<tool id="pacu_map" name="PACU - mapping" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Map ONT / Illumina reads to a reference genome for PACU</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='xrefs'/>
    <expand macro="requirements" />
    <expand macro="version_command"/>
    <command detect_errors="exit_code">
        <![CDATA[
        PACU_map

        ## FASTA input
        --ref-fasta '$ref_fasta'
        --ref-fasta-name '$ref_fasta.element_identifier'

        ## FASTQ input
        --read-type $fastq_tech.read_type
        #if str($fastq_tech.read_type) == 'illumina':
            --fastq-illumina $fastq_tech.fastq_illumina_1 $fastq_tech.fastq_illumina_2
            --fastq-illumina-names '$fastq_tech.fastq_illumina_1.element_identifier' '$fastq_tech.fastq_illumina_2.element_identifier'
        #elif str($fastq_tech.read_type) == 'ont':
            --fastq-ont $fastq_tech.fastq_ont
            --fastq-ont-name '$fastq_tech.fastq_ont.element_identifier'
        #end if

        ## Output
        --output '$bam'

        ## Other options
        $trim
        --dir-working \$PWD
        --threads \${GALAXY_SLOTS}
        ]]>
    </command>
    <inputs>
        <param argument="--ref-fasta" type="data" format="fasta" label="Reference genome"/>
        <conditional name="fastq_tech">
            <param argument="--read-type" type="select" label="FASTQ type">
                <option value="illumina">Illumina paired-end reads</option>
                <option value="ont">ONT single-end reads</option>
            </param>
            <when value="illumina">
                <param name="fastq_illumina_1" type="data" format="fastq,fastqsanger.gz" label="Forward reads"/>
                <param name="fastq_illumina_2" type="data" format="fastq,fastqsanger.gz" label="Reverse reads"/>
            </when>
            <when value="ont">
                <param name="fastq_ont" type="data" format="fastq,fastqsanger.gz" label="ONT reads"/>
            </when>
        </conditional>
        <param argument="--trim" type="boolean" label="Trim reads" checked="true" truevalue="--trim" falsevalue=""/>
    </inputs>
    <outputs>
        <data name="bam" format="bam" label="Mapping on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <!-- The line differences correspond to the three commands in the SAM header -->
            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
            <conditional name="fastq_tech">
                <param name="read_type" value="ont"/>
                <param name="fastq_ont" value="TIAC1151-ont.gz"/>
            </conditional>
            <param name="trim" value="false" />
            <output name="bam" ftype="bam" file="mapped_reads-ont.bam" lines_diff="6"/>
        </test>
        <test>
            <!-- The line differences correspond to the three commands in the SAM header -->
            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
            <conditional name="fastq_tech">
                <param name="read_type" value="illumina"/>
                <param name="fastq_illumina_1" value="TIAC1151_1P.fastq.gz"/>
                <param name="fastq_illumina_2" value="TIAC1151_2P.fastq.gz"/>
            </conditional>
            <param name="trim" value="false" />
            <output name="bam" ftype="bam" file="mapped_reads-ilmn.bam" lines_diff="6"/>
        </test>
                <test>
            <!-- The line differences correspond to the three commands in the SAM header -->
            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
            <conditional name="fastq_tech">
                <param name="read_type" value="ont"/>
                <param name="fastq_ont" value="TIAC1151-ont.gz"/>
            </conditional>
            <param name="trim" value="true" />
            <output name="bam" ftype="bam" file="mapped_reads_trimmed-ont.bam" lines_diff="6"/>
        </test>
        <test>
            <!-- The line differences correspond to the three commands in the SAM header -->
            <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
            <conditional name="fastq_tech">
                <param name="read_type" value="illumina"/>
                <param name="fastq_illumina_1" value="TIAC1151_1P.fastq.gz"/>
                <param name="fastq_illumina_2" value="TIAC1151_2P.fastq.gz"/>
            </conditional>
            <param name="trim" value="true" />
            <output name="bam" ftype="bam" file="mapped_reads_trimmed-ilmn.bam" lines_diff="6"/>
        </test>
    </tests>
    <help>
        This script maps Illumina or ONT reads to an input reference genome in FASTA format.
        It also writes a custom tag to the BAM file to propagate the sample name to PACU within Galaxy.
        The sample name is derived from the name of the input FASTQ files.
    </help>
    <expand macro="citations"/>
</tool>