<tool id="demultiplex-emc" name="Demultiplex" version="1.0.0">
    <description></description>
    <requirements>
        <requirement type="package" version="3.7.0">python</requirement>
        <requirement type="package" version="1.72">biopython</requirement>
    </requirements>
    
    <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="__designation_and_ext__" directory="outputs"/>
            <!--<discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;.+)" directory="outputs"/>-->
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input" value="input.fastq"/>
            <param name="mapping" value="mapping.txt"/>
            <output_collection name="demultiplex_out" type="list">
                <element name="sequence1" file="sequence1.fastq"/>
                <element name="sequence2" file="sequence2.fastq"/>
            </output_collection>
        </test>
        <test>
            <param name="input" value="input.fasta"/>
            <param name="mapping" value="mapping.txt"/>
            <output_collection name="demultiplex_out" type="list">
                <element name="sequence1" file="sequence1.fasta"/>
                <element name="sequence2" file="sequence2.fasta"/>
            </output_collection>
        </test>
    </tests>
    <help>
There is no help
    </help>
    <citations>
        <citation type="bibtex">@misc{Demultplex-EMC,
            author = {Erasmus MC},
            title = {Demultiplex-EMC},
            year = {2018},
            howpublished = {https://github.com/ErasmusMC-Bioinformatics/Demultiplex}
        }</citation>
    </citations>
</tool>