Mercurial > repos > artbio > mapping_quality_stats

comparison mapping_quality_stats.r @ 2:ce2d8f611a51 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
author artbio
date Sat, 10 Feb 2024 01:32:48 +0000
parents f00479673d47
children
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1:7883d97fa479 2:ce2d8f611a51
1 ## Setup R error handling to go to stderr 1 ## Setup R error handling to go to stderr
2 options(show.error.messages = FALSE, 2 options(show.error.messages = FALSE,
3 error = function() { 3 error = function() {
4 cat(geterrmessage(), file = stderr()) 4 cat(geterrmessage(), file = stderr())
5 q("no", 1, FALSE) 5 q("no", 1, FALSE)
6 } 6 }
7 ) 7 )
8 8
9 9
10 warnings() 10 warnings()
11 library(optparse) 11 library(optparse)
12 library(ggplot2) 12 library(ggplot2)
13 13
14 option_list <- list( 14 option_list <- list(
15 make_option(c("-i", "--input"), type = "character", help = "Path to tabular file"), 15 make_option(c("-i", "--input"), type = "character", help = "Path to tabular file"),
16 make_option(c("-o", "--output"), type = "character", help = "path to the pdf plot") 16 make_option(c("-o", "--output"), type = "character", help = "path to the pdf plot")
17 ) 17 )
18 18
19 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) 19 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
20 args <- parse_args(parser) 20 args <- parse_args(parser)
21 21
22 # data frame implementation 22 # data frame implementation