# HG changeset patch
# User artbio
# Date 1615126866 0
# Node ID e66b91475343bb9e861337e6dcad2cc0fd5f91d3
# Parent  88e03bac1e36b7ad950315f8bfd6e7f06dc5c099
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 7df896b940e80984168b1fa6326c4d862e7e208c"

diff -r 88e03bac1e36 -r e66b91475343 segmentation_sequenza.R
--- 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"),
diff -r 88e03bac1e36 -r e66b91475343 sequenza_index.xml
--- 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>
diff -r 88e03bac1e36 -r e66b91475343 sequenza_to_hrdtools_input.R
--- 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))
diff -r 88e03bac1e36 -r e66b91475343 snvtocnv.xml
--- 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