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comparison cloning_similation.xml @ 13:7d1778f5e164 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 26 May 2025 10:10:46 +0000
parents 07e902da89ad
children 16ccb36aa8e3
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12:556649b3f9bb 13:7d1778f5e164
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' && echo DEBUG && ls 'outdir_gb'
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="Assemby 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"/>
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">linear</option>
58 <option value="circular">circular</option> 58 <option value="circular" selected="True">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="enzyme" type="text" label="Enzyme" value="auto" optional="True"/> 61 <param name="enzyme" type="text" label="Enzyme" value="auto" optional="True"/>
62 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" /> 62 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" />
63 </section> 63 </section>