<tool id="sequenzaindex" name="create GC_wiggle of reference genome" version="3.0.0+galaxy1">
    <description>
    </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="3.0.0">sequenza-utils</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occured" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
    @pipefail@
    sequenza-utils gc_wiggle  --fasta $reference -o $refwig -w $window
    ]]></command>
    <inputs>
        <param name="reference" type="data" format="fasta" label="Genome in fasta format"
               help="the fasta genome whose GC content will be indexed"/>
        <param name="window" type="integer" value="50" label="window size" help="The size of the wiggle for GC content calculation" />
     </inputs>
    <outputs>
        <data name="refwig" format="wig" label="reference_wig" />
    </outputs>
    <tests>
        <test>
            <param name="window" value="100" ftype="vcf" />
            <param name="reference" value="hg19_chr22.fa.gz" />
            <output name="refwig" file="hg19.GCref.txt" ftype="wig" />
        </test>
        <test>
            <param name="window" value="100" ftype="vcf" />
            <param name="reference" value="hg38_chr22.fa.gz" />
            <output name="refwig" file="hg38.GCref.txt" ftype="wig" />
        </test>

    </tests>
    <help>

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

Analyzes 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.

This tools builds the GC wigle index of the reference genome required to perform analysis
of the somatic single nucleotide variations using the tool "Infer CNVs from SNVs"

    
Inputs
--------

The reference genome in a fasta format

*Warning* the genome fasta must be sorted according to the chromosomes
(e.g. chr1, chr2, .. chr21, chr22)

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