Mercurial > repos > artbio > snvtocnv
changeset 1:d2833cfb3f08 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
| author | artbio |
|---|---|
| date | Thu, 19 May 2022 20:35:24 +0000 |
| parents | b77d7a0a45e8 |
| children | e0724d649885 |
| files | segmentation_sequenza.R snvtocnv.xml test-data/hg19_CN_histo.pdf test-data/hg19_chrom_depths.pdf test-data/hg19_chrom_view.pdf test-data/hg19_genome_view.pdf test-data/hg19_model.pdf test-data/hg38_CN_histo.pdf test-data/hg38_chrom_depths.pdf test-data/hg38_chrom_view.pdf test-data/hg38_genome_view.pdf test-data/hg38_model.pdf |
| diffstat | 12 files changed, 21 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/segmentation_sequenza.R Sun Mar 07 23:19:59 2021 +0000 +++ b/segmentation_sequenza.R Thu May 19 20:35:24 2022 +0000 @@ -40,9 +40,9 @@ ## Processing seqz files : normalisation and segmentation for chromosomes 1 to 22 message(sprintf("\nExtraction step for %s", data_file)) -chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", - "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", - "chr18", "chr19", "chr20", "chr21", "chr22") + chrom_list <- c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", + "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", + "chr18", "chr19", "chr20", "chr21", "chr22", "chrX") Sys.setenv(TZDIR = "/usr/share/zoneinfo/") Sys.setenv(TZ = "US/Eastern")
--- a/snvtocnv.xml Sun Mar 07 23:19:59 2021 +0000 +++ b/snvtocnv.xml Thu May 19 20:35:24 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.7.0"> +<tool id="snvtocnv" name="Infer CNVs from SNVs" version="3.0.0+galaxy0"> <description> </description> <macros> @@ -26,7 +26,8 @@ Rscript $__tool_directory__/sequenza_to_hrdtools_input.R -i test/sample_segments.txt -s test/sample_alternative_solutions.txt - -o '$cnvs' + -o '$cnvs' && + ls test ]]></command> <inputs> <param name="refwig" type="data" format="txt" label="GC wigle of reference genome"/> @@ -37,17 +38,32 @@ <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>