Mercurial > repos > artbio > snvtocnv
changeset 7:e66b91475343 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 7df896b940e80984168b1fa6326c4d862e7e208c"
| author | artbio |
|---|---|
| date | Sun, 07 Mar 2021 14:21:06 +0000 |
| parents | 88e03bac1e36 |
| children | 67213c4eefa6 |
| files | segmentation_sequenza.R sequenza_index.xml sequenza_to_hrdtools_input.R snvtocnv.xml |
| diffstat | 4 files changed, 7 insertions(+), 16 deletions(-) [+] |
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--- a/segmentation_sequenza.R Sun Mar 07 12:01:21 2021 +0000 +++ b/segmentation_sequenza.R Sun Mar 07 14:21:06 2021 +0000 @@ -1,17 +1,10 @@ +options(warn = -1) + # load packages that are provided in the conda env -# options(show.error.messages = F, -# error = function() { -# cat(geterrmessage(), file = stderr()); q("no", 1, F)}) - library(optparse) library(sequenza) library(BiocParallel) library(tidyverse) -Sys.setenv(TZ = "Etc/UTC") # turnaround the tidyverse bug "In OlsonNames() : no Olson database found" -tzdirs <- c(Sys.getenv("TZDIR"), file.path(R.home("share"), - "zoneinfo"), "/usr/share/zoneinfo", "/usr/share/lib/zoneinfo", - "/usr/lib/zoneinfo", "/usr/local/etc/zoneinfo", "/etc/zoneinfo", - "/usr/etc/zoneinfo") option_list <- list( make_option( c("-i", "--input"),
--- a/sequenza_index.xml Sun Mar 07 12:01:21 2021 +0000 +++ b/sequenza_index.xml Sun Mar 07 14:21:06 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="sequenzaindex" name="create GC_wiggle of reference genome" version="0.5.0"> +<tool id="sequenzaindex" name="create GC_wiggle of reference genome" version="0.6.1"> <description> </description> <macros>
--- a/sequenza_to_hrdtools_input.R Sun Mar 07 12:01:21 2021 +0000 +++ b/sequenza_to_hrdtools_input.R Sun Mar 07 14:21:06 2021 +0000 @@ -1,7 +1,6 @@ +options(warn = -1) + # load packages that are provided in the conda env -options(show.error.messages = F, error = function() { - cat(geterrmessage(), file = stderr()); q("no", 1, F) }) -Sys.setenv(TZ = "Pacific/Auckland") # turnaround the tidyverse bug "In OlsonNames() : no Olson database found" library(optparse) library(tidyverse) @@ -62,6 +61,6 @@ print(reformatted) reformatted %>% - write_tsv(opt$output) + write.table(opt$output, quote=F, row.names=F, sep="\t") message(sprintf("Output written to %s", opt$output))
--- a/snvtocnv.xml Sun Mar 07 12:01:21 2021 +0000 +++ b/snvtocnv.xml Sun Mar 07 14:21:06 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.5.0"> +<tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.6.1"> <description> </description> <macros> @@ -17,7 +17,6 @@ </stdio> <command detect_errors="exit_code"><![CDATA[ @pipefail@ -## sequenza-utils gc_wiggle --fasta reference.fa -o $refwig -w 50 && sequenza-utils snp2seqz -v '$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