<tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="21.09" license="MIT">
    <description>DNA assembly using BASIC on OpenTrons</description>
    <macros>
        <token name="@TOOL_VERSION@">4.1.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">dnabot</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python -m dnabot.dnabot_app
        #if $adv.default_settings_file
            --default_settings_file '$adv.default_settings_file'
        #end if
        nogui
        --construct_path '$construct_file'
        #set files = '" "'.join([str($file) for $file in $plate_files])
        --source_paths "${files}"
        --etoh_well '$adv.etoh_well'
        --soc_column '$adv.soc_column'
        --output_dir 'output'
        && tar -cvf '$dnabot_scripts' 'output'
    ]]></command>
    <inputs>
        <param name="construct_file" type="data" format="csv" label="Source Construct" help="CSV file listing constructs to be implemented where each row corresponds to one construct and consists of a sequence of BASIC linker and DNA part IDs (in an operon format)"/>
        <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" help="File(s) listing parts to be used in constructs." />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="default_settings_file" type="data" format="yaml" optional="true" label="Lab settings file" help="Yaml file providing labware IDs and parameter to be used in the Opentrons scripts." />
            <param argument="--etoh_well" type="select" label="Well coordinate for Ethanol" help="Coordinates of the well plate providing ethanol for the purification step.">
                <option value="A2" >A2</option>
                <option value="A3" >A3</option>
                <option value="A4" >A4</option>
                <option value="A5" >A5</option>
                <option value="A6" >A6</option>
                <option value="A7" >A7</option>
                <option value="A8" >A8</option>
                <option value="A9" >A9</option>
                <option value="A10" >A10</option>
                <option value="A11" selected="true">A11</option>
            </param>
            <param argument="--soc_column" type="select" label="Column coordinate for SOC" help="Coordinate of the column plate providing SOC (Super Optimal broth with Catabolite repression) media for the transformation step. SOC is a nutrient-rich culture media typically used for bacterial transformation."> 
                <option value="1" selected="true">1</option>
                <option value="2" >2</option>
                <option value="3" >3</option>
                <option value="4" >4</option>
                <option value="5" >5</option>
                <option value="6" >6</option>
                <option value="7" >7</option>
                <option value="8" >8</option>
                <option value="9" >9</option>
                <option value="10" >10</option>
                <option value="11" >11</option>
                <option value="12" >12</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="dnabot_scripts" format="tar" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with compress option -->
            <param name="construct_file" value="constructs.csv" />
            <param name="plate_files" value="user_parts_coords.csv,linker_parts_coords.csv"/>
            <output name="dnabot_scripts" ftype="tar">
                <assert_contents>
                    <has_size value="160000" delta="10000"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
DNA-Bot
============

**DNA-Bot** tool reads the list of constructs where each row corresponds to one construct and consists of a sequence of BASIC (Biopart Assembly Standard for Idempotent Cloning) linker and DNA part IDs (in an operon format), and the DNA-parts position on the source plates. The tool generates a set of python scripts to drive an Opentrons liquid handling robot for building the plasmids using BASIC assembly method, as decribed by Storch et al. (10.1021/sb500356d).

These python scripts implement the **4 assembly steps**: clip reactions, purification, assembly and strain transformation. In short, the **Clip reactions** step prepares the mixes for the ligation of the individual DNA parts with the linkers; the **Purification** step purifies the linker-ligated DNA parts using magnetic beads and the Opentrons magnetic module; the **Assembly** step mixes the DNA purified parts to build the final constructs; while the **Transformation** step transforms the chassis micro-organism with the plasmid and inoculates onto agar.

.. image:: ${static_path}/images/DNABOT_WF.PNG
    :width: 90 %
    :align: center

|

Optional parameters can be set by the user to define the plastic labwares to be used, and set protocol parameters such as washing or incubation times for purification step by providing a YAML settings file. Default settings: `<https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/dnabot/default_settings.yaml>`_

Inputs
------

* **Source Construct**: CSV file listing constructs to be implemented where each row corresponds to one construct and consists of a sequence of BASIC linker and DNA part IDs (in an operon format).
* **Plate files**: File(s) listing parts to be used in constructs.
* **Well coordinate for Ethanol**: (string) Coordinates of the well plate providing ethanol for the purification step. Default: A11
* **Column coordinate for SOC**: (integer) Coordinate of the column plate providing SOC (Super Optimal broth with Catabolite repression) media for the transformation step. SOC is a nutrient-rich culture media typically used for bacterial transformation. Default: 1.
* **Lab settings file**: Yaml file providing labware IDs and parameter to be used in the Opentrons scripts: `Default settings <https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/dnabot/default_settings.yaml>`_.


Ouput
-----

* **Dnabot scripts**: DNA-Bot scripts in TAR format which implement the 4 assembly steps and metainformation to keep track of parameters.

Authors
-------

* **Matthew C Haines**
* Thomas Duigou

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

* Marko Storch
* Geoff Baldwin
    ]]></help>
    <citations>
        <citation type="doi">10.1093/synbio/ysaa010</citation>
    </citations>
</tool>