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Uploaded rpbasicdesign 0.3.4
author | tduigou |
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date | Thu, 18 Nov 2021 13:17:02 +0000 |
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<tool id="rpbasicdesign" name="BasicDesign" version="0.3.4"> <description>Build DNA-BOT input files from rpSBML</description> <requirements> <requirement type="package" version="0.3.4">rpbasicdesign</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ python -m rpbasicdesign.cli --rpsbml_file '$rpsbml_file' #if $adv.parts_files #set files = '" "'.join([str($file) for $file in $adv.parts_files]) --parts_files "${files}" #end if --lms_id '$adv.lms_id' --lmp_id '$adv.lmp_id' --backbone_id '$backbone_id' --sample_size '$sample_size' #if str($adv.cds_permutation) == "true" --cds_permutation true #else --cds_permutation false #end if --o_dnabot_dir 'out/dnabot_in' --o_sbol_dir 'out/sbol_export' ]]></command> <inputs> <param name="rpsbml_file" type="data" format="xml" label="rpSBML file"/> <param name="backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" /> <param name="sample_size" type="integer" value="3" label="Number of construct to generate" /> <section name="adv" title="Advanced Options" expanded="false"> <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" /> <param name="lms_id" type="text" value="LMS" label="LMS part ID" /> <param name="lmp_id" type="text" value="LMP" label="LMP part ID" /> <param name="cds_permutation" type="boolean" label="Perform CDS permutation?" checked="true" /> </section> </inputs> <outputs> <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} - ${rpsbml_file.name}: constructs" /> <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} - ${rpsbml_file.name}: User parts plate"/> <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} - ${rpsbml_file.name}: Biolegio plate"/> <collection name="sbol_dir" type="list" label="${tool.name} - ${rpsbml_file.name}: SBOL constructs"> <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" /> </collection> </outputs> <tests> <test> <!-- test 1: check if identical outputs are produced --> <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" /> <param name="sample_size" value="3" /> <output name="Constructs" file="constructs.csv" ftype="csv" compare="diff"/> <output name="User parts plate" file="user_parts_plate.csv" ftype="csv" compare="diff"/> <output name="Biolegio plate" file="biolegio_plate.csv" ftype="csv" compare="diff"/> <output_collection name="sbol_dir" type="list"> <discovered_dataset designation="BASIC_construct_A1" ftype="xml" file="BASIC_construct_A1.xml"/> <discovered_dataset designation="BASIC_construct_B1" ftype="xml" file="BASIC_construct_B1.xml"/> <discovered_dataset designation="BASIC_construct_C1" ftype="xml" file="BASIC_construct_C1.xml"/> </output_collection> </test> </tests> <help><![CDATA[ rpbasicdesign ================ Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly chosen from a default list. CDSs, in other words gene variants, of enzymes are randomly chosen from amongst the UniProt IDs extracted. Constructs generated can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL files. Input ----- Required: * **rpsbml_file**\ : (string) rpSBML file from which enzymes UniProt IDs will be collected. Advanced options: * **parts_files**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, user_parts.csv] * **lms_id**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. * **lmp_id**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP. * **backbone_id**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1. * **sample_size**\ : (int) Number of construct to generate.Default: 3. * **cds_permutation**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. Output ------ * **o_dnabot_dir**\ : (string) Output folder to write construct and plate files. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/dnabot_in. * **o_sbol_dir**\ : (string) Output folder to write SBOL depictions of constructs. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/sbol_export. Project Links ------------------ * `GitHub <https://github.com/brsynth/rpbasicdesign>`_ License ------- * `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_ ]]></help> <citations> <citation type="bibtex"> @article{10.1093/synbio/ysaa010, author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S}, title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology}, journal = {Synthetic Biology}, volume = {5}, number = {1}, year = {2020}, month = {07}, issn = {2397-7000}, doi = {10.1093/synbio/ysaa010}, url = {https://doi.org/10.1093/synbio/ysaa010}, note = {ysaa010}, eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf}, } </citation> </citations> </tool>