_assembly_dataset/BBa_K611094_bar.gb" /> 245 <element name="BBa_K611094_bar" value="BioBrick_assembly_dataset/BBa_K611094_bar.gb" />
243 </collection> 246 </collection>
244 </param> 247 </param>
245 <param name="assembly_csv" value="BioBrick_assembly_dataset/hierarchical_biobrick.csv" /> 248 <param name="assembly_csv" value="BioBrick_assembly_dataset/hierarchical_biobrick.csv" />
246 <conditional nam="json_use"> 249 <conditional name="json_use">
247 <param name='use_json_paramers' value='false' /> 250 <param name='use_json_paramers' value='false' />
248 <param name='assembly_plan_name' value='BioBrickStandardAssembly' /> 251 <param name='assembly_plan_name' value='BioBrickStandardAssembly' />
249 <param name="topology" value="circular"/> 252 <param name="topology" value="circular"/>
250 </conditional> 253 </conditional>
251 <param name="use_file_names_as_ids" value="True" /> 254 <param name="use_file_names_as_ids" value="True" />
287 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" /> 290 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
288 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" /> 291 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
289 </collection> 292 </collection>
290 </param> 293 </param>
291 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" /> 294 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
292 <conditional nam="json_use"> 295 <conditional name="json_use">
293 <param name='use_json_paramers' value='false' /> 296 <param name='use_json_paramers' value='false' />
294 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' /> 297 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
295 <param name="topology" value="circular"/> 298 <param name="topology" value="circular"/>
296 </conditional> 299 </conditional>
297 <param name="use_file_names_as_ids" value="True" /> 300 <param name="use_file_names_as_ids" value="True" />
352 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" /> 355 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
353 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" /> 356 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
354 </collection> 357 </collection>
355 </param> 358 </param>
356 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" /> 359 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
357 <conditional nam="json_use"> 360 <conditional name="json_use">
358 <param name='use_json_paramers' value='false' /> 361 <param name='use_json_paramers' value='false' />
359 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' /> 362 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
360 <param name="topology" value="circular"/> 363 <param name="topology" value="circular"/>
361 </conditional> 364 </conditional>
362 <param name="use_file_names_as_ids" value="True" /> 365 <param name="use_file_names_as_ids" value="True" />
408 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" /> 411 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
409 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" /> 412 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
410 </collection> 413 </collection>
411 </param> 414 </param>
412 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" /> 415 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
413 <conditional nam="json_use"> 416 <conditional name="json_use">
414 <param name="use_json_paramers" value='true'/> 417 <param name="use_json_paramers" value='true'/>
415 <param name="json_conf" value="test-JSON.json" /> 418 <param name="json_conf" value="test-JSON.json" />
416 </conditional> 419 </conditional>
417 <param name="use_file_names_as_ids" value="True" /> 420 <param name="use_file_names_as_ids" value="True" />
418 <output name="output_zip" ftype='zip'> 421 <output name="output_zip" ftype='zip'>
448 </test> 451 </test>
449 </tests> 452 </tests>
450 453
451 <help><![CDATA[ 454 <help><![CDATA[
452 Cloning_Simulation 455 Cloning_Simulation
453 ==================== 456 ====================
454 457
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/>`_). 458 The Cloning Simulation tool is based on the DnaCauldron package developed by the EGF Biofoundry. It enables rapid and accurate assembly simulation of DNA parts for modular cloning systems, such as Golden Gate Assembly (complete documentation `here <https://edinburgh-genome-foundry.github.io/DnaCauldron/>`_).
456 459
457 **Parameters**: 460 **Parameters**:
458 --------------- 461 ----------------
459 * **Use parameters from JSON**: Yes/No parameter to ask user if he wants to set parameters manually or using JSON file. 462 * **Use parameters from JSON**: Yes/No parameter to ask user if he wants to set parameters manually or using JSON file.
460 * **Assemby csv**: csv file containes the construct names with their parts. (Without Header) 463 * **Assemby csv**: csv file containes the construct names with their parts. (Without Header)
461 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s). 464 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s).
462 * **Domesticated GenBank**: Dimesticated GenBank list (Optional) 465 * **Domesticated GenBank**: Dimesticated GenBank list (Optional)
463 * **Topology**: Can be "circular", "linear". 466 * **Topology**: Can be "circular", "linear".
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>`_ 467 * **Enzyme**: It will be selected automatically, or you can set one from this dictionnary : `dict <https://github.com/biopython/biopython/blob/master/Bio/Restriction/Restriction_Dictionary.py>`_
465 * **Assembly Class**: 468 * **Assembly Class**:
466 - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_golden_gate>`_ 469 - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `Golden Gate dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_golden_gate>`_
467 - "gibson_assembly": GibsonAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/gibson_assembly>`_ 470 - "gibson_assembly": GibsonAssembly `Gibson dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/gibson_assembly>`_
468 - "BASIC_assembly": BASICAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/BASIC_assembly>`_ 471 - "BASIC_assembly": BASICAssembly `BASIC dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/BASIC_assembly>`_
469 - "biobrick_assembly": BioBrickStandardAssembly, `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_biobrick>`_ 472 - "biobrick_assembly": BioBrickStandardAssembly, `biobrick dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_biobrick>`_
470 - "lcr_assembly": LigaseCyclingReactionAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/lcr_assembly>`_ 473 - "lcr_assembly": LigaseCyclingReactionAssembly `lcr dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/lcr_assembly>`_
471 ]]></help> 474 ]]></help>
472 <citations> 475 <citations>
473 <citation type="bibtex"> 476 <citation type="bibtex">
474 @unpublished{cloning_simulation 477 @unpublished{cloning_simulation
475 author = {Ramiz Khaled}, 478 author = {Ramiz Khaled},