comparison rpbasicdesign.xml @ 5:e743b6118dae draft

"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"

4:9ba4dab7f0ba

<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@">1.1.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement>
    </requirements>

        </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 construct 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).
* **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>
    </citations>
</tool>

5:e743b6118dae

<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>
        <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement>
    </requirements>

        </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 construct 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).
* **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>
    </citations>
</tool>