<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.1.1">
    <description>converter</description>
    <edam_topics>
        <edam_topic>topic_0622</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_3434</edam_operation>
    </edam_operations>
    <command><![CDATA[
python '$__tool_directory__/tabular_to_fastq.py' '$input_file' '$output_file' '$identifier' '$sequence' '$quality'
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="tabular" label="Tabular file to convert" />
        <param name="identifier" type="data_column" data_ref="input_file" label="Identifier column" />
        <param name="sequence" type="data_column" data_ref="input_file" label="Sequence column" />
        <param name="quality" type="data_column" data_ref="input_file" label="Quality column" />
    </inputs>
    <outputs>
        <data name="output_file" format="fastq" />
    </outputs>
    <tests>
        <!-- basic test -->
        <test>
            <param name="input_file" value="fastq_to_tabular_out_1.tabular" ftype="tabular" />
            <param name="identifier" value="1" />
            <param name="sequence" value="2" />
            <param name="quality" value="3" />
            <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
        </test>
        <!-- color space test -->
        <test>
            <param name="input_file" value="fastq_to_tabular_out_2.tabular" ftype="tabular" />
            <param name="identifier" value="1" />
            <param name="sequence" value="2" />
            <param name="quality" value="3" />
            <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btq281</citation>
    </citations>
</tool>