<tool id="subset" name="Subset" description="only keeps the n lines of a text-based file">
    <command interpreter="python">
    subset.py
        $singlePaired.sPaired
        $size
        $input.ext
        ${ os.getcwd() }/${ $__app__.config.tool_path }
        #if str( $singlePaired.sPaired ) == "single"
        $input
        $output
        #else
        $input
        $output1
        $singlePaired.input2
        $output2
        #end if
    </command>

    <inputs>

    <param name="input" type="data" label="Input file" format="fastq,fastqillumina,fastqsanger,export,sam" checked="true" />

    <conditional name="singlePaired">
        <param name="sPaired" type="select" label="Is this library paired?">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
        </param>
        <when value="single" />
        <when value="paired">
        <param name="input2" type="data" label="Input file" format="fastq,fastqillumina,fastqsanger,export,sam" checked="true" />
        </when> <!-- paired -->
    </conditional> <!-- singlePaired -->

    <param name="size" type="select" label="The output file extension">
            <option value="1000000">1,000,000</option>
            <option value="100000" selected="true">100,000</option>
            <option value="10000">10,000</option>
    </param>

    </inputs>

    <outputs>
    <data format_source="input" name="output">
        <filter>(singlePaired['sPaired'] == 'single')</filter>
    </data>
    <data format_source="input" name="output1" label="${tool.name} on ${on_string}: Mates A">
        <filter>(singlePaired['sPaired'] == 'paired')</filter>
    </data>
    <data format_source="input2" name="output2"  label="${tool.name} on ${on_string}: Mates B">
        <filter>(singlePaired['sPaired'] == 'paired')</filter>
    </data>
    </outputs>
    <help>
.. class:: warningmark

This tool is meant only for testing purposes

It makes a random selection of lines from the input file(s) and prints them in the output file(s).

    </help>
</tool>