comparison rpbasicdesign.xml @ 1:e73c927dc332 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign commit b4fb63a436c6c8711bacb4f35c1eab17a17efd16

0:cdd6a526bdcf

<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[

        --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="">

                    <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">

                <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"/>

* **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.

1:e73c927dc332

<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>
    <command detect_errors="exit_code"><![CDATA[

        --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
        --max_gene_per_construct $adv.max_gene_per_construct
    ]]></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="">

                    <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 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" 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">

                <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."/>
            <param argument="--max_gene_per_construct" type="integer" value="3" min="1" max="10" label="Maximum number of genes per construct" help="If more genes are required, i.e. more reactions are described in the input SBML file, then the execution will failed."/>
        </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"/>

* **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.