<tool id="random_select" name="Choose Randomly" version="0.1.0" profile="16.10">
    <description>one pair of reads from a collection of paired reads</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if not $seed
        #from hashlib import md5
        #set $seed = md5(str($input.name)).hexdigest()
        #end if
        echo "seed: " $seed &&
        echo $seed > $output_seed &&
        #import random
        #set $_ = random.seed($seed)
        #set $choice = random.choice(list($input))
        cp $choice.forward $selection.forward && cp $choice.reverse $selection.reverse
    ]]></command>
    <inputs>
		<param label="List of paired datasets" name="input" type="data_collection" collection_type="list:paired" format="fastqsanger" />
        <param label="Random seed (optional)" name="seed" type="text" />
    </inputs>
    <outputs>
    	<collection name="selection" label="Selected pair" type="paired">
    		<data name="forward" format="fastqsanger" />
            <data name="reverse" format="fastqsanger" />
        </collection>
        <data name="output_seed" label="Seed" format_source="seed" hidden="true" />
    </outputs>
    <tests>
        <test>
            <param name="mul" value="single" />
            <param name="seed" value="TESTTEST" />
            <param name="input">
                <collection type="list">
                    <element name="sample1">
                        <collection type="paired">
                            <element name="forward" value="sample1_1.fastq" />
                            <element name="reverse" value="sample1_2.fastq" />
                        </collection>
                    </element>
                    <element name="sample2">
                        <collection type="paired">
                            <element name="forward" value="sample2_1.fastq" />
                            <element name="reverse" value="sample2_2.fastq" />
                        </collection>
                    </element>
                    <element name="sample3">
                        <collection type="paired">
                            <element name="forward" value="sample3_1.fastq" />
                            <element name="reverse" value="sample3_2.fastq" />
                        </collection>
                    </element>
                    <element name="sample4">
                        <collection type="paired">
                            <element name="forward" value="sample4_1.fastq" />
                            <element name="reverse" value="sample4_2.fastq" />
                        </collection>
                    </element>
                </collection>
            </param>
            <output_collection name="selection" type="paired" >
                <element name="forward" file="sample4_1.fastq" />
                <element name="reverse" file="sample4_2.fastq" />
            </output_collection>
        </test>
    </tests>
    <help>Choose one pair at random from a paired dataset. 
            If you re-use the seed, the choice should be the same 
            (this is for reproducability of analysis.) 
            Provide a blank seed value to use a seed created 
            as an MD5 sum of the dataset's name.
    </help>
    <citations>
    </citations>
</tool>