Mercurial > repos > artbio > snvtocnv
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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
author | artbio |
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date | Sun, 07 Mar 2021 23:19:59 +0000 |
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children | d2833cfb3f08 |
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<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.7.0"> <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' ]]></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" /> </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" /> </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" /> </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>