<tool id="fast_fastq_filter" name="fastq-filter" version="0.3.0" python_template_version="3.5" profile="16.04">
    <description>filter FASTQ reads fast</description>
    <requirements>
        <requirement type="package" version="0.3.0">fastq-filter</requirement>
        <!-- TODO: Remove this once biocontainer is published -->
        <container type="docker">quay.io/rhpvorderman/fastq-filter:0.3.0</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        set -e;
        fastq-filter
        #if str($filters.minimum_length.enabled) == "true"
        --min-length $filters.minimum_length.threshold
        #end if
        #if str($filters.maximum_length.enabled) == "true"
        --max-length $filters.maximum_length.threshold
        #end if
        #if str($filters.average_error_rate.enabled) == "true"
        --average-error-rate $filters.average_error_rate.threshold
        #end if
        #if str($filters.mean_quality.enabled) == "true"
        --mean-quality $filters.mean_quality.threshold
        #end if
        #if str($filters.median_quality.enabled) == "true"
        --median-quality $filters.median_quality.threshold
        #end if
        --verbose
        -o '${output1}.gz'
        #if str($library.type) == "paired":
        -o ${output2}.gz
        #end if

        '$library.input_1'
        #if str($library.type) == "paired":
        '$library.input_2'
        #end if
        ;

        mv '${output1}.gz' '$output1';
        #if str($library.type) == "paired":
        mv '${output2}.gz' '$output2';
        #end if
    ]]></command>
    <inputs>
        <conditional name="library">
            <param name="type" type="select" label="Single-end or Paired-end reads?">
                <option value="single">Single-end</option>
                <option value="paired">Paired-end</option>
            </param>
            <when value="single">
                <param type="data" name="input_1" label="Input FASTQ file" format="fastqsanger,fastqsanger.gz" />
            </when>
            <when value="paired">
                <param type="data" name="input_1" label="Input FASTQ file #1" format="fastqsanger,fastqsanger.gz" />
                <param type="data" name="input_2" label="Input FASTQ file #2" format="fastqsanger,fastqsanger.gz" />
            </when>
        </conditional>
        <section name="filters" title="Filters" expanded="true">
            <conditional name="minimum_length">
                <param name="enabled" type="boolean" label="Minimum length"
                       help="The minimum length for a read."/>
                <when value="true">
                    <param name="threshold" type="integer" label="Threshold"
                           value="20" min="1"/>
                </when>
                <when value="false"/>
            </conditional>
            <conditional name="maximum_length">
                <param name="enabled" type="boolean" label="Maximum length"
                       help="The maximum length for a read."/>
                <when value="true">
                    <param name="threshold" type="integer" label="Threshold"
                           value="1000" min="1"/>
                </when>
                <when value="false"/>
            </conditional>
            <conditional name="average_error_rate">
                <param name="enabled" type="boolean" label="Average error rate"
                       help="The minimum average per base error rate."/>
                <when value="true">
                    <param name="threshold" type="float" label="Threshold"
                           value="0.001" min="0"/>
                </when>
                <when value="false"/>
            </conditional>
            <conditional name="mean_quality">
                <param name="enabled" type="boolean" label="Mean quality">
                    <help>
                        Average quality. Same as the 'Average error rate' option but
                        specified with a phred score. I.e a mean quality of 30 is
                        equivalent to an average error rate of 0.001'.
                    </help>
                </param>
                <when value="true">
                    <param name="threshold" type="integer" label="Threshold"
                           value="30" min="0"/>
                </when>
                <when value="false"/>
            </conditional>
            <conditional name="median_quality">
                <param name="enabled" type="boolean" label="Median quality">
                    <help>
                        DEPRECATED: The minimum median phred score. This is not as
                        informative as the average error rate. It is also slower to
                        calculate. This filter is only included for backwards
                        compatibility reasons.
                    </help>
                </param>
                <when value="true">
                    <param name="threshold" type="integer" label="Threshold"
                           value="30" min="0"/>
                </when>
                <when value="false"/>
            </conditional>
        </section>
    </inputs>
    <outputs>
        <data name="output1" format="fastqsanger.gz" />
        <data name="output2" format="fastqsanger.gz">
            <filter>library['type'] == 'paired'</filter>
        </data>
    </outputs>
    <help><![CDATA[
    When paired FASTQ data is given, fastq-filter makes sure the output is in
    sync. The filters behave as follows for paired-end data:

    + average error rate: The average of the combined phred scores is used.
    + median quality: The median of the combined phred scores is used.
    + Minimum length: at least one of the records of the pair must meet the minimum length.
    + Maximum length: None of the records in the pair must exceed the maximum length.

    The rationale for the length filters is that R1 and R2 both sequence the same
    molecule and the canonical length is the longest of both.

    ]]></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>