<macros>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@TOOL_VERSION@">0.9.12</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">cnvkit</requirement>
            <requirement type="package" version="1.21">samtools</requirement>
        </requirements>
    </xml>
    <xml name="reference_interface">
        <conditional name="reference_source">
            <param name="ref_selector" type="select" label="Choose the source for the reference genome">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param argument="--fasta" optional="true" type="select" label="Reference genome">
                    <options from_data_table="fasta_indexes">
                        <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param argument="--fasta" type="data" optional="true" format="fasta" label="Reference" help="Reference sequence" />
            </when>
        </conditional>
    </xml>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">cnvkit</xref>
        </xrefs>
    </xml>
    <xml name="creators">
        <creator>
            <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" />
            <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" />
            <person givenName="Katarzyna" familyName="Kamieniecka" url="https://github.com/kkamieniecka" />
            <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" />
            <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" />
        </creator>
    </xml>
    <xml name="creators_and_zahra">
        <creator>
            <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" />
            <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" />
            <person givenName="Katarzyna" familyName="Kamieniecka" url="https://github.com/kkamieniecka" />
            <person givenName="zahra" familyName="Karimi" url="https://github.com/zahraK20" />
            <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" />
            <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" />
        </creator>
    </xml>
    <xml name="shared">
            <param argument="--method" type="select" label="Select the sequencing method of the input files" help="">
                <option value="hybrid" selected="True">hybridization capture </option>
                <option value="amplicon">targeted amplicon sequencing </option>
                <option value="wgs">whole genome sequencing </option>
            </param>
            <param argument="--segment-method" type="select" label="Method used in the 'segment' step" help="">
                <option value="cbs" selected="True">CBS: Circular Binary Segmentation (default, precise)</option>
                <option value="flasso">Flasso: Fused Lasso; smoother segments, fewer breakpoints</option>
                <option value="haar">Haar: Haar wavelet transform; detects abrupt changes</option>
                <option value="none">None: No segmentation; outputs bin-level data as segments</option>
                <option value="hmm">Hmm: Basic Hidden Markov Model (generic use)</option>
                <option value="hmm-tumor">Hmm-tumor: HMM tailored for tumor samples (somatic CNVs)</option>
                <option value="hmm-germline">Hmm-germline: HMM for germline (inherited) variants (diploid assumption)</option>
            </param>
            <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Use or assume a male reference" help="female samples will have +1 log-CNR of chrX; otherwise male samples would have -1 chrX" />
            <param argument="--countreads" type="boolean" checked="false" truevalue="--countreads" falsevalue="" label="Get read depths by counting read midpoints within each bin" help="" />
            <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples" />
    </xml>
    <xml name="create_CNV_reference_file">
        <param name="input_sample_file" type="data" format="bam" label="Sample BAM file" help="" />
        <param argument="--normal" optional="true" type="data" format="bam" label="Control BAM file" help="It is optional only if You have a single sample or are working with WGS data with no normal samples" />
        <param argument="--targets" type="data" format="bed" label="Capture BED regions" help="" />
    </xml>
    <xml name="advanced_no_reference">
        <param argument="--antitargets" optional="true" type="data" format="bed,tabular" label="Antitarget intervals" help="BED or list" />
        <param argument="--annotate" optional="true" type="data" format="bed,gff,tabular" label="Use gene models from this file to assign names to the target regions" help="Format: UCSC refFlat.txt or ensFlat.txt file preferred, or BED, interval list, GFF, or similar" />
        <param argument="--short-names" type="boolean" checked="false" truevalue="--short-names" falsevalue="" label="Reduce multi-accession bait labels" help="" />
        <param argument="--target-avg-size" type="integer" optional="true" label="Average size of split target bins" min="1" value="" help="" />
        <param argument="--access" optional="true" type="data" format="bed" label="Regions of accessible sequence on chromosomes BED" help="" />
        <param argument="--antitarget-avg-size" optional="true" type="integer" label="Average size of antitarget bins" min="1" value="" help="" />
        <param argument="--antitarget-min-size" optional="true" type="integer" label="Minimum size of antitarget bins" min="1" value="" help="" />
        <param argument="--cluster" optional="true" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Calculate and use cluster-specific summary stats in the reference pool" help="" />
    </xml>
