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comparison cloning_similation.xml @ 6:e1e985913204 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Wed, 21 May 2025 14:53:05 +0000
parents b0134502203b
children 296e5145a862
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5:b0134502203b 6:e1e985913204
14 <requirement type="package" version="0.1.8">sequenticon</requirement> 14 <requirement type="package" version="0.1.8">sequenticon</requirement>
15 <requirement type="package" version="3.1.5">dna_features_viewer</requirement> 15 <requirement type="package" version="3.1.5">dna_features_viewer</requirement>
16 </requirements> 16 </requirements>
17 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
18 #set genbank_file_paths = ','.join([str(f) for f in $genbank_files]) 18 #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
19 #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files]) 19 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
20 #if $domesticated_input 20 #set domesticated_input_paths = ','.join([str(f) for f in $domesticated_input])
21 #set domesticated_input_paths = ','.join([str(f) for f in $domesticated_input]) 21 #set file_name_mapping_dom = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
22 #set file_name_mapping_dom = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input]) 22 #if $domesticated_input_paths != '' and $genbank_file_paths == ''
23 #else 23 #set genbank_file_paths = ','.join([str(f) for f in $domesticated_input])
24 #set domesticated_input_paths = "" 24 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $domesticated_input])
25 #set file_name_mapping_dom = "" 25 #set domesticated_input_paths = ''
26 #set file_name_mapping_dom = ''
26 #end if 27 #end if
27 mkdir 'outdir_zip' && mkdir 'outdir_gb' && 28 mkdir 'outdir_zip' && mkdir 'outdir_gb' &&
28 cp '$assembly_csv' 'assembly_csv.csv' && 29 cp '$assembly_csv' 'assembly_csv.csv' &&
29 python '$__tool_directory__/cloning_simulation.py' 30 python '$__tool_directory__/cloning_simulation.py'
30 --parts_files '$genbank_file_paths' 31 --parts_files '$genbank_file_paths'
36 --use_file_names_as_id '$adv.use_file_names_as_ids' 37 --use_file_names_as_id '$adv.use_file_names_as_ids'
37 --outdir_simulation 'outdir_zip' 38 --outdir_simulation 'outdir_zip'
38 --outdir_gb 'outdir_gb' 39 --outdir_gb 'outdir_gb'
39 --output_simulation 'output_zip.zip' 40 --output_simulation 'output_zip.zip'
40 --enzyme '$adv.enzyme' 41 --enzyme '$adv.enzyme'
41 --topology '$topology'&& 42 --topology '$topology' &&
42 cp 'output_zip.zip' '$output_zip' 43 cp 'output_zip.zip' '$output_zip'
43 ]]></command> 44 ]]></command>
44 <inputs> 45 <inputs>
45 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)"/> 46 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" optional="True"/>
46 <param name="assembly_csv" type="data" format="csv" label="assemnby csv"/> 47 <param name="assembly_csv" type="data" format="csv" label="assemnby csv"/>
47 <param name="domesticated_input" type="data_collection" collection_type="list" format="genbank" label="Domesticated GenBank" value="None" optional="True"/> 48 <param name="domesticated_input" type="data_collection" collection_type="list" format="genbank" label="Domesticated GenBank" optional="True"/>
48 <param name="assembly_plan_name" type="select" label="assembly calss" help="select the assambly class"> 49 <param name="assembly_plan_name" type="select" label="assembly calss" help="select the assambly class">
49 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option> 50 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
50 <option value="GibsonAssembly">Gibson_assembly</option> 51 <option value="GibsonAssembly">Gibson_assembly</option>
51 <option value="BASICAssembly">BASIC_assembly</option> 52 <option value="BASICAssembly">BASIC_assembly</option>
52 <option value="BioBrickStandardAssembly">biobrick_assembly</option> 53 <option value="BioBrickStandardAssembly">biobrick_assembly</option>
303 <has_n_lines min="20" /> 304 <has_n_lines min="20" />
304 </assert_contents> 305 </assert_contents>
305 </element> 306 </element>
306 </output_collection> 307 </output_collection>
307 </test> 308 </test>
309 <!--test only domestication input-->
310 <test>
311 <param name="domesticated_input">
312 <collection type="list">
313 <element name="part_A" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_A.gb" />
314 <element name="part_B" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_B.gb" />
315 <element name="part_C" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_C.gb" />
316 <element name="part_D" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_D.gb" />
317 <element name="part_E" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_E.gb" />
318 <element name="part_F" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_F.gb" />
319 <element name="part_G" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_G.gb" />
320 <element name="part_H" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_H.gb" />
321 <element name="part_I" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_I.gb" />
322 <element name="part_J" value="2-step_golden_gate_parts/parts_for_2-step_golden_gate/part_J.gb" />
323 <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" />
325 </collection>
326 </param>
327 <param name="assembly_csv" value="2-step_golden_gate_parts/2-step-golden_gate_plan.csv" />
328 <param name='assembly_plan_name' value='Type2sRestrictionAssembly' />
329 <param name="topology" value="circular"/>
330 <param name="adv|use_file_names_as_ids" value="True" />
331 <output name="output_zip" ftype='zip'>
332 <assert_contents>
333 <has_archive_member path=".*" n="62"/>
334 <has_archive_member path="assambly_simulation/assembly_plan_graph.pdf">
335 <has_size min="5"/>
336 </has_archive_member>
337 </assert_contents>
338 </output>
339 <output_collection name="construct_gb" type="list" count="4">
340 <element name="construct_1">
341 <assert_contents>
342 <has_n_lines min="20" />
343 </assert_contents>
344 </element>
345 <element name="construct_2">
346 <assert_contents>
347 <has_n_lines min="20" />
348 </assert_contents>
349 </element>
350 <element name="construct_3">
351 <assert_contents>
352 <has_n_lines min="20" />
353 </assert_contents>
354 </element>
355 <element name="construct_4">
356 <assert_contents>
357 <has_n_lines min="20" />
358 </assert_contents>
359 </element>
360 </output_collection>
361 </test>
308 </tests> 362 </tests>
309 363
310 <help><![CDATA[ 364 <help><![CDATA[
311 Cloning_Simulation 365 Cloning_Simulation
312 ==================== 366 ====================
313 367
314 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/>`_). 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/>`_).
315 369
316 **Parameters**: 370 **Parameters**:
317 --------------- 371 ---------------