Mercurial > repos > artbio > snvtocnv
changeset 2:9265faa93098 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit fd049d0796cbfaa6c41a7d80e84d3a734b30acc8-dirty"
| author | artbio |
|---|---|
| date | Fri, 19 Feb 2021 14:56:45 +0000 |
| parents | 7421ab885b27 |
| children | 15b26e44b18d |
| files | segmentation_sequenza.R snvtocnv.xml |
| diffstat | 2 files changed, 10 insertions(+), 5 deletions(-) [+] |
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--- a/segmentation_sequenza.R Thu Feb 18 19:03:54 2021 +0000 +++ b/segmentation_sequenza.R Fri Feb 19 14:56:45 2021 +0000 @@ -42,9 +42,13 @@ ## 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") + segfile <- sequenza.extract(data_file, - verbose = TRUE) # , - # chromosome.list = as.character(c(1:22))) + verbose = TRUE, + chromosome.list = chrom_list) ## Estimation of cellularity and ploidy
--- a/snvtocnv.xml Thu Feb 18 19:03:54 2021 +0000 +++ b/snvtocnv.xml Fri Feb 19 14:56:45 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.1"> +<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.2"> <description> </description> <macros> @@ -25,9 +25,9 @@ #end if sequenza-utils gc_wiggle --fasta reference.fa -o reference.gc50Base.wig.gz -w 50 && sequenza-utils snp2seqz -v '$input_snvs' -gc reference.gc50Base.wig.gz -o sample.seqz.gz && - sequenza-utils seqz_binning --seqz sample.seqz.gz -w 50 -o sample.binned.seqz.gz && + sequenza-utils seqz_binning --seqz sample.seqz.gz -w 50 -o '$wiggle' && Rscript $__tool_directory__/segmentation_sequenza.R - -i sample.binned.seqz.gz + -i '$wiggle' -s sample -O test && Rscript $__tool_directory__/sequenza_to_hrdtools_input.R @@ -45,6 +45,7 @@ </param> </inputs> <outputs> + <data name="wiggle" format="binary" 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" />