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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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0:3a3b0f7cb5c2 1:2655e08cd61a
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@">0</token> 4 <token name="@VERSION_SUFFIX@">1</token>
5 <token name="@TOOL_VERSION@">0.1.0</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>
10 <requirement type="package" version="0.1.10">proglog</requirement> 10 <requirement type="package" version="0.1.10">proglog</requirement>
29 cp '$assembly_csv' 'assembly_csv.csv' && 29 cp '$assembly_csv' 'assembly_csv.csv' &&
30 python '$__tool_directory__/cloning_simulation.py' 30 python '$__tool_directory__/cloning_simulation.py'
31 --parts_files '$genbank_file_paths' 31 --parts_files '$genbank_file_paths'
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 --assembly_plan_name '$assembly_plan_name'
35 --file_name_mapping '$file_name_mapping' 34 --file_name_mapping '$file_name_mapping'
36 --file_name_mapping_dom '$file_name_mapping_dom' 35 --file_name_mapping_dom '$file_name_mapping_dom'
37 --use_file_names_as_id '$adv.use_file_names_as_ids' 36 --use_json_paramers '$json_use.use_json_paramers'
37 #if not $json_use.use_json_paramers:
38 --enzyme '$json_use.enzyme'
39 --topology '$json_use.topology'
40 --assembly_plan_name '$json_use.assembly_plan_name'
41 #else:
42 --json_conf '$json_use.json_conf'
43 #end if
44 --use_file_names_as_id '$use_file_names_as_ids'
38 --outdir_simulation 'outdir_zip' 45 --outdir_simulation 'outdir_zip'
39 --outdir_gb 'outdir_gb' 46 --outdir_gb 'outdir_gb'
40 --output_simulation 'output_zip.zip' 47 --output_simulation 'output_zip.zip' &&
41 --enzyme '$adv.enzyme'
42 --topology '$topology' &&
43 cp 'output_zip.zip' '$output_zip' 48 cp 'output_zip.zip' '$output_zip'
44 ]]></command> 49 ]]></command>
45 <inputs> 50 <inputs>
46 <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"/>
47 <param name="assembly_csv" type="data" format="csv" label="Assemby csv"/> 52 <param name="assembly_csv" type="data" format="csv" label="Assemby csv"/>
48 <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"/>
49 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class"> 54 <conditional name="json_use">
50 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option> 55 <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" />
51 <option value="GibsonAssembly">Gibson_assembly</option> 56 <when value="false">
52 <option value="BASICAssembly">BASIC_assembly</option> 57 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
53 <option value="BioBrickStandardAssembly">biobrick_assembly</option> 58 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
54 <option value="LigaseCyclingReactionAssembly">lcr_assembly</option> 59 <option value="GibsonAssembly">Gibson_assembly</option>
55 </param> 60 <option value="BASICAssembly">BASIC_assembly</option>
56 <param name="topology" type="select" label="Assambly Topology" help="select circular or linear topology"> 61 <option value="BioBrickStandardAssembly">biobrick_assembly</option>
57 <option value="linear">linear</option> 62 <option value="LigaseCyclingReactionAssembly">lcr_assembly</option>
58 <option value="circular" selected="True">circular</option> 63 </param>
59 </param> 64 <param name="topology" type="select" label="Assambly Topology" help="select circular or linear topology">
60 <section name="adv" title="Advanced Options" expanded="false"> 65 <option value="linear">linear</option>
61 <param name="enzyme" type="text" label="Enzyme" value="auto" optional="True"/> 66 <option value="circular" selected="True">circular</option>
62 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" /> 67 </param>
63 </section> 68 <param name="enzyme" type="text" label="Enzyme" value="auto" optional="True"/>
69 </when>
70 <when value="true">
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" />
72 </when>
73 </conditional>
74 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" />
64 </inputs> 75 </inputs>
65 <outputs> 76 <outputs>
66 <data format="zip" name="output_zip" label="simulation results (zip)"/> 77 <data format="zip" name="output_zip" label="simulation results (zip)"/>
67 <collection name="construct_gb" type="list" label="simulation results (gb)"> 78 <collection name="construct_gb" type="list" label="simulation results (gb)">
