| Previous changeset 2:8a087d7546b8 (2022-03-28) Next changeset 4:9ba4dab7f0ba (2022-05-06) |
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Commit message:
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty" |
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modified:
rpbasicdesign.xml |
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| diff -r 8a087d7546b8 -r e4821c820f7c rpbasicdesign.xml --- a/rpbasicdesign.xml Mon Mar 28 14:16:59 2022 +0000 +++ b/rpbasicdesign.xml Wed Mar 30 09:04:23 2022 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="19.09">\n+<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09">\n <description>Build DNA-BOT input files from rpSBML</description>\n <macros>\n <token name="@TOOL_VERSION@">1.0.1</token>\n@@ -23,7 +23,7 @@\n --max_enz_per_rxn $adv.max_enz_per_rxn\n ]]></command>\n <inputs>\n- <param name="rpsbml_file" type="data" format="xml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/>\n+ <param name="rpsbml_file" type="data" format="sbml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/>\n <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.">\n <sanitizer invalid_char="">\n <valid initial="string.letters,string.digits">\n@@ -34,11 +34,10 @@\n </valid>\n </sanitizer>\n <validator type="empty_field" message="Backbone ID is required"/>\n- <validator type="regex">[0-9a-zA-Z_:-]+</validator>\n </param>\n- <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Number of constructs to generate" help="Number of construct to generate."/>\n+ <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Sample size" help="Number of construct to generate."/>\n <section name="adv" title="Advanced Options" expanded="false">\n- <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" />\n+ <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)" />\n <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." >\n <sanitizer invalid_char="">\n <valid initial="string.letters,string.digits">\n@@ -62,21 +61,21 @@\n <validator type="empty_field" message="LMP ID is required"/>\n </param>\n <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." />\n- <param argument="--sbol_output" type="boolean" checked="false" truevalue="--o_sbol_dir out/sbol_export" falsevalue="" label="Output SBOL results?" help="Output folder to write SBOL depictions of constructs." />\n+ <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" />\n <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."/>\n </section>\n </inputs>\n <outputs>\n <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" />\n- <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/>\n- <data name="B'..b' <output name="Biolegio_plate" file="biolegio_plate_muconate.csv" ftype="csv" compare="diff"/>\n </test>\n </tests>\n <help><![CDATA[\n rpbasicdesign\n ================\n \n-Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding\n-enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly\n-chosen from a default list. CDSs, in other words gene variants, of enzymes are\n-randomly chosen from amongst the UniProt IDs extracted. Constructs generated\n-can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL\n-files.\n+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.\n \n Input\n -----\n \n Required:\n \n-* **rpsbml_file**\\ : (string) rpSBML file from which enzymes UniProt IDs will be collected.\n+* **rpSBML file**\\ : rpSBML file from which enzymes UniProt IDs will be collected.\n \n Advanced options:\n \n-* **parts_files**\\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, data/user_parts.csv]\n-* **lms_id**\\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.\n-* **lmp_id**\\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.\n-* **backbone_id**\\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.\n-* **sample_size**\\ : (int) Number of construct to generate. Default: 88.\n-* **cds_permutation**\\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.\n-* **max_enz_per_rxn**\\ : (integer) 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). \n+* **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).\n+* **LMS part ID**\\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.\n+* **LMP part ID**\\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.\n+* **Backbone part ID**\\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.\n+* **Sample size**\\ : (int) Number of construct to generate. Default: 88.\n+* **Perform CDS permutation?**\\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.\n+* **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). \n \n Output\n ------\n \n-* **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.\n-* **o_sbol_dir**\\ : (string) Output folder to write SBOL depictions of constructs. Existing files will be overwritten. Default: not output.\n+* **constructs**\\ : CSV construct file listing the constructs to be built.\n+* **User parts plate**\\ : CSV file listing the DNA parts to be included into each construct.\n+* **Biolegio plate**\\ : CSV file listing the plate coordinates of the BASIC linkers.\n+* **SBOL constructs**\\ : (optional) one SBOL (Synthetic Biology Open Language) file is produced for each construct generated in XML format. \n \n Project Links\n ------------------\n' |