<tool id="quality" name="Quality control" version="0.4.2">
    <description>Performs quality control on FASTQ reads.</description>
    <requirements>
          <requirement type="package" version="0.4.2">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        quasitools quality

        ## Preparing file input.
        #if $data_type.type == "paired":

            '$data_type.fastq_input1'
            '$data_type.fastq_input2'

        #elif $data_type.type == "collection":

            '$data_type.fastq_input1.forward'
            '$data_type.fastq_input1.reverse'

        #elif $data_type.type == "single":

            '$data_type.fastq_input1'

        #end if

        #if $length_cutoff:
            -lc '$length_cutoff'
        #end if

        #if $score_cutoff:
            -sc '$score_cutoff'
        #end if

        #if $min_read_qual:
            -rq '$min_read_qual'
        #end if

        #if $low_quality.qual_selector == "filter_ns":
            --ns
        #elif $low_quality.qual_selector == "mask_reads":
            --mask_reads
        #end if

        #if $score_type.score_selector == "median":
            --median
        #elif $score_type.score_selector == "mean":
            --mean
        #end if

        $trim_reads

        -o output

    ]]></command>
    <inputs>
        <conditional name="data_type">
            <param name="type" type="select" label="Specify the read type.">
                <option value="single">Single-end Data</option>
                <option value="paired">Paired-end Data</option>
                <option value="collection">Collection Paired-end Data</option>
            </param>
            <when value="single">
                <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/>
            </when>
            <when value="paired">
                <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/>
                <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/>
            </when>
            <when value="collection">
                <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" />
            </when>
        </conditional>
        <param name="length_cutoff" type="integer" optional="true" min="1" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." />
        <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose median or mean quality score (depending on the score type specified) is less than the specified score cutoff value will be filtered out. Defaults to 30." />
        <param name="min_read_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for a position in a read not to be masked, is masking is enabled. Defaults to 30." />
        <param name="trim_reads" type="boolean" optional="true" checked="false" truevalue="-tr" falsevalue="" label="Trim reads" help="Iteratively trim reads based on filter values if enabled." />
        <conditional name="low_quality">
            <param name="qual_selector" type="select" label="Filter out regions masked, or mask low coverage regions with n's." multiple="false" display="radio">
                <option value="filter_ns">Filter out regions with n's</option>
                <option value="mask_reads">Mask low coverage regions with n's</option>
                <option value="neither" selected="true">Do not filter or mask low coverage regions.</option>
            </param>
            <when value="filter_ns">
            </when>
            <when value="mask_reads">
            </when>
            <when value="neither">
            </when>
        </conditional>
        <conditional name="score_type">
            <param name="score_selector" type="select" label="Use either median score (default) or mean score for the score cutoff value." multiple="false" display="radio">
                <option value="median" selected="true">Use median score</option>
                <option value="mean">Use mean score</option>
            </param>
            <when value="median">
            </when>
            <when value="mean">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="fastq" label="Quality control output" name="output_filtered" from_work_dir="output/filtered.fastq" />
    </outputs>
    <tests>
        <test>
            <param name="type" value="single"/>
            <param name="fastq_input1" value="forward.fastq" />
            <param name="score_selector" value="median" />
            <output name="output_filtered">
                <assert_contents>
                    <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" />
                    <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="type" value="single"/>
            <param name="fastq_input1" value="forward.fastq" />
            <param name="score_selector" value="median" />
            <param name="qual_selector" value="filter_ns" />
            <output name="output_filtered">
                <assert_contents>
                    <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" />
                    <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="type" value="single"/>
            <param name="fastq_input1" value="forward.fastq" />
            <param name="score_selector" value="median" />
            <param name="trim_reads" value="-tr" />
            <output name="output_filtered">
                <assert_contents>
                    <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" />
                    <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="type" value="single"/>
            <param name="fastq_input1" value="forward.fastq" />
            <param name="score_selector" value="median" />
            <param name="qual_selector" value="mask_reads" />
            <output name="output_filtered">
                <assert_contents>
                    <has_text text="@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86" />
                    <has_text text="NNNNNNTACCACATCCCNCNNNNTTNNNNNNNNNNANNTCNNTNNCNNTNCTNNNTNTNNNTGNTGCNTNTTTTTCAGTTCCCTTNGNTGNNGNCTTCAGNNNNTATACTGCATTTACCNTNCNT" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="type" value="single"/>
            <param name="fastq_input1" value="forward.fastq" />
            <param name="score_selector" value="mean" />
            <output name="output_filtered">
                <assert_contents>
                    <has_text text="@M01647:10:000000000-ACPHB:1:1101:10485:1674 1:N:0:86" />
                    <has_text text="CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Quality Control
===============

Perform quality control on FASTQ reads.]]></help>
    <citations>
    </citations>
</tool>