<tool id="fast_fastq_filter" name="fastq-filter" version="0.1.0" python_template_version="3.5" profile="16.04">
    <description>filter FASTQ reads fast</description>
    <requirements>
        <requirement type="package" version="0.1.0">fastq-filter</requirement>
        <!-- TODO: Remove this once biocontainer is published -->
        <container type="docker">quay.io/rhpvorderman/fastq-filter:0.1.0</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #set all_filters = [str(filter['filter']) + ":" + str(filter['filter_threshold']) for filter in $filters]
        fastq-filter -o '$output1'
        #echo "'" + "|".join($all_filters) + "'"
        '$input1'
    ]]></command>
    <inputs>
        <param type="data" name="input1" label="Input FASTQ file" format="fastqsanger,fastqsanger.gz" />
        <repeat name="filters" title="Filter" min="1">
            <param name="filter" type="select" label="Filter on">
              <option value="min_length">minimum length</option>
              <option value="max_length">maximum length</option>
              <option value="mean_quality" selected="true">mean quality</option>
              <option value="median_quality">median quality</option>
            </param>
            <param name="filter_threshold" type="integer" label="Filter threshold" value="20"/>
        </repeat>
    </inputs>
    <outputs>
        <!--Fastqsanger format for now. For conditionally applying fastqsanger.gz the tool needs
         to be updated. An option is using format auto_detect, so we do not have to conditionally set
         fastqsanger or fastqsanger.gz-->
        <data name="output1" format="fastqsanger" />
        <!--When the tool is updated for paired input, the optional paired output can probably be
        found in the cutadapt wrapper -->
    </outputs>
    <tests>
        <test>
            <param name="input1" value="input.fastq.gz"/>
            <output name="output1" file="output.fastq.gz"/>
        </test>
    </tests>
    <help><![CDATA[
    The following filters are available:

    + mean_quality:<quality>         The mean quality of the FASTQ record is equal or above the given quality value.
    + median_quality:<quality>       The median quality of the FASTQ record is equal or above the given quality value.
    + min_length:<length>            The length of the sequence in the FASTQ record is at least min_length
    + max_length:<length>            The length of the sequence in the FASTQ record is at most max_length

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubfastq-filter,
  author = {Vorderman, Ruben Harmen Paul},
  year = {2021},
  title = {fastq-filter},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/LUMC/fastq-filter},
}</citation>
    </citations>
</tool>