<tool id="sbml2sbol" name="SbmlToSbol" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
    <description>Convert sbml to sbol format</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">0.1.13</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">sbml2sbol</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python -m sbml2sbol
        --input '$sbml_single_input'
        --outfile '$sbol_outfile'
        $adv.rbs
        --max_prot_per_react '$adv.max_prot_per_react'
        #if $adv.tirs 
            --tirs '$adv.tirs'
        #end if
        --pathway_id '$adv.pathway_id'
        --uniprotID_key '$adv.uniprotID_key'
    ]]></command>
    <inputs>
        <param name="sbml_single_input" type="data" format="sbml" label="Pathway (SBML)" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param argument="--rbs" type="boolean" truevalue="--rbs True" falsevalue="--rbs False" label="Calculate the RBS strength?" checked="true" help="Calculate or not the RBS (Ribosome Binding Site) strength (default: True)"/>
            <param argument="--max_prot_per_react" type="integer" value="3" min="1" max="20" label="The maximum number of proteins per reaction" />
            <param argument="--tirs" type="text" optional="true" label="Space separated RBS strength values" />
            <param argument="--pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" >
                <validator type="empty_field" message="Pathway ID is required"/>
            </param>
            <param argument="--uniprotID_key" type="text" value="selenzy" label="Uniprot ID" >
                <validator type="empty_field" message="Uniprot ID is required"/>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="sbol_outfile" format="xml" label="${tool.name}: sbol outfile" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with default parameters  -->
            <param name="sbml_single_input" value="lycopene.xml" />
            <output name="sbol_outfile" file="sbol_lycopene_output.xml" ftype="xml" compare="diff" sort="true"/>
        </test>
        <test>
        <!-- test 2: check if identical outputs are produced without RBS calculation  -->
            <param name="sbml_single_input" value="lycopene.xml" />
            <param name="rbs" value="--rbs False" />
            <param name="max_prot_per_react" value="5" />
            <output name="sbol_outfile" file="sbol_lycopene_output2.xml" ftype="xml" compare="diff" sort="true"/>
        </test>
    </tests>
    <help><![CDATA[
SBML to SBOL
================

This tool takes a pathway model (encoded in SBML) as input and returns a collection of placeholders for the subsequent design of the synthetic DNA that is required to encode the enzymes defined in the pathway model (encoded in SBOL).

Input
-----

Required:

* **Pathway (SBML)**\ : Pathway file in SBML format.

Advanced options:

* **Calculate the RBS strength?**\ : (boolean) Calculate or not the RBS (Ribosome Binding Site) strength (default: True).
* **The maximum number of proteins per reaction**\ : (int) The maximum number of proteins per reaction (default: 3).
* **Space separated RBS strength values**\ : (int) The RBS (Ribosome Binding Site) strength values (default: None)
* **Group ID of the heterologous pathway**\ : (string) Group ID of the heterologous pathway (default: rp_pathway)
* **Uniprot ID**\ : (string) Uniprot ID of the heterologous pathway (default: selenzy)

Output
------

* **sbol outfile**\ : output (SBOL) file.
    ]]></help>
    <creator>
        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
    </creator>
    <citations>
        <citation type="bibtex">
            @unpublished{SbmlToSbol
                author = {Neil Swainston},
                title = {{SbmlToSbol}},
                url = {https://github.com/neilswainston/SbmlToSbol},
            }
        </citation>
    </citations>
</tool>