<tool id="lcrgenie" name="Ligase Chain Reaction Genie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
    <description>Web-based tool for supporting the design of bridging oligos</description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.2</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">lcr_genie</requirement>
    </requirements>
    <stdio>
        <regex match="WARNING:" level="warning" />
        <regex match="ERROR:" level="fatal" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m lcr_genie
            '$LCR_input'
            'out.xlsx'
            --melting_temp '$adv.melting_temp'
        && mv 'out.xlsx' '$LCR_output'
    ]]></command>
    <inputs>
        <param name="LCR_input" type="data" format="xml" label="Constructs" help="SBOL file containing constructs designs and sequences" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="melting_temp" value="60.0" type="float" label="Melting temperature" help="Target melting temperature for the bridging oligos"/>
        </section>
    </inputs>
    <outputs>
        <data name="LCR_output" format="xlsx" label="LCR Genie: Assembly Plan" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with default parameters  -->
            <param name="LCR_input" value="LCR_input_lycopene.xml" />
            <output name="LCR_output" >
                <assert_contents>
                    <has_size value="58196" delta="100" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
LCRGenie
========

LCR Genie is a web-based tool for supporting the design of bridging oligos, which are required for annealing together individual synthetic DNA parts (designed by PartsGenie) into multi-gene plasmid assemblies, designed by OptDoE.

Enzyme identifiers are randomly chosen and combined with the aforementioned parts to explore the combinatorics of possible constructs.

LCR Genie takes as input an SBOL (Synthetic Biology Open Language) document containing numerous combinatorial plasmid assemblies, and designing bridging oligos necessary for assembly via the ligase cycling reaction method. The LCR Genie node performs analogous functionality to the `DNA weaver <https://github.com/Edinburgh-Genome-Foundry/DnaWeaver>`_ node (supporting multi-part assembly but by a different experimental method) and as such, its output format matches that of DNA Weaver.


Input
-----

* **Constructs**\ : SBOL (Synthetic Biology Open Language) file containing constructs designs and sequences
* **Melting temperature**\ : (float) is the target melting temperature for the bridging oligos (default=60.0)

Output
------

* **Assembly Plan**\ : Output spreadsheet
    ]]></help>
    <creator>
        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
    </creator>
    <citations>
        <citation type="bibtex">
            @unpublished{LCRGenie
                author = {Neil Swainston},
                title = {{LCRGenie}},
                url = {https://github.com/neilswanston/LCRGenie/},
            }
        </citation>
    </citations>
</tool>