<tool id="snvtocnv" name="Infer CNVs from SNVs" version="3.0.0+galaxy0">
    <description>
    </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="3.0.0">sequenza-utils</requirement>
        <requirement type="package" version="3.0.0">r-sequenza</requirement>
        <requirement type="package" version="1.6.6">r-optparse</requirement>
        <requirement type="package" version="1.24.0">bioconductor-biocparallel</requirement>
        <requirement type="package" version="1.3.0">r-tidyverse</requirement>
        <requirement type="package" version="2021a=he74cb21_0">tzdata</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occured" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
    @pipefail@
    sequenza-utils snp2seqz -v '$input_snvs'  -gc $refwig -o sample.seqz.gz &&
    sequenza-utils seqz_binning --seqz sample.seqz.gz -w 50 -o '$wiggle' &&
    Rscript $__tool_directory__/segmentation_sequenza.R
            -i '$wiggle'
            -s sample
            -O test &&
    Rscript $__tool_directory__/sequenza_to_hrdtools_input.R
            -i test/sample_segments.txt
            -s test/sample_alternative_solutions.txt
            -o '$cnvs' &&
    ls test
    ]]></command>
    <inputs>
        <param name="refwig" type="data" format="txt" label="GC wigle of reference genome"/>
        <param name="input_snvs" type="data" format="vcf" label="SNVs to process in a vcf file"/>
    </inputs>
    <outputs>
        <data name="wiggle" format="txt" label="binned wiggle" />
        <data name="sample_segment" format="txt" label="sample segments" from_work_dir="test/sample_segments.txt" />
        <data name="alt_solutions" format="txt" label="alternate solutions" from_work_dir="test/sample_alternative_solutions.txt" />
        <data name="cnvs" format="tabular" label="Annotated CNVs" />
        <data name="chrom_depths" format="pdf" label="Chromosomes sequencing depth" from_work_dir="test/sample_chromosome_depths.pdf"/>
        <data name="chrom_view" format="pdf" label="Chromosomes views" from_work_dir="test/sample_chromosome_view.pdf"/>
        <data name="genome_view" format="pdf" label="Genome view" from_work_dir="test/sample_genome_view.pdf"/>        
        <data name="model_fit" format="pdf" label="Cellularity and Diploidy model" from_work_dir="test/sample_model_fit.pdf"/>        
        <data name="CN_histo" format="pdf" label="Copy Numbers histogram" from_work_dir="test/sample_CN_bars.pdf"/>        
    </outputs>
    <tests>
        <test>
            <param name="input_snvs" value="hg19_chr22.vcf" ftype="vcf" />
            <param name="refwig" value="hg19.GCref.txt" />
            <output name="cnvs" file="hg19.cnv.tab" ftype="tabular" />
            <output name="chrom_depths" ftype="pdf" file="hg19_chrom_depths.pdf"/>
            <output name="chrom_view" ftype="pdf" file="hg19_chrom_view.pdf"/>
            <output name="genome_view" ftype="pdf" file="hg19_genome_view.pdf"/>        
            <output name="model_fit" ftype="pdf" file="hg19_model.pdf"/>        
            <output name="CN_histo" ftype="pdf" file="hg19_CN_histo.pdf"/>        
        </test>
        <test>
            <param name="input_snvs" value="hg38_chr22.vcf" ftype="vcf" />
            <param name="refwig" value="hg38.GCref.txt" />
            <output name="cnvs" file="hg38.cnv.tab" ftype="tabular" />
            <output name="chrom_depths" ftype="pdf" file="hg38_chrom_depths.pdf"/>
            <output name="chrom_view" ftype="pdf" file="hg38_chrom_view.pdf"/>
            <output name="genome_view" ftype="pdf" file="hg38_genome_view.pdf"/>        
            <output name="model_fit" ftype="pdf" file="hg38_model.pdf"/>        
            <output name="CN_histo" ftype="pdf" file="hg38_CN_histo.pdf"/>        
        </test>
    </tests>
    <help>

snvtocnv
============================

Analyze genomic sequencing data from paired normal-tumor samples, including
cellularity and ploidy estimation; mutation and copy number (allele-specific and total
copy number) detection, quantification and visualization.

    
Inputs
--------

A GC wigle of genome index generated with the tool "create GC_wiggle of reference genome"
available from this galaxy wrapper

A vcf file of somatic *single* nucleotide variations observed in a tumor sample


    </help>
    <citations>
        <citation type="doi">10.1093/annonc/mdu479</citation>
    </citations>
</tool>