<tool id="fastq_filter_n" name="FASTQ filterer" profile="18.01" version="0.25.1+galaxy0">
    <description>Discards reads with more than x% of uncalled bases (N)</description>
    <requirements>
        <requirement type="package" version="0.25.1">fastq_utils</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
    fastq_filter_n -n '$threshold' '$file' > $outfile
    ]]></command>
    <inputs>
        <param name="file" label="Input file" type="data" format="fastqsanger.gz" optional="false" help="Fastq (optional gzipped) file name"/>
        <param name="threshold" label="Filter threshold" argument="-n" optional="true" value="0" type="integer" min="0" max="100" help="[0-100] Maximum percentage of uncalled bases in a read. Default is 0."/>
    </inputs>
    <outputs>
        <data label="${tool.name} on ${on_string}: Output file" name="outfile" format="fastqsanger.gz" />
    </outputs>
    <tests>
        <test>
            <param name="file" value="test_21_2.fastq.gz"/>
            <param name="threshold" value="5"/>
            <output name="outfile" md5="019ce04559162b973e13a514a5c01595"/>
        </test>
    </tests>
    <help><![CDATA[
============================================================
FASTQ filterer (fastq_filter_n)
============================================================

Outputs a gzipped fastq file where reads with more than the
maximum number of allowed uncalled bases are not included.

Threshold is the maximum percentage (ranging from 0 to 100)
of uncalled bases that a read can have. Default value is 0,
which means that a read with a single N would be discarded.

     ]]></help>
    <citations>
        <citation type="bibtex"><![CDATA[
            @ARTICLE{Fonseca2017,
            author = {Fonseca, N.},
            title = {fastq_utils},
            year = {2017},
            publisher = {GitHub},
            journal = {GitHub repository},
            howpublished = {\url{https://github.com/nunofonseca/fastq_utils}},
            commit = {c6cf3f954c5286e62fbe36bb9ffecd89d7823b07}
            }]]></citation>
    </citations>
</tool>