<tool id="eBCSgen_simulate" name="eBCSgen simulation" version="@TOOL_VERSION@_galaxy0">
    <description>- simulate given model</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <container type="docker">sybila/ebcsgen:v@TOOL_VERSION@</container>
    </requirements>

    <command>python3 ${__tool_directory__}/ebcsgen_simulate.py
        --model '$model'
        --output '$output'
        --deterministic '$type.deterministic_choice'
        #if $type.deterministic_choice == "True":
            --direct False
            --runs 1
            --volume '$type.volume'
            --step '$type.step'
        #else:
            --direct '$type.network_free_choice'
            --runs '$type.num_of_runs'
            --volume 1
            --step 0.01
        #end if
        --max_time '$max_time'
    </command>

    <inputs>
        <param format="bcsl.model" name="model" type="data" label="Model file" help="Provide a BCSL model file"/>
        <conditional name="type">
            <param name="deterministic_choice" type="select" label="Choose simulation method:">
                <option value="False" selected="true">Stochastic</option>
                <option value="True">Deterministic</option>
            </param>
            <when value="False">
                <param name="network_free_choice" type="select" label="Choose network-free approach:">
                    <option value="False" selected="true">Indirect</option>
                    <option value="True">Direct</option>
                </param>
                <param name="num_of_runs" min="1" type="integer" value="1" label="Number of runs:"/>
            </when>
            <when value="True">
                <param name="volume" min="0" type="integer" value="1" label="Volume (liters):"/>
                <param name="step" min="0" type="float" value="0.01" label="Simulation step:"/>
            </when>
        </conditional>
        <param name="max_time" min="0" type="integer" value="1" label="Maximum simulation time:"/>
    </inputs>

    <outputs>
        <data format="csv" name="output"/>
    </outputs>

    <tests>
        <test>
            <param name="model" value="repressilator.bcsl.model" ftype="bcsl.model"/>
            <section name="type">
                <param name="deterministic_choice" value="True"/>
                <param name="step" value="0.1"/>
            </section>
            <param name="max_time" value="100"/>
            <output name="output" value="simulation_determ.csv" ftype="csv"/>
        </test>
        <test>
            <param name="model" value="repressilator.bcsl.model" ftype="bcsl.model"/>
            <section name="type">
                <param name="deterministic_choice" value="False"/>
                <param name="network_free_choice" value="False"/>
                <param name="num_of_runs" value="2"/>
            </section>
            <param name="max_time" value="200"/>
            <output name="output" ftype="csv">
                <assert_contents>
                    <has_n_columns n="4" sep=","/>
                    <has_n_lines min="10"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="model" value="repressilator.bcsl.model" ftype="bcsl.model"/>
            <section name="type">
                <param name="deterministic_choice" value="False"/>
                <param name="network_free_choice" value="True"/>
                <param name="num_of_runs" value="1"/>
            </section>
            <param name="max_time" value="100"/>
            <output name="output" ftype="csv">
                <assert_contents>
                    <has_n_columns n="4" sep=","/>
                    <has_n_lines min="10"/>
                </assert_contents>
            </output>
        </test>
    </tests>
</tool>