annotate optdoe.xml @ 0:7f13e58f1532 draft

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

<tool id="OptDoE" name="Design of Experiment" version="2.0.1">
    <description>An optimal design of experiments (DoE) base package for synthetic biology</description>
    <requirements>
        <requirement type="package" version="v2.0.1">doebase</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python -m doebase
            --func doeGetSBOL
            #if $adv.genes_sbol_file
                --sbol_file '$adv.genes_sbol_file'
            #end if
            #if $adv.ref_parts_file
                --ref_parts_file '$adv.ref_parts_file'
            #end if
            --libsize '$adv.libsize'
            --get_sequences '$adv.get_sequences'
            --backtranslate '$adv.backtranslate'
            --codon_table '$adv.codon_table'
            '$genes_file'
            '$constructs'
    ]]></command>
    <inputs>
        <param name="genes_file" type="data" format="csv" label="Genes" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="genes_sbol_file" type="data" format="xml" label="Optimised Genes" optional="true"/>
            <param name="ref_parts_file" type="data" format="xml" value="None" label="Ref Parts" optional="true"/>
            <param name="libsize" type="integer" value="32" label="Maximal library size" />
            <param name="get_sequences" type="boolean" label="" checked="true" />
            <param name="backtranslate" type="boolean" label="" checked="true" />
            <param name="codon_table" type="text" value="Eecoli.cut" label="" />
        </section>
    </inputs>
    <outputs>
        <data name="constructs" format="xml" label="Constructs" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with default parameters  -->
            <param name="genes_file" value="genes_lycopene.csv" />
            <output name="constructs" file="constructs_lycopene.xml" ftype="xml" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
OptDoE
===========
This tool takes as input a rpSBML file, that contains for each heterologous reaction a ranked list of UniProt identifiers for the sequences, and the list of links to the DNA registry SynBioHub for the desired vector backbones, resistance cassette, and promoters (generated using the tool "OptDoE Parts Reference Generator"). An optimal design of experiments is performed by using OptBioDes based on logistic regression analysis with an assumed linear model for the response. The design is evaluated by its D-efficiency, defined as:

.. math:: D_{eff} = \frac{1}{n}\abs{X^{T}X}^{\frac{1}{p}}

|

Where n is the number of experimental runs or library size, p is the number of independent variables, and X is the model matrix, i.e., a row for each experimental run and a column for each term in the model. The library size n can be selected and should be above a minimal threshold depending on the number of combinatorial complexity of the library. 
The experimental design can be evaluated through the provided diagnostics for D-efficiency, power analysis, and relative prediction variance, allowing the optimal selection of library size. 
The resulting design is provided as an SBOL collection containing the definition of each DNA component and the combinatorial library of constructs.

.. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/OptDoE/img/image3.png
	:width: 80 %
	:align: center


.. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/OptDoE/img/image46.png
	:width: 80 %
	:align: center

|

Above are examples of two constructs generated through optimal combinatorial design and represented using SBOL Visual in SynBioHub. 
Note: if advanced parameter "input_parts" is left empty, the following parts are used:


    +---------+------------+--------------------------------------------------+
    | Name    | Type       | SynBioHub                                        |
    +=========+============+==================================================+
    | PlacUV5 | Promoter   | https://synbiohub.org/public/igem/BBa_K1847014/1 |
    +---------+------------+--------------------------------------------------+
    | Ptrc    | Promoter   | https://synbiohub.org/public/igem/BBa_J56012/1   |
    +---------+------------+--------------------------------------------------+
    | BBR1    | Origin     | https://synbiohub.org/public/igem/BBa_I50041/1   |
    +---------+------------+--------------------------------------------------+
    | p15A    | Origin     | https://synbiohub.org/public/igem/BBa_I50032/1   |
    +---------+------------+--------------------------------------------------+
    | ColE1   | Origin     | https://synbiohub.org/public/igem/BBa_J64101/1   |
    +---------+------------+--------------------------------------------------+
    | res1    | Resistance | https://synbiohub.org/public/igem/BBa_I13800/1   |
    +---------+------------+--------------------------------------------------+
    | Ter     | Terminator | https://synbiohub.org/public/igem/BBa_B1006/1    |
    +---------+------------+--------------------------------------------------+
	  
To generate another CSV

Input
-----

Required:

* **genes_file**\ : (string) Path to either tar.xz input collection of rpSBML files or a single rpSBML file.
* **-input_format**\ : (string) Format of the input
* **-input_sbol**\ : (string) Path to the SBOL input file
* **-input_parts**\ : (string) CSV with the genetic parts. Default (if left empty) is the above table. To generate a new compatible CSV file, please use the "OptDoE Parts Reference Generator" tool

Advanced options:

* **genes_sbol_file**\ : (string) Path to the optimised gens file (SBOL)
* **ref_parts_file**\ : (string) CSV with the genetic parts. Default (if left empty) is the above table. To generate a new compatible CSV file, please use the "OptDoE Parts Reference Generator" tool
* **libsize**\ : (integer, default: 32) Maximal library size 
* **get_sequences**\ : (boolean, default: True)
* **backtranslate**\ : (boolean, default: True)
* **codon_table**\ : (text, default: Eecoli.cut)

Output
------

* **constructs**\ : (string) Path to the output SBOL file

Project Link
------------

* `Original Project <https://github.com/pablocarb/doebase>`_

Authors
-------

* **Pablo Carbonell**

License
-------

`MIT <https://raw.githubusercontent.com/pablocarb/appoptdes/master/LICENSE>`_

Acknowledgments
---------------

* Joan Hérisson
* Thomas Duigou
    ]]></help>
</tool>