| Previous changeset 4:9ba4dab7f0ba (2022-05-06) Next changeset 6:ce36e195a61b (2023-05-01) |
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Commit message:
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty" |
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modified:
rpbasicdesign.xml |
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| diff -r 9ba4dab7f0ba -r e743b6118dae rpbasicdesign.xml --- a/rpbasicdesign.xml Fri May 06 16:26:26 2022 +0000 +++ b/rpbasicdesign.xml Tue May 17 14:50:31 2022 +0000 |
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| @@ -1,6 +1,7 @@ -<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09"> +<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> <description>Build DNA-BOT input files from rpSBML</description> <macros> + <token name="@VERSION_SUFFIX@">0</token> <token name="@TOOL_VERSION@">1.1.0</token> </macros> <requirements> @@ -129,18 +130,12 @@ <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. @@ -149,25 +144,18 @@ * **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). * **Maximum number of genes per construct**\ : (int) If more genes are required, i.e. more reactions are described in the input SBML file, then the execution will failed. (Default: 3). - 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> |