<tool id="halfdeep" name="HalfDeep" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>identifies genomic regions with half-depth coverage based on sequencing read mappings.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ##
        ## Set up the directory structure expected by bam_depth.sh and halfdeep.sh
        ## See: https://github.com/makovalab-psu/HalfDeep?tab=readme-ov-file#expected-directory-layout
        ##
        mkdir -p reads halfdeep/ref/mapped_reads &&
        ##
        ## reference
        ##
        ln -s '$ref' 'ref.$ref.ext' &&
        #if not $mapped_reads
            minimap2 -x map-pb -d ref.idx 'ref.$ref.ext' &&
        #else
            touch ref.idx &&
        #end if
        ##
        ## reads
        ##
        #import re
        #set $reads_base = re.sub('[^\w\-\s]', '_', str($reads.element_identifier))
        ln -s '$reads' 'reads/${reads_base}.$reads.ext' &&
        echo 'reads/${reads_base}.$reads.ext' >> input.fofn &&
        ##
        ## mapped reads
        ##
        #if $mapped_reads
            ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}.${reads.ext}.bam' &&
            ln -s '${reads_base}.${reads.ext}.bam' 'halfdeep/ref/mapped_reads/${reads_base}.${reads.ext}.sort.bam' &&
            ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}.${reads.ext}.sort.bam.bai' &&
        #end if
        ##
        ## run bam_depth.sh
        ##
        bam_depth.sh 'ref.$ref.ext' 1 &&
        ##
        ## run halfdeep.sh
        ##
        halfdeep.sh 'ref.$ref.ext'
    ]]></command>
    <inputs>
        <param name="ref" type="data" format="fasta,fasta.gz" label="Genome Assembly" help="A Genome Assembly in FASTA format."/>
        <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Sequencing Reads" help="Sequencing Reads for the Genome Assembly in FASTQ format."/>
         <param name="mapped_reads" type="data" format="bam" value="" optional="true" label="Aligned Reads" help="Alignments of the Sequencing Reads to the Genome Assembly in BAM format."/>
    </inputs>
    <outputs>
        <data name="halfdeep_dat" format="bed" from_work_dir="halfdeep/ref/halfdeep.dat" label="HalfDeep on ${on_string}"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="ref" value="ref.fasta.gz" ftype="fasta.gz"/>
            <param name="reads" value="reads.fasta.gz" ftype="fasta.gz"/>
            <param name="mapped_reads" value="mapped_reads.bam" ftype="bam"/>
            <output name="halfdeep_dat" file="halfdeep.bed" ftype="bed"/>
        </test>
        <test expect_num_outputs="1">
            <param name="ref" value="ref.fasta.gz" ftype="fasta.gz"/>
            <param name="reads" value="reads.fasta.gz" ftype="fasta.gz"/>
            <output name="halfdeep_dat" file="halfdeep.bed" ftype="bed"/>
        </test>
    </tests>
    <help><![CDATA[

HalfDeep identifies genomic regions with half-depth coverage based on sequencing read mappings. These regions may reveal insights into heterogametic sex chromosomes, haplotype-specific variation, or potential assembly errors such as heterotypic duplications.

Given the following inputs:

1. A genome assembly in FASTA format.
2. Reads in FASTQ format.
3. Mapped reads in BAM format (optional)

HalfDeep automates the following tasks:

1. Mapping reads and merging individual mapping files.
2. Calculating per-base read depth.
3. Smoothing read coverage using a defined window with genodsp.
4. Determining the percentile of read coverage.
5. Identifying genomic regions with half-depth coverage based on a specified percentile threshold (e.g., 40–60%) and exporting them in BED file format

HalfDeep produces the following output:

1. HalfDeep: BED file containing regions of the genome assembly that are "covered at half depth"
    ]]></help>
    <expand macro="citations"/>
</tool>