<tool id ="fastuniq" name="FastUniq" version="1.1">
    <description></description>
    <requirements>
        <requirement type="package" version="1.1">fastuniq</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
    python $__tool_directory__/create_input_list.py
    --fastq_R1 "$fastq_R1"
    --fastq_R2 "$fastq_R2"
    --output_list output_list &&
    fastuniq
    -i output_list
    -t "$select_output_format"
    -o "$fastq_R1_rmdup"
    -p "$fastq_R2_rmdup"
    -c 0
    ]]></command>
    <inputs>
        <param format="fastq" name="fastq_R1" type="data" label="R1 reads"/>
        <param format="fastq" name="fastq_R2" type="data" label="R2 reads"/>
        <param name="select_output_format" type="select" label="Select Output Format">
            <option value="q" selected="true">FASTQ</option>
            <option value="f">FASTA</option>
        </param>
    </inputs>
    <outputs>
        <data format="fastq" name="fastq_R1_rmdup" type="data" label="${fastq_R1.element_identifier} Unique Reads">
            <change_format>
                <when input="select_output_format" value="f" format="fasta"/>
            </change_format>
        </data>
        <data format="fastq" name="fastq_R2_rmdup" type="data" label="${fastq_R2.element_identifier} Unique Reads">
            <change_format>
                <when input="select_output_format" value="f" format="fasta"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="fastq_R1" value="input_R1.fastq" ftype="fastq"/>
            <param name="fastq_R2" value="input_R2.fastq" ftype="fastq"/>
            <param name="select_output_format" value="q"/>
            <param name="fastq_R1_rmdup" value="output_R1.fastq" ftype="fastq"/>
            <param name="fastq_R2_rmdup" value="output_R2.fastq" ftype="fastq"/>
        </test>
    </tests>
    <help> <![CDATA[
**FastUniq** is an ultrafast de novo tool for removal of duplicates in paired short DNA sequence reads in FASTQ format.
It identifies duplicates by comparing sequences between read pairs and does not require complete genome sequences as prerequisites.
It is also capable of simultaneously handling reads with different lengths and results in highly efficient running time.

The input files required are two paired forward and reverse read files in fastq format.
     ]]> </help>
    <citations>
        <citation type="doi">doi:10.1371/journal.pone.0052249</citation>
    </citations>
</tool>