<tool id="dnabot" name="DNA-Bot" version="@TOOL_VERSION@" profile="21.09">
    <description>DNA assembly using BASIC on OpenTrons</description>
    <macros>
        <token name="@TOOL_VERSION@">3.1.0</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="File listing constructs to be implemented."/>
        <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 media for the transformation step."> 
                <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" file="dnabot_scripts.tar" compare="sim_size" decompress="True"/>
        </test>
    </tests>
    <help><![CDATA[
DNA-Bot
============

 **DNA-Bot** tool reads the list of constructs (previously produced by `rpBasicDesign <https://toolshed.g2.bx.psu.edu/view/iuc/rpbasicdesign/cdd6a526bdcf>`_) and the DNA-parts position on the source plates and generates a set of python scripts to drive an Opentrons liquid handling robot for building the plasmids using BASIC assembly method (as decribed in `Storch2015 <https://doi.org/10.1021/sb500356d>`_). 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.

Inputs
------

* **Source Construct**: CSV file listing constructs to be implemented.
* **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 media for the transformation step. 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.

Version
-------

3.1.0

Authors
-------

* **Matthew C Haines**
* Thomas Duigou

License
-------

`MIT <https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT/blob/master/LICENSE>`_


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

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