<tool id="demultiplex-emc" name="Demultiplex" version="1.0.0">
    <requirements>
        <requirement type="package" version="3.7.0">python</requirement>
        <requirement type="package" version="1.72">biopython</requirement>
    </requirements>
    <description></description>
    <command>
        mkdir outputs;
        python3 $__tool_directory__/demultiplex.py 
        --input $input
        --format auto
        --output-dir ./outputs
        --mapping-file $mapping
    </command>
    <inputs>
        <param name="input" type="data" format='fasta,fastq' label="The input fasta/fastq"/>
        <param name="mapping" type="data" format='tabular' label="The mapping file"/>
    </inputs>
    <outputs>
        <!--<data name="debug" format="txt" label="debug"/>-->
        <collection name='demultiplex_out' format_source='input' type='list'>
            <discover_datasets pattern="__name_and_ext__" directory="outputs" format_source='input'/>
        </collection>
    </outputs>
    <tests>
    <!--
        <test>
            <param name="input1" value="1.bed"/>
            <param name="input2" value="2.bed"/>
            <output name="out_file1" file="cat_wrapper_out1.bed"/>
        </test>
        TODO: if possible, enhance the underlying test code to handle this test
            the problem is multiple params with the same name "input2"
        <test>
            <param name="input1" value="1.bed"/>
            <param name="input2" value="2.bed"/>
            <param name="input2" value="3.bed"/>
            <output name="out_file1" file="cat_wrapper_out2.bed"/>
        </test>
    -->
    </tests>
    <help>
There is no help
    </help>
</tool>