    <xml name="reuse_an_existing_cnv_reference_file">
        <param name="input_sample_file" type="data" format="bam" label="Sample file" help="" />
        <param argument="--reference" type="data" format="cnn" label="CNV reference CNN File" help="" />
    </xml>
    <xml name="output_section">
        <section name="output_section" title="Outputs" expanded="false">
            <param argument="--scatter" type="boolean" checked="false" truevalue="--scatter" falsevalue="" label="Create a whole-genome copy ratio profile as a PNG scatter plot" help="" />
            <param argument="--diagram" type="boolean" checked="false" truevalue="--diagram" falsevalue="" label="Create an ideogram of copy ratios on chromosomes as a PDF" help="" />
        </section>
    </xml>
    <xml name="autobin_optional">
            <param argument="--method" type="select" label="Select the sequencing method of the input files" help="">
                <option value="hybrid" selected="True">hybridization capture </option>
                <option value="amplicon">targeted amplicon sequencing </option>
                <option value="wgs">whole genome sequencing </option>
            </param>
            <param argument="--access" optional="true" type="data" format="bed" label="Sequencing-accessible genomic regions, or exons to use as possible targets" help="The output of refFlat2bed.py" />
            <param argument="--bp-per-bin" optional="true" type="integer" label=" Desired average number of sequencing read bases mapped to each bin" min="1" value="100000" help="" />
            <param argument="--target-max-size" optional="true" type="integer" label="Maximum size of target bins" min="1" value="20000" help="" />
            <param argument="--target-min-size" optional="true" type="integer" label="Minimum size of target bins" min="1" value="20" help="" />
            <param argument="--antitarget-max-size" optional="true" type="integer" label="Maximum size of antitarget bins" min="1" value="500000" help="" />
            <param argument="--antitarget-min-size" optional="true" type="integer" label="Minimum size of antitarget bins" min="1" value="500" help="" />
            <param argument="--annotate" optional="true" type="data" format="bed,gff,tabular" label="Use gene models from this file to assign names to the target regions" help="Format: UCSC refFlat.txt or ensFlat.txt file preferred, or BED, interval list, GFF, or similar" />
            <param argument="--short-names" type="boolean" checked="false" truevalue="--short-names" falsevalue="" label="Reduce multi-accession bait labels to be short and consistent" help="" />
            <param argument="--target-output-bed" optional="true" type="data" format="bed" label="Filename for target BED output" help="If not specified, constructed from the input file basename" />
            <param argument="--antitarget-output-bed" optional="true" type="data" format="bed" label="Filename for antitarget BED output" help="If not specified, constructed from the input file basename" />
    </xml>
    <xml name="filter">
        <param argument="--filter" type="select" multiple="true" label="Merge segments flagged by the specified filter(s) with the adjacent segment(s)." help="">
            <option value="ampdel" selected="True">ampdel</option>
            <option value="cn">cn</option>
            <option value="ci">ci</option>
            <option value="sem">sem</option>
        </param>
    </xml>
    <xml name="sample_sex">
        <param argument="--sample-sex" type="select" label="Method used in the 'segment' step" help="">
            <option value="Male" selected="True">Male</option>
            <option value="Female">Female</option>
        </param>
    </xml>
    <xml name="call_optional">
            <param argument="--method" type="select" label="Select the sequencing method of the input files" help="">
                <option value="threshold" selected="True">hybridization capture </option>
                <option value="clonal">targeted amplicon sequencing </option>
                <option value="none">whole genome sequencing </option>
            </param>
            <param argument="--center" type="select" label="Method used in the 'segment' step" help="">
                <option value="mean">mean</option>
                <option value="median" selected="True">median</option>
                <option value="mode">mode</option>
                <option value="biweight">biweight</option>
            </param>
            <param argument="--center-at" optional="true" type="float" label="Subtract a constant number from all log2 ratios" value="" help="For manual re-centering, in case the --center option gives unsatisfactory results" />
            <param argument="--thresholds" type="text" label="Hard thresholds for calling each integer copy number, separated by commas" value="=-1.1,-0.25,0.2,0.7" help="Apply cutoffs to either original or rescaled log2 values" />
            <param argument="--ploidy" optional="true" type="integer" label="Ploidy of the sample cells" min="1" max="2" value="2" help="" />
            <param argument="--purity" optional="true" type="float" label="Estimated tumor cell fraction, a.k.a. purity or cellularity" min="0" max="1" value="" help="" />
            <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples" />
            <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Use or assume a male reference" help="Was a male reference used? If so, expect half ploidy on chrX and chrY; otherwise, only chrY has half ploidy. In CNVkit, if a male reference was used, the neutral copy number ploidy of chrX is 1; chrY is haploid for either reference sex" />
