<tool id="deeptools_bam_coverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
    <description>generates a coverage bigWig file from a given BAM file</description>
    <macros>
        <token name="@BINARY@">bamCoverage</token>
        <import>deepTools_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command>
<![CDATA[
        ln -s '$bamInput' one.bam &&
        ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&

        @BINARY@
            @THREADS@

            --bam one.bam
            --outFileName '$outFileName'
            --outFileFormat '$outFileFormat'

            --binSize $binSize

            #if $scaling.type=='rpkm':
                --normalizeUsingRPKM
            #elif $scaling.type=='1x':
                #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
                    --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
                #else:
                    --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
                #end if
            #elif $scaling.type=='own':
                --scaleFactor $scaling.scaleFactor
            #end if

            #if str($region).strip() != '':
                --region '$region'
            #end if

            #if $advancedOpt.showAdvancedOpt == "yes":
                #if $advancedOpt.smoothLength:
                    --smoothLength '$advancedOpt.smoothLength'
                #end if

                @ADVANCED_OPTS_READ_PROCESSING@
                $advancedOpt.skipNAs

                #if str($advancedOpt.ignoreForNormalization).strip() != '':
                    --ignoreForNormalization $advancedOpt.ignoreForNormalization
                #end if
            #end if
]]>
    </command>

    <inputs>
        <param name="bamInput" format="bam" type="data" label="BAM file"
            help="The BAM file must be sorted."/>

        <param name="binSize" type="integer" value="50" min="1"
            label="Bin size in bases"
            help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads)  will be reported. If only half a fragment overlaps, this fraction will be reported. "/>

        <conditional name="scaling">
            <param name="type" type="select" label="Scaling/Normalization method" >
                <option value="1x">Normalize coverage to 1x</option>
                <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
                <option value="no">Do not normalize or scale</option>
            </param>
            <when value="rpkm">
                <expand macro="scaleFactor" />
            </when>
            <when value="no"/>
            <when value="1x">
                <expand macro="effectiveGenomeSize" />
                <expand macro="scaleFactor" />
            </when>
        </conditional>

        <param name="outFileFormat" type="select" label="Coverage file format">
            <option value="bigwig" selected="true">bigwig</option>
            <option value="bedgraph">bedgraph</option>
        </param>

        <expand macro="region_limit_operation" />

        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <expand macro="smoothLength" />

                <param argument="ignoreForNormalization" type="text" value=""
                    label="Regions that should be excluded for normalization"
                    help="A list of chromosome names separated by spaces
                        containing those chromosomes that should be excluded
                        during normalization. This is useful when
                        considering samples with unequal coverage across
                        chromosomes, like male and female samples. Example: chrX chrM" />

                <expand macro="skipNAs" />
                <expand macro="read_processing_options" />

                <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
                    label="Determine nucleosome positions from MNase-seq data"
                    help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." />

            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="bigwig" name="outFileName">
            <change_format>
                <when input="outFileFormat" value="bigwig" format="bigwig" />
                <when input="outFileFormat" value="bedgraph" format="bedgraph" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
            <param name="outFileFormat" value="bigwig" />
            <param name="showAdvancedOpt" value="no" />
            <param name="binSize" value="10" />
            <param name="type" value="no" />
            <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" />
        </test>
        <test>
            <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
            <param name="outFileFormat" value="bigwig" />
            <param name="showAdvancedOpt" value="no" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
        </test>
        <test>
            <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
            <param name="outFileFormat" value="bedgraph" />
            <param name="showAdvancedOpt" value="no" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" />
        </test>
        <test>
            <param name="bamInput" value="phiX.bam" ftype="bam" />
            <param name="outFileFormat" value="bigwig" />
            <param name="showAdvancedOpt" value="no" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
        </test>
        <test>
            <param name="bamInput" value="phiX.bam" ftype="bam" />
            <param name="outFileFormat" value="bedgraph" />
            <param name="showAdvancedOpt" value="yes" />
            <param name="binSize" value="10" />
            <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
read coverages. The way the method works is by first calculating all the
number of reads (either extended to match the fragment length or not) that
overlap each bin in the genome. The resulting read counts can be normalized
using either a given scaling factor, the RPKM formula or to get a 1x depth of
coverage (RPGC). In the case of paired-end mapping, each read mate is treated
independently to avoid a bias when a mixture of concordant and discordant
pairs is present. This means that *each end* will be extended to match the
fragment length.

.. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png


You can find more details on the bamCoverage doc page: https://deeptools.readthedocs.org/en/master/content/tools/bamCoverage.html


**Output files**:

- coverage file either in bigWig or bedGraph format

-----

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>