68 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" /> 79 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
86 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" /> 97 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
87 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" /> 98 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
88 </collection> 99 </collection>
89 </param> 100 </param>
90 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" /> 101 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
91 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' /> 102 <conditional nam="json_use">
92 <param name="topology" value="circular"/> 103 <param name='use_json_paramers' value='false' />
93 <param name="adv|use_file_names_as_ids" value="True" /> 104 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
105 <param name="topology" value="circular"/>
106 </conditional>
107 <param name="use_file_names_as_ids" value="True" />
94 <output name="output_zip" ftype='zip'> 108 <output name="output_zip" ftype='zip'>
95 <assert_contents> 109 <assert_contents>
96 <has_archive_member path=".*" n="62"/> 110 <has_archive_member path=".*" n="62"/>
97 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf"> 111 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
98 <has_size min="5"/> 112 <has_size min="5"/>
128 <collection type="list"> 142 <collection type="list">
129 <element name="gibson_sequences" value="Gibson_assembly_dataset/gibson_sequences.fa" /> 143 <element name="gibson_sequences" value="Gibson_assembly_dataset/gibson_sequences.fa" />
130 </collection> 144 </collection>
131 </param> 145 </param>
132 <param name="assembly_csv" value="Gibson_assembly_dataset/gibson_assembly.csv" /> 146 <param name="assembly_csv" value="Gibson_assembly_dataset/gibson_assembly.csv" />
133 <param name='assembly_plan_name' value='GibsonAssembly' /> 147 <conditional nam="json_use">
134 <param name="topology" value="circular"/> 148 <param name='use_json_paramers' value='false' />
135 <param name="adv|use_file_names_as_ids" value="True" /> 149 <param name='assembly_plan_name' value='GibsonAssembly' />
150 <param name="topology" value="circular"/>
151 </conditional>
152 <param name="use_file_names_as_ids" value="True" />
136 <output name="output_zip" ftype='zip'> 153 <output name="output_zip" ftype='zip'>
137 <assert_contents> 154 <assert_contents>
138 <has_archive_member path=".*" n="78"/> 155 <has_archive_member path=".*" n="78"/>
139 <has_archive_member path="assambly_simulation/Report.pdf"> 156 <has_archive_member path="assambly_simulation/Report.pdf">
140 <has_size min="5"/> 157 <has_size min="5"/>
166 <element name="RFP_GFP_plasmid_BOs" value="lcr_assembly_dataset/RFP_GFP_plasmid_BOs.fa" /> 183 <element name="RFP_GFP_plasmid_BOs" value="lcr_assembly_dataset/RFP_GFP_plasmid_BOs.fa" />
167 <element name="RFP_GFP_plasmid_parts" value="lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa" /> 184 <element name="RFP_GFP_plasmid_parts" value="lcr_assembly_dataset/RFP_GFP_plasmid_parts.fa" />
168 </collection> 185 </collection>
169 </param> 186 </param>
170 <param name="assembly_csv" value="lcr_assembly_dataset/assembly_plan.csv" /> 187 <param name="assembly_csv" value="lcr_assembly_dataset/assembly_plan.csv" />
171 <param name='assembly_plan_name' value='LigaseCyclingReactionAssembly' /> 188 <conditional nam="json_use">
172 <param name="topology" value="circular"/> 189 <param name='use_json_paramers' value='false' />
173 <param name="adv|use_file_names_as_ids" value="True" /> 190 <param name='assembly_plan_name' value='LigaseCyclingReactionAssembly' />
191 <param name="topology" value="circular"/>
192 </conditional>
193 <param name="use_file_names_as_ids" value="True" />
174 <output name="output_zip" ftype='zip'> 194 <output name="output_zip" ftype='zip'>
175 <assert_contents> 195 <assert_contents>
176 <has_archive_member path=".*" n="68"/> 196 <has_archive_member path=".*" n="68"/>
177 <has_archive_member path="assambly_simulation/Report.pdf"> 197 <has_archive_member path="assambly_simulation/Report.pdf">
178 <has_size min="5"/> 198 <has_size min="5"/>
192 <element name="RFP" value="BASIC_assembly_dataset/RFP.gb" /> 212 <element name="RFP" value="BASIC_assembly_dataset/RFP.gb" />
193 <element name="oligos" value="BASIC_assembly_dataset/oligos.fa" /> 213 <element name="oligos" value="BASIC_assembly_dataset/oligos.fa" />