    </xml>
    <xml name="additionally_SNP_process">
        <param argument="--vcf" optional="true" type="data" format="vcf" label="VCF file" help="VCF file name containing variants for calculation of b-allele frequencies" />
        <param argument="--sample-id" type="text" label="Name of the sample in the VCF to use for b-allele frequency extraction" help="" />
        <param argument="--normal-id" type="text" label="Corresponding normal sample ID in the input VCF" help="This sample is used to select only germline SNVs to calculate b-allele frequencies" />
        <param argument="--min-variant-depth" type="integer" min="1" value="20" optional="true" label="Minimum read depth for a SNV to be used in the b-allele frequency calculation" help="" />
        <param argument="--zygosity-freq" type="float" min="0" value="0.25" optional="true" label="Ignore VCF's genotypes and instead infer zygosity from allele frequencies" help="" />
    </xml>
    <xml name="diagram_optional">
            <param argument="--segment" optional="true" type="data" format="cns,cnr" label="Segment" help="Segmentation calls cns, the output of the 'segment' command" />
            <param argument="--threshold" optional="true" type="float" label="Threshold" min="0" value="0.5" help="Copy number change threshold to label genes" />
            <param argument="--min-probes" optional="true" type="integer" label="Minimum propes" min="1" value="3" help="Minimum number of covered probes to label a gene" />
            <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
            <param argument="--no-shift-xy" type="boolean" checked="false" truevalue="--no-shift-xy" falsevalue="" label="Don't adjust the X and Y chromosomes according to sample sex" help="" />
            <param argument="--chromosome" type="text" label="Chromosome to display" help="e.g. 'chr1' no chromosomal range allowed" />
    </xml>
    <xml name="diagram_plot">
        <param argument="--title" type="text" label="Plot title" help="" />
        <param argument="--no-gene-labels" type="boolean" checked="false" truevalue="--no-gene-labels" falsevalue="" label="Disable gene_name labels on plot useful when a lot of CNV were called" help="" />
    </xml>
    <xml name="heatmap_optional">
            <param argument="--by-bin" type="boolean" checked="false" truevalue="--by-bin" falsevalue="" label="Plot data x-coordinates by bin indices instead of genomic coordinates" help="" />
            <param argument="--chromosome" type="text" label="Chromosome range" help="Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000'" />
            <param argument="--desaturate" type="boolean" checked="false" truevalue="--desaturate" falsevalue="" label="Tweak color saturation to focus on significant changes" help="" />
            <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
            <param argument="--no-shift-xy" type="boolean" checked="false" truevalue="--no-shift-xy" falsevalue="" label="Don't adjust the X and Y chromosomes according to sample sex" help="" />
            <param argument="--vertical" type="boolean" checked="false" truevalue="--vertical" falsevalue="" label="Plot heatmap with samples as X-axis instead of Y-axis" help="" />
            <param argument="--delimit-samples" type="boolean" checked="false" truevalue="--delimit-samples" falsevalue="" label="Add an horizontal delimitation line between each sample" help="" />
            <param argument="--title" type="text" label="Plot title" help="" />
    </xml>
    <xml name="reference_optional">
            <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Calculate and store summary stats for clustered subsets of the normal samples with similar coverage profiles" help="" />
            <param argument="--min-cluster-size" optional="true" type="integer" label="Minimum cluster size to keep in reference profiles" min="1" value="4" help="" />
            <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Create a male reference" help="shift female samples' chrX log-coverage by -1, so the reference chrX average is -1. Otherwise, shift male samples' chrX by +1, so the reference chrX average is 0" />
    </xml>
    <xml name="construct_CNV_ref_with_natural_expected_number">
        <param argument="--targets" optional="true" type="data" format="bed" label="Target intervals bed file" help="" />
        <param argument="--antitargets" optional="true" type="data" format="bed" label="Antitarget intervals bed file" help="" />
    </xml>
    <xml name="disable_specific_automatic_bias_corrections">
        <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" />
        <param argument="--no-edge" type="boolean" checked="false" truevalue="--no-edge" falsevalue="" label="skip edge-effect correction" help="" />
        <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label="skip repeat master correction" help="" />
    </xml>
    <xml name="scatter_optional">
            <param argument="--segment" optional="true" type="data" format="cns,cnr" label="Segment" help="Segmentation calls cns, the output of the 'segment' command" />
            <param argument="--chromosome" type="text" label="Chromosome range" help="Chromosome or chromosomal range, e.g. 'chr1' or 'chr1:2333000-2444000'" />
            <param argument="--gene" type="text" label="Name of gene or genes comma-separated to display" help="" />
            <param argument="--range-list" optional="true" type="data" format="bed" label="Range list" help="File listing the chromosomal ranges to display, as BED"/>
            <param argument="--width" optional="true" type="integer" label="Width" min="1" value="1000000" help="Width of margin to show around the selected genes or small chromosomal region" />
