Mercurial > repos > iuc > rpbasicdesign
diff rpbasicdesign.xml @ 0:cdd6a526bdcf draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign commit bdac148247c9c3d3da3420220d006e723c718277"
author | iuc |
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date | Wed, 30 Mar 2022 13:05:31 +0000 |
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children | e73c927dc332 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpbasicdesign.xml Wed Mar 30 13:05:31 2022 +0000 @@ -0,0 +1,172 @@ +<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09"> + <description>Build DNA-BOT input files from rpSBML</description> + <macros> + <token name="@TOOL_VERSION@">1.0.1</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">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' + $adv.cds_permutation + --o_dnabot_dir 'out/dnabot_in' + $adv.sbol_output + --max_enz_per_rxn $adv.max_enz_per_rxn + ]]></command> + <inputs> + <param name="rpsbml_file" type="data" format="sbml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/> + <param argument="--backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" help="Part ID to be used as the backbone."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value=":" /> + <add value="." /> + <add value="-" /> + <add value="_" /> + </valid> + </sanitizer> + <validator type="empty_field" message="Backbone ID is required"/> + </param> + <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Sample size" help="Number of constructs 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" help="List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: Standard Biolegio Parts (BBP-18500)" /> + <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." > + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value=":" /> + <add value="-" /> + <add value="_" /> + <add value="." /> + </valid> + </sanitizer> + <validator type="empty_field" message="LMS ID is required"/> + </param> + <param argument="--lmp_id" type="text" value="LMP" label="LMP part ID" help="Part ID to be used as the LMP methylated linker."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value=":" /> + <add value="-" /> + <add value="_" /> + <add value="." /> + </valid> + </sanitizer> + <validator type="empty_field" message="LMP ID is required"/> + </param> + <param argument="--cds_permutation" type="boolean" truevalue="--cds_permutation true" falsevalue="--cds_permutation false" checked="true" label="Perform CDS permutation?" help="Whether all combinations of CDS permutation should be built." /> + <param argument="--sbol_output" type="boolean" checked="false" truevalue="--o_sbol_dir out/sbol_export" falsevalue="" label="Output SBOL results?" help="Whether SBOL (Synthetic Biology Open Language) depictions of constructs should be outputted" /> + <param argument="--max_enz_per_rxn" type="integer" value="1" min="1" max="99" label="Maximum number of enyzme to consider per reaction." help="Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept."/> + </section> + </inputs> + <outputs> + <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" /> + <data name="User_parts_plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/> + <data name="Biolegio_plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} on ${rpsbml_file.name}: Biolegio plate"/> + <collection name="sbol_dir" type="list" label="${tool.name} on ${rpsbml_file.name}: SBOL constructs"> + <filter> adv['sbol_output'] </filter> + <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" /> + </collection> + </outputs> + <tests> + <test expect_num_outputs="4"> + <!-- test 1: check if identical outputs are produced (Lycopene input)--> + <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" /> + <param name="sample_size" value="3" /> + <output name="Constructs" file="constructs_lycopene.csv" ftype="csv" compare="diff"> + <assert_contents> + <has_n_lines n="4"/> + </assert_contents> + </output> + <output name="User_parts_plate" file="user_parts_plate_lycopene.csv" ftype="csv" compare="diff"/> + <output name="Biolegio_plate" file="biolegio_plate_lycopene.csv" ftype="csv" compare="diff"/> + <param name="sbol_output" value="true" /> + <output_collection name="sbol_dir" type="list" count="3"> + <element name="BASIC_construct_A1"> + <assert_contents> + <is_valid_xml /> + <has_text text="BASIC_construct_A1" /> + <has_n_lines n="339" /> + </assert_contents> + </element> + <element name="BASIC_construct_B1"> + <assert_contents> + <is_valid_xml /> + <has_text text="BASIC_construct_B1" /> + <has_n_lines n="339" /> + </assert_contents> + </element> + <element name="BASIC_construct_C1"> + <assert_contents> + <is_valid_xml /> + <has_text text="BASIC_construct_C1" /> + <has_n_lines n="339" /> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="3"> + <!-- test 2: check if identical outputs are produced (Muconate input)--> + <param name="rpsbml_file" value="muconate_example.xml" /> + <param name="sample_size" value="88" /> + <output name="Constructs" file="constructs_muconate.csv" ftype="csv" compare="diff"> + <assert_contents> + <has_n_lines n="89"/> + </assert_contents> + </output> + <output name="User_parts_plate" file="user_parts_plate_muconate.csv" ftype="csv" compare="diff"/> + <output name="Biolegio_plate" file="biolegio_plate_muconate.csv" ftype="csv" compare="diff"/> + </test> + </tests> + <help><![CDATA[ +rpbasicdesign +================ + +rpbasicdesign extracts enzyme IDs from rpSBML (System Biology Markup Language) files containing additionnal annotations (e.g. reaction rules ID) and produced by the RP (RetroPath) suite available in `SynBioCAD Galaxy platform <https://galaxy-synbiocad.org/>`_, to generate genetic constructs compliant with the BASIC (Biopart Assembly Standard for Idempotent Cloning) assembly approach. CSV files produced are ready to be used with DNA-Bot to generate instructions for automated build of the genetic constructs using OpenTrons liquid handling robots. + +Input +----- + +Required: + +* **rpSBML file**\ : rpSBML file from which enzymes UniProt IDs will be collected. + +Advanced options: + +* **Linkers and user parts**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: ( `Standard Biolegio Parts <https://www.biolegio.com/>`_: BBP-18500). +* **LMS part ID**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. +* **LMP part ID**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP. +* **Backbone part ID**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1. +* **Sample size**\ : (int) Number of constructs to generate. Default: 88. +* **Perform CDS permutation?**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. +* **Maximum number of enyzme to consider per reaction**\ : (int) Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept. (Default: 1). + +Output +------ + +* **constructs**\ : CSV construct file listing the constructs to be built. +* **User parts plate**\ : CSV file listing the DNA parts to be included into each construct. +* **Biolegio plate**\ : CSV file listing the plate coordinates of the BASIC linkers. +* **SBOL constructs**\ : (optional) one SBOL (Synthetic Biology Open Language) file is produced for each construct generated in XML format. + +Project Links +------------------ + +* `GitHub <https://github.com/brsynth/rpbasicdesign>`_ + +License +------- + +* `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_ + + ]]></help> + <citations> + <citation type="doi">10.1093/synbio/ysaa010</citation> + </citations> +</tool> \ No newline at end of file