194 </collection> 214 </collection>
195 </param> 215 </param>
196 <param name="assembly_csv" value="BASIC_assembly_dataset/basic_assembly.csv" /> 216 <param name="assembly_csv" value="BASIC_assembly_dataset/basic_assembly.csv" />
197 <param name='assembly_plan_name' value='BASICAssembly' /> 217 <conditional nam="json_use">
198 <param name="topology" value="circular"/> 218 <param name='use_json_paramers' value='false' />
199 <param name="adv|use_file_names_as_ids" value="True" /> 219 <param name='assembly_plan_name' value='BASICAssembly' />
220 <param name="topology" value="circular"/>
221 </conditional>
222 <param name="use_file_names_as_ids" value="True" />
200 <output name="output_zip" ftype='zip'> 223 <output name="output_zip" ftype='zip'>
201 <assert_contents> 224 <assert_contents>
202 <has_archive_member path=".*" n="47"/> 225 <has_archive_member path=".*" n="47"/>
203 <has_archive_member path="assambly_simulation/Report.pdf"> 226 <has_archive_member path="assambly_simulation/Report.pdf">
204 <has_size min="5"/> 227 <has_size min="5"/>
218 <element name="BBa_J61048_term" value="BioBrick_assembly_dataset/BBa_J61048_term.gb" /> 241 <element name="BBa_J61048_term" value="BioBrick_assembly_dataset/BBa_J61048_term.gb" />
219 <element name="BBa_K611094_bar" value="BioBrick_assembly_dataset/BBa_K611094_bar.gb" /> 242 <element name="BBa_K611094_bar" value="BioBrick_assembly_dataset/BBa_K611094_bar.gb" />
220 </collection> 243 </collection>
221 </param> 244 </param>
222 <param name="assembly_csv" value="BioBrick_assembly_dataset/hierarchical_biobrick.csv" /> 245 <param name="assembly_csv" value="BioBrick_assembly_dataset/hierarchical_biobrick.csv" />
223 <param name='assembly_plan_name' value='BioBrickStandardAssembly' /> 246 <conditional nam="json_use">
224 <param name="topology" value="circular"/> 247 <param name='use_json_paramers' value='false' />
225 <param name="adv|use_file_names_as_ids" value="True" /> 248 <param name='assembly_plan_name' value='BioBrickStandardAssembly' />
249 <param name="topology" value="circular"/>
250 </conditional>
251 <param name="use_file_names_as_ids" value="True" />
226 <output name="output_zip" ftype='zip'> 252 <output name="output_zip" ftype='zip'>
227 <assert_contents> 253 <assert_contents>
228 <has_archive_member path=".*" n="47"/> 254 <has_archive_member path=".*" n="47"/>
229 <has_archive_member path="assambly_simulation/Report.pdf"> 255 <has_archive_member path="assambly_simulation/Report.pdf">
230 <has_size min="5"/> 256 <has_size min="5"/>
261 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" /> 287 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
262 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" /> 288 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
263 </collection> 289 </collection>
264 </param> 290 </param>
265 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" /> 291 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
266 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' /> 292 <conditional nam="json_use">
293 <param name='use_json_paramers' value='false' />
294 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
295 <param name="topology" value="circular"/>
296 </conditional>
297 <param name="use_file_names_as_ids" value="True" />
267 <param name="domesticated_input"> 298 <param name="domesticated_input">
268 <collection type="list"> 299 <collection type="list">
269 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" /> 300 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
270 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" /> 301 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
271 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" /> 302 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
272 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" /> 303 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
273 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" /> 304 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
274 </collection> 305 </collection>
275 </param> 306 </param>
276 <param name="topology" value="circular"/>
277 <param name="adv|use_file_names_as_ids" value="True" />
278 <output name="output_zip" ftype='zip'> 307 <output name="output_zip" ftype='zip'>
279 <assert_contents> 308 <assert_contents>
280 <has_archive_member path=".*" n="62"/> 309 <has_archive_member path=".*" n="62"/>
