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<tool id="complex_splitter" name="Complex_Splitter" version="0.5.0">
    <description>Creates ensembles of individual chains for downstream RMSF processing</description>
    <requirements>
       <requirement type="package" version="8">openjdk</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[        
        java -Djava.awt.headless=true -jar '$__tool_directory__/ComplexSplitter.jar' '$input1' '$input2' '$input3'
	&& cp ChainA.pdb '$output1'
	&& cp ChainB.pdb '$output2'
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="pdb" label="input1"/>
	<param name="input2" size="2" type="text" label="First chain:"/>
	<param name="input3" size="2" type="text" label="Second chain:"/>
    </inputs>      
    <outputs>
        <data name="output1" format="pdb" label="First chain ensemble from ${on_string}"/>
	<data name="output2" format="pdb" label="Second chain ensemble from ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="pdb" value="2hdx-READY-ALIGNED.pdb"/>
            <output name="output1">
                <assert_contents>
                    <has_text text="813"/>
		</assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This program creates separate, individual ensembles of the two chains to be analyzed
    ]]></help>
</tool>