<tool id="cfsan-qaqc" name="CFSAN QA/QC process" version="0.1.0">
    <requirements>
        <requirement type="package" version="1.65">biopython</requirement>
        <requirement type="package" version="1.4.3">matplotlib</requirement>
        <requirement type="package" version="1.9.2">numpy</requirement>
        <requirement type="package" version="0.16.1">pandas</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $reads.reads_select == 'collection'
            #set name=$reads.coll.name
            #set forward=$reads.coll.forward
            #set reverse=$reads.coll.reverse
        #else
            #set name=$forward.name
        #end if
        mkdir plots &&
        qa_core/gims_core.py --sequencingType "Illumina MiSeq"
                             --approximateGenomeSize $genomeSize
                             --coverageThreshold $covThreshold
                             --minimumQScore $minQ
                             --output_plots plots
                             --parallelism \${GALAXY_SLOTS:-6}
                             --annotate $name
                             --log -
                             suite
                             $forward
                             $reverse
                             -o $output
    ]]></command>
    <inputs>
        <conditional name="reads">
            <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
                <option value="collection">Paired collection from your history</option>
                <option value="history">Two FASTQ datasets from your history</option>
            </param>
            <when value="collection">
                <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
            </when>
            <when value="history">
                <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
                <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
            </when>
        </conditional>
        <param name="genomeSize" type="text" label="Approximate genome size" value="4700000" />
        <param name="covThreshold" type="text" label="Coverage threshold" value="20" />
        <param name="minQ" type="text" label="Minimum average Q score" value="27.0" />
    </inputs>
    <outputs>
        <data label="QA/QC Results" name="output" format="tabular" />
        <data label="Nucleotide plot" name="nucleo_plot" format="png" from_work_dir="nucleotide_distribution.png" />
        <data label="QScore Distribution" name="qscore_dist" format="png" from_work_dir="qscore_distribution.png" />
        <data label="QScore Histogram" name="qscore_histro" format="png" from_work_dir="qscore_histogram.png" />
    </outputs>
    <tests>
        <test>
            <param name="reads_select" value="collection" />
            <param name="coll">
                <collection type="list:paired">
                <element name="TEST TEST TEST">
                <collection type="paired">
                    <element name="forward" value="Input/forward_big.fastq.gz" ftype="fastqsanger.gz" />
                    <element name="reverse" value="Input/reverse_big.fastq.gz" ftype="fastqsanger.gz" />
                </collection>
                </element>
                </collection>
            </param>
            <output name="output" value="Output/output.tsv" />
        </test>
    </tests>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>