<tool id="concatenate_ordered" name="Concatenate Ordered Dataset Collection" version="0.1.0">
    <description> Concatenates files in dataset collection based on orginial file name stored in first column.</description>
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
		$__tool_directory__/./concatenate_ordered.bash "$input1" "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="tabular" multiple="true" label="Read Counts Files"/>
    </inputs>
    <outputs>
        <data name="output1" format="tabular" label="Read Counts"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="dataset_692.dat,dataset_684.dat,dataset_688.dat,dataset_686.dat,dataset_690.dat"/>
            <output name="output1" file="read_counts_ordered.txt"/>
        </test>
    </tests>
    <help><![CDATA[
        This tools takes a series of input files and concatenates the contents in order according to the alphabetical order of the first column of the input files containing the original file name.
    ]]></help>
    <citations>
        <citation type="doi">doi:10.1038/nmeth.4663</citation>
    </citations>
</tool>