    </xml>
    <xml name="scatter_plot">
        <param argument="--antitarget-marker" type="text" label="Antitarget marker" value="same as targets" help="Plot antitargets using this symbol when plotting in a selected chromosomal region"/>
        <param argument="--by-bin" type="boolean" checked="false" truevalue="--by-bin" falsevalue="" label="Plot data x-coordinates by bin indices instead of genomic coordinates" help=""/>
        <param argument="--segment-color" type="text" label="Segment color" value="red" help=""/>
        <param argument="--title" type="text" label="Plot title" help=""/>
        <param argument="--trend" type="boolean" checked="false" truevalue="--trend" falsevalue="" label="Draw a smoothed local trendline on the scatter plot" help=""/>
        <param argument="--y-max" optional="true" type="integer" label="y-axis upper limit" min="1" value="" help=""/>
        <param argument="--y-min" optional="true" type="integer" label="y-axis lower limit" min="1" value="" help=""/>
        <param argument="--fig-size" optional="true" type="float" label="Width and height of the plot in inches" value="" help="Example 6.4 4.8, the space between the two inputs is important"/>
    </xml>
    <xml name="segment_optional">
            <param argument="--dataframe" type="text" label="Data frame" help="File name to save the raw R dataframe emitted by CBS or Fused Lasso, example dataframe.r"/>
            <param argument="--method" type="select" label="Segmentation method" help="">
                <option value="cbs" selected="True">CBS: Circular Binary Segmentation (default, precise)</option>
                <option value="flasso">Flasso: Fused Lasso; smoother segments, fewer breakpoints</option>
                <option value="haar">Haar: Haar wavelet transform; detects abrupt changes</option>
                <option value="none">None: No segmentation; outputs bin-level data as segments</option>
                <option value="hmm">Hmm: Basic Hidden Markov Model (generic use)</option>
                <option value="hmm-tumor">Hmm-tumor: HMM tailored for tumor samples (somatic CNVs)</option>
                <option value="hmm-germline">Hmm-germline: HMM for germline (inherited) variants (diploid assumption)</option>
            </param>
            <param argument="--threshold" optional="true" type="integer" label="Significance threshold" min="1" help="To accept breakpoints during segmentation. For HMM methods, this is the smoothing window size"/>
            <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples"/>
            <param argument="--drop-outliers" optional="true" type="integer" label="Drop outliers" min="1" value="10" help=""/>
            <param argument="--smooth-cbs" type="boolean" checked="false" truevalue="--smooth-cbs" falsevalue="" label="Perform an additional smoothing before CBS segmentations" help=""/>
    </xml>
    <xml name="sample_sex_condition">
        <conditional name="Sample_sex">
            <param name="sex" type="select" label="Sample sex availabel" help="">
                <option value="no" selected="True">Sample sex unknown</option>
                <option value="yes">Select sample sex</option>
            </param>
            <when value="yes">
                <expand macro="sample_sex" />
            </when>
            <when value="no">
            </when>
        </conditional>
    </xml>
    <xml name="genemetrics_segmetrics_statistics">
          <param argument="--mean" type="boolean" checked="true" truevalue="--mean" falsevalue="" label="Mean log2-ratio" help="" />
          <param argument="--median" type="boolean" checked="false" truevalue="--median" falsevalue="" label="Median" help="" /> 
          <param argument="--mode" type="boolean" checked="false" truevalue="--mode" falsevalue="" label="mode" help="peak density of log2 ratios" />
          <param argument="--ttest" type="boolean" checked="false" truevalue="--ttest" falsevalue="" label="One-sample t-test" help="bin log2 ratios versus 0.0" />
          <param argument="--stdev" type="boolean" checked="false" truevalue="--stdev" falsevalue="" label="Standard deviation" help="" />
          <param argument="--sem" type="boolean" checked="false" truevalue="--sem" falsevalue="" label="Standard error of the mean" help="" />
          <param argument="--mad" type="boolean" checked="false" truevalue="--mad" falsevalue="" label="Median absolute deviation" help="" />
          <param argument="--mse" type="boolean" checked="false" truevalue="--mse" falsevalue="" label="mean squared error" help="" />
          <param argument="--iqr" type="boolean" checked="false" truevalue="--iqr" falsevalue="" label="Inter-quartile range" help="" />
          <param argument="--bivar" type="boolean" checked="false" truevalue="--bivar" falsevalue="" label="Tukeys biweight midvariance" help="" />
          <param argument="--ci" type="boolean" checked="false" truevalue="--ci" falsevalue="" label="confidence interval" help="" />
          <param argument="--pi" type="boolean" checked="false" truevalue="--pi" falsevalue="" label="prediction interval" help="" />
          <param argument="--alpha" type="boolean" checked="false" truevalue="--alpha" falsevalue="" label="alpha" help="" />
          <param argument="--bootstrap" type="boolean" checked="false" truevalue="--bootstrap" falsevalue="" label="estimate confidence interval" help="number of bootstrp interations" />
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1371/journal.pcbi.1004873</citation>
        </citations>
    </xml>
</macros>