<tool id="dnabot" name="DNA-Bot" version="3.0.0">
    <description>DNA assembly using BASIC on OpenTrons</description>
    <requirements>
        <requirement type="package" version="3.0.0">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 '$dnabot_scripts' 'output'
    ]]></command>
    <inputs>
        <param name="construct_file" type="data" format="csv" label="Source Construct" />
        <param name="plate_files" type="data" format="csv" multiple="true" label="Plate files" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="default_settings_file" type="data" format="yaml" optional="true" label="Yaml file providing labware IDs and parameter to be used" />
            <param name="etoh_well" type="select" label="Well coordinate for Ethanol">
                <option value="A2" >A2</option>
                <option value="A3" >A3</option>
                <option value="A4" >A4</option>
                <option value="A5" >A5</option>
                <option value="A6" >A6</option>
                <option value="A7" >A7</option>
                <option value="A8" >A8</option>
                <option value="A9" >A9</option>
                <option value="A10" >A10</option>
                <option value="A11" selected="true">A11</option>
            </param>
            <param name="soc_column" type="select" label="Column coordinate for SOC">
                <option value="1" selected="true">1</option>
                <option value="2" >2</option>
                <option value="3" >3</option>
                <option value="4" >4</option>
                <option value="5" >5</option>
                <option value="6" >6</option>
                <option value="7" >7</option>
                <option value="8" >8</option>
                <option value="9" >9</option>
                <option value="10" >10</option>
                <option value="11" >11</option>
                <option value="12" >12</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="dnabot_scripts" format="tar" label="${tool.name} scripts" />
    </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 assembly using BASIC on OpenTrons

Input
-----

* **default_settings_file**: (string) file providing labware IDs and parameter to be used. Default: dnabot/default_settings.yaml.
* **construct_path**: (string) Construct CSV file.
* **source_paths**: (string) Source CSV files.
* **etoh_well**: (string) Well coordinate for Ethanol. Default: A11.
* **soc_column**: (integer) Column coordinate for SOC. Default: 1.
* **template_dir**: (string) Template directory. Default: "template_ot2_scripts" located next to the present script.

Ouput
-----

* **output_dir**: (string) Output directory. Default: same directory than the one containing the "construct_path" file.

Version
-------

3.0.0

Authors
-------

* **Matthew C Haines**
* Thomas Duigou

License
-------

`MIT <https://github.com/brsynth/DNA-BOT/blob/DNA-BOT-APIv2/LICENSE>`_


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

* Marko Storch
* Geoff Baldwin
    ]]></help>
    <citations>
        <citation type="bibtex">
            @article{10.1093/synbio/ysaa010,
                author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S},
                title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology},
                journal = {Synthetic Biology},
                volume = {5},
                number = {1},
                year = {2020},
                month = {07},
                issn = {2397-7000},
                doi = {10.1093/synbio/ysaa010},
                url = {https://doi.org/10.1093/synbio/ysaa010},
                note = {ysaa010},
                eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf},
            }
        </citation>
    </citations>
</tool>