<tool id="sbol_converter" name="SBOL Converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
    <description>Convert between SBOL3 and other genetic design formats</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">1.0a16</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">sbol-utilities</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($convert_type.type) == "SBOL2 to SBOL3"
            ln -sv '$sbol2_input' 'input.$sbol2_input.ext' &&
            sbol2to3 -o '$output' 'input.$sbol2_input.ext'
        #elif str($convert_type.type) == "SBOL3 to SBOL2"
            ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
            sbol3to2 -o '$output' 'input.$sbol3_input.ext'
        #elif str($convert_type.type) == "SBOL3 to GENBANK"
            ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
            sbol2genbank -o '$output' 'input.$sbol3_input.ext'
        #elif str($convert_type.type) == "GENBANK to SBOL3"
            ln -sv '$genbank_input' 'input.$genbank_input.ext' &&
            genbank2sbol -o '$output' 'input.$genbank_input.ext' --namespace '$convert_type.namespace'
        #elif str($convert_type.type) == "SBOL3 to FASTA"
            ln -sv '$sbol3_input' 'input.$sbol3_input.ext' &&
            sbol2fasta -o '$output' 'input.$sbol3_input.ext'
        #elif str($convert_type.type) == "FASTA to SBOL3"
            ln -sv '$fasta_input' 'input.$fasta_input.ext' &&
            fasta2sbol -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace'
        #elif str($convert_type.type) == "SBOL2 to FASTA"
            ln -sv '$sbol2_input' 'input.$sbol2_input.ext' &&
            sbol-converter SBOL2 FASTA -o '$output' 'input.$sbol2_input.ext'
        #elif str($convert_type.type) == "FASTA to SBOL2"
            ln -sv '$fasta_input' 'input.$fasta_input.ext' &&
            sbol-converter FASTA SBOL2 -o '$output' 'input.$fasta_input.ext' --namespace '$convert_type.namespace'
        #end if
    ]]></command>
    <inputs>
        <conditional name="convert_type">
            <param name="type" type="select" label="Converting type" help="Choose the format (input/ouput) for SBOL conversion">
                <option value="SBOL2 to SBOL3" selected="True">From SBOL2 to SBOL3</option>
                <option value="SBOL2 to FASTA" >From SBOL2 to FASTA</option>
                <option value="SBOL3 to SBOL2" >From SBOL3 to SBOL2</option>
                <option value="SBOL3 to FASTA" >From SBOL3 to FASTA</option>
                <option value="SBOL3 to GENBANK" >From SBOL3 to GENBANK</option>
                <option value="GENBANK to SBOL3" >From GENBANK to SBOL3</option>
                <option value="FASTA to SBOL3" >From FASTA to SBOL3</option>
                <option value="FASTA to SBOL2" >From FASTA to SBOL2</option>
            </param>
            <when value="SBOL2 to SBOL3">
                <param name="sbol2_input" type="data" format="xml,rdf,nt" label="SBOL2 input" help="SBOL2 file in XML or RDF or NT format"/>
            </when>
            <when value="SBOL3 to SBOL2">
                <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/>
            </when>
            <when value="SBOL3 to GENBANK">
                <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/>
            </when>
            <when value="GENBANK to SBOL3">
                <param name="genbank_input" type="data" format="gb" label="Genbank input" help="Genbank file in GB format"/>
                <param argument="--namespace" type="text" value="https://synbiohub.org/public/igem" label="Namespace URL" help="Namespace URL, required for conversions from GenBank. Default=https://synbiohub.org/public/igem" />
            </when>
            <when value="SBOL3 to FASTA">
                <param name="sbol3_input" type="data" format="xml,rdf,nt" label="SBOL3 input" help="SBOL3 file in XML or RDF or NT format"/>
            </when>
            <when value="FASTA to SBOL3">
                <param name="fasta_input" type="data" format="fasta" label="FASTA input" help="FASTA input file"/>
                <param argument="--namespace" type="text" value="https://synbiohub.org/public/igem" label="Namespace URL" help="Namespace URL, required for conversions from FASTA. Default=https://synbiohub.org/public/igem" />
            </when>
            <when value="SBOL2 to FASTA">
                <param name="sbol2_input" type="data" format="xml,rdf,nt" label="SBOL2 input" help="SBOL2 file in XML or RDF or NT format" />
            </when>
            <when value="FASTA to SBOL2">
                <param name="fasta_input" type="data" format="fasta" label="FASTA input" help="FASTA input file"/>
                <param argument="--namespace" type="text" value="https://synbiohub.org/public/igem" label="Namespace URL" help="Namespace URL, required for conversions from FASTA. Default=https://synbiohub.org/public/igem" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="nt" label="${tool.name} on ${on_string}: ${convert_type.type}" >
            <change_format>
                <when input="convert_type.type" value="SBOL3 to GENBANK" format="gb" />
                <when input="convert_type.type" value="SBOL3 to FASTA" format="fasta" />
                <when input="convert_type.type" value="SBOL2 to FASTA" format="fasta" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced sbol2 to sbol3-->
        <conditional name="convert_type">
            <param name="type" value="SBOL2 to SBOL3"/>
        </conditional>
        <param name="sbol2_input" value="BASIC_construct_A1_sbol2_input.xml" />
        <output name="output" file="BASIC_construct_A1_sbol3_output.nt" ftype="nt" compare="diff"/>
        </test>
        <test>
        <!-- test 2: check if identical outputs are produced sbol3 to genbank-->
        <conditional name="convert_type">
            <param name="type" value="SBOL3 to GENBANK"/>
        </conditional>
        <param name="sbol3_input" value="BBa_J23101.nt" />
        <output name="output" file="BBa_J23101.gb" ftype="gb" compare="diff"/>
        </test>

        <test>
        <!-- test 2: check if identical outputs are produced sbol3 to fasta-->
        <conditional name="convert_type">
            <param name="type" value="SBOL3 to FASTA"/>
        </conditional>
        <param name="sbol3_input" value="BBa_J23101.nt" />
        <output name="output" >
            <assert_contents>
            <has_text text=">BBa_J23101 constitutive promoter family member" />
            <has_text text="tttacagctagctcagtcctaggtattatgctagc" />
            </assert_contents>
        </output>
        </test>
    </tests>
    <help><![CDATA[
SBOL Converter
==============

Convert between SBOL3 and other genetic design formats.

Input
-----
Required:
* **INPUT_FILE**\ : SBOL2 or SBOL3 or GENBANK or FASTA input file.
* **Namespace URL**\ : Namespace URL, required for conversions from GenBank or from Fasta. Default=https://synbiohub.org/public/igem"

Output
------
* **OUTPUT_FILE**\ : SBOL2 or SBOL3 or GENBANK or FASTA output file.
    ]]></help>
    <creator>
        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
    </creator>
    <citations>
        <citation type="doi">10.1021/acssynbio.1c00188</citation>
    </citations>
</tool>