281 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf"> 310 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
282 <has_size min="5"/> 311 <has_size min="5"/>
323 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" /> 352 <element name="part_K" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_K.gb" />
324 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" /> 353 <element name="part_L" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_L.gb" />
325 </collection> 354 </collection>
326 </param> 355 </param>
327 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" /> 356 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
328 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' /> 357 <conditional nam="json_use">
329 <param name="topology" value="circular"/> 358 <param name='use_json_paramers' value='false' />
330 <param name="adv|use_file_names_as_ids" value="True" /> 359 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
360 <param name="topology" value="circular"/>
361 </conditional>
362 <param name="use_file_names_as_ids" value="True" />
363 <output name="output_zip" ftype='zip'>
364 <assert_contents>
365 <has_archive_member path=".*" n="62"/>
366 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
367 <has_size min="5"/>
368 </has_archive_member>
369 </assert_contents>
370 </output>
371 <output_collection name="construct_gb" type="list" count="4">
372 <element name="construct_1">
373 <assert_contents>
374 <has_n_lines min="20" />
375 </assert_contents>
376 </element>
377 <element name="construct_2">
378 <assert_contents>
379 <has_n_lines min="20" />
380 </assert_contents>
381 </element>
382 <element name="construct_3">
383 <assert_contents>
384 <has_n_lines min="20" />
385 </assert_contents>
386 </element>
387 <element name="construct_4">
388 <assert_contents>
389 <has_n_lines min="20" />
390 </assert_contents>
391 </element>
392 </output_collection>
393 </test>
394 <!--test JSON param-->
395 <test>
396 <param name="genbank_files">
397 <collection type="list">
398 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
399 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
400 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
401 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
402 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
403 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
404 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
405 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
406 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
407 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
408 <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" />
410 </collection>
411 </param>
412 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
413 <conditional nam="json_use">
414 <param name="use_json_paramers" value='true'/>
415 <param name="json_conf" value="test-JSON.json" />
416 </conditional>
417 <param name="use_file_names_as_ids" value="True" />
331 <output name="output_zip" ftype='zip'> 418 <output name="output_zip" ftype='zip'>
332 <assert_contents> 419 <assert_contents>
333 <has_archive_member path=".*" n="62"/> 420 <has_archive_member path=".*" n="62"/>
334 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf"> 421 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
335 <has_size min="5"/> 422 <has_size min="5"/>
367 454
368 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/>`_). 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/>`_).
369 456
370 **Parameters**: 457 **Parameters**:
371 --------------- 458 ---------------
459 * **Use parameters from JSON**: Yes/No parameter to ask user if he wants to set parameters manually or using JSON file.
372 * **Assemby csv**: csv file containes the construct names with their parts. (Without Header) 460 * **Assemby csv**: csv file containes the construct names with their parts. (Without Header)
373 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s). 461 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s).
374 * **Domesticated GenBank**: Dimesticated GenBank list (Optional) 462 * **Domesticated GenBank**: Dimesticated GenBank list (Optional)
375 * **Topology**: Can be "circular", "linear". 463 * **Topology**: Can be "circular", "linear".
376 * **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>`_ 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>`_