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comparison cloning_similation.xml @ 7:296e5145a862 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 23 May 2025 12:53:50 +0000
parents e1e985913204
children 07e902da89ad
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6:e1e985913204 7:296e5145a862
36 --file_name_mapping_dom '$file_name_mapping_dom' 36 --file_name_mapping_dom '$file_name_mapping_dom'
37 --use_file_names_as_id '$adv.use_file_names_as_ids' 37 --use_file_names_as_id '$adv.use_file_names_as_ids'
38 --outdir_simulation 'outdir_zip' 38 --outdir_simulation 'outdir_zip'
39 --outdir_gb 'outdir_gb' 39 --outdir_gb 'outdir_gb'
40 --output_simulation 'output_zip.zip' 40 --output_simulation 'output_zip.zip'
41 --enzyme '$adv.enzyme' 41 --enzyme '$adv.enzyme'
42 --topology '$topology' && 42 --topology '$topology' &&
43 cp 'output_zip.zip' '$output_zip' 43 cp 'output_zip.zip' '$output_zip'
44 ]]></command> 44 ]]></command>
45 <inputs> 45 <inputs>
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="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="assemnby csv"/> 47 <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"/> 48 <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"> 49 <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
50 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option> 50 <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
51 <option value="GibsonAssembly">Gibson_assembly</option> 51 <option value="GibsonAssembly">Gibson_assembly</option>
52 <option value="BASICAssembly">BASIC_assembly</option> 52 <option value="BASICAssembly">BASIC_assembly</option>
53 <option value="BioBrickStandardAssembly">biobrick_assembly</option> 53 <option value="BioBrickStandardAssembly">biobrick_assembly</option>
54 <option value="LigaseCyclingReactionAssembly">lcr_assembly</option> 54 <option value="LigaseCyclingReactionAssembly">lcr_assembly</option>
55 </param> 55 </param>
56 <param name="topology" type="select" label="assambly topology" help="select circular or linear topology"> 56 <param name="topology" type="select" label="Assambly Topology" help="select circular or linear topology">
57 <option value="linear" selected="True">linear</option> 57 <option value="linear" selected="True">linear</option>
58 <option value="circular">circular</option> 58 <option value="circular">circular</option>
59 </param> 59 </param>
60 <section name="adv" title="Advanced Options" expanded="false"> 60 <section name="adv" title="Advanced Options" expanded="false">
61 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use file names as sequence IDs?" /> 61 <param name="enzyme" type="text" label="Enzyme" value="auto" optional="True"/>
62 <param name="enzyme" type="text" label="restrintion enzyme" value="auto" optional="True"/> 62 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" />
63 </section> 63 </section>
64 </inputs> 64 </inputs>
65 <outputs> 65 <outputs>
66 <data format="zip" name="output_zip" label="simulation results"/> 66 <data format="zip" name="output_zip" label="simulation results"/>
67 <collection name="construct_gb" type="list" label="All constrauct GenBank"> 67 <collection name="construct_gb" type="list" label="All Constract GenBank">
68 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" /> 68 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
69 </collection> 69 </collection>
70 </outputs> 70 </outputs>
71 <tests> 71 <tests>
72 <!--test type2s_assembly class--> 72 <!--test type2s_assembly class-->
367 367
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/>`_). 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/>`_).
369 369
370 **Parameters**: 370 **Parameters**:
371 --------------- 371 ---------------
372 * **assemnby csv**: csv file containes the construct names with their parts. 372 * **Assemby csv**: csv file containes the construct names with their parts.
373 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s). 373 * **GenBank files**: Upload all the parts sequences for your assembli(es). Don't forget the receptor vector(s).
374 * **topology**: Can be "circular", "linear". 374 * **Domesticated GenBank**: Dimesticated GenBank list (Optional)
375 * **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>`_ 375 * **Topology**: Can be "circular", "linear".
376 * **assembly_class**: 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>`_
377 * **Assembly Class**:
377 - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_golden_gate>`_ 378 - "GoldenGate_assembly": Type2sRestrictionAssembly (recommended in Domesticated dataset) `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_golden_gate>`_
378 - "gibson_assembly": GibsonAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/gibson_assembly>`_ 379 - "gibson_assembly": GibsonAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/gibson_assembly>`_
379 - "BASIC_assembly": BASICAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/BASIC_assembly>`_ 380 - "BASIC_assembly": BASICAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/BASIC_assembly>`_
380 - "biobrick_assembly": BioBrickStandardAssembly, `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_biobrick>`_ 381 - "biobrick_assembly": BioBrickStandardAssembly, `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/hierarchical_biobrick>`_
381 - "lcr_assembly": LigaseCyclingReactionAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/lcr_assembly>`_ 382 - "lcr_assembly": LigaseCyclingReactionAssembly `ex. dataset <https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master/examples/lcr_assembly>`_