<tool id="sbml2sbol" name="SbmlToSbol" version="0.1.12">
    <description>Convert sbml to sbol format</description>
    <requirements>
        <requirement type="package" version="0.1.12">sbml2sbol</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python -m sbml2sbol
            --input '$sbml_single_input'
            --outfile '$sbol_outfile'
        #if str($adv.rbs) == "true"
            --rbs True
        #else
            --rbs False
        #end if
        --max_prot_per_react '$adv.max_prot_per_react'
        #if $adv.tirs 
            --tirs $adv.tirs
        #end if
        --pathway_id '$adv.pathway_id'
        --uniprotID_key '$adv.uniprotID_key'
    ]]></command>
    <inputs>
        <param name="sbml_single_input" type="data" format="xml" label="Pathway (SBML)" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="rbs" type="boolean" label="Calculate the RBS strength?" checked="true" />
            <param name="max_prot_per_react" type="integer" value="3" label="The maximum number of proteins per reaction" />
            <param name="tirs" type="text" optional="true" label="Space separated RBS strength values" />
            <param name="pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" />
            <param name="uniprotID_key" type="text" value="selenzy" label="Uniprot ID" />
        </section>
    </inputs>
    <outputs>
        <data name="sbol_outfile" format="xml" label="${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>
    </tests>
    <help><![CDATA[
SBML to SBOL
================

Convert a single or multiple SBML files to SBOL.

Input
-----

Required:

* **input**\ : (string) path to folder(s) containing rpSBML files and/or rpSBML file path(s).

Advanced options:

* **rbs**\ : (boolean) Calculate or not the RBS strength (default: True).
* **max_prot_per_react**\ : (int) The maximum number of proteins per reaction (default: 3).
* **tirs**\ : (int) The RBS strength values (default: None)
* **pathway_id**\ : (string) Group ID of the heterologous pathway (default: rp_pathway)
* **uniprotID_key**\ : (string) Group ID of the heterologous pathway (default: selenzy)

Output
------

* **outfile**\ : (string) specify output (SBOL) file.

Project Links
------------------

* `GitHub <https://github.com/neilswainston/SbmlToSbol>`_

Version
----------
0.1.12

License
-------

* `MIT <https://raw.githubusercontent.com/neilswainston/SbmlToSbol/master/LICENSE>`_

    ]]></help>
</tool>