<tool id="normalize_readsizes" name="Normalize readsizes" version="0.5.24">
    <description>of multiple fastq files</description>
    <requirements>
        <requirement type="package" version="0.5.24">readtagger</requirement>
    </requirements>
    <version_command>normalize_readsizes --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
#for $i, $element in enumerate($input):
    ln -fs '$element' '${i}.${element.ext}' &&
#end for
normalize_readsizes
#for $i, $element in enumerate($input):
    -i '${i}.${element.ext}'
    -o '${i}.out.${element.ext}'
#end for
#for $i, $element in enumerate($output):
    && mv '${i}.out.${element.ext}' '$element'
#end for
    ]]></command>
    <inputs>
        <param name="input" type="data_collection" collection_type="list" label="Select collection of fastq datasets to normalize" format="fastqsanger,fastqsanger.gz"/>
    </inputs>
    <outputs>
        <collection name="output" type="list" structured_like="input" inherit_format="true"/>
    </outputs>
    <tests>
        <test>
            <param name="input">
                <collection type="list">
                  <element name="a" value="long_reads_a.fastq" />
                  <element name="b" value="long_reads_b.fastq" />
                </collection>
            </param>
            <param name="insert_reference" value="transposon"/>
            <output_collection name="output">
                <element name="a" value="long_reads_a_normalized.fastq" ftype="fastqsanger"/>
                <element name="b" value="long_reads_b_normalized.fastq" ftype="fastqsanger"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Normalizes read size distributions across a collection of fastq files so that the read size distribution is the same
across all datasets.
    ]]></help>
</tool>