| Previous changeset 6:7c4feda2d9c7 (2020-01-07) Next changeset 8:0adb846ca056 (2024-02-20) |
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Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 6dc66b89f0792e4da40719ec83494a1fcee5e105" |
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modified:
probecoverage.r probecoverage.xml |
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| diff -r 7c4feda2d9c7 -r bea8435e1e79 probecoverage.r --- a/probecoverage.r Tue Jan 07 06:08:56 2020 -0500 +++ b/probecoverage.r Thu Jun 03 23:59:31 2021 +0000 |
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| @@ -1,74 +1,74 @@ ## Setup R error handling to go to stderr -options( show.error.messages=F, - error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +options(show.error.messages = F, + error = function() { + cat(geterrmessage(), file = stderr()); q("no", 1, F) + } + ) warnings() library(optparse) library(ggplot2) library(reshape2) option_list <- list( - make_option(c("-i", "--input"), type="character", help="Path to dataframe"), - make_option(c("-t", "--title"), type="character", help="Main Title"), - make_option("--xlab", type = "character", help="X-axis legend"), - make_option("--ylab", type = "character", help="Y-axis legend"), - make_option("--sample", type = "character", help="a space separated of sample labels"), - make_option("--method", type = "character", help="bedtools or pysam"), - make_option(c("-o", "--output"), type = "character", help="path to the pdf plot") + make_option(c("-i", "--input"), type = "character", help = "Path to dataframe"), + make_option(c("-t", "--title"), type = "character", help = "Main Title"), + make_option("--xlab", type = "character", help = "X-axis legend"), + make_option("--ylab", type = "character", help = "Y-axis legend"), + make_option("--sample", type = "character", help = "a space separated of sample labels"), + make_option("--method", type = "character", help = "bedtools or pysam"), + make_option(c("-o", "--output"), type = "character", help = "path to the pdf plot") ) parser <- OptionParser(usage = "%prog [options] file", option_list = option_list) -args = parse_args(parser) -samples = substr(args$sample, 2, nchar(args$sample)-2) -samples = strsplit(samples, ", ") +args <- parse_args(parser) +samples <- substr(args$sample, 2, nchar(args$sample) - 2) +samples <- strsplit(samples, ", ") # data frames implementation -Table <- read.delim(args$input, header=F) -headers = c("chromosome", "start", "end", "id") -for (i in seq(1, length(Table)-4)) { +table <- read.delim(args$input, header = F) +headers <- c("chromosome", "start", "end", "id") +for (i in seq(1, length(table) - 4)) { headers <- c(headers, samples[[1]][i]) -colnames(Table) <- headers +colnames(table) <- headers } ## function -if (args$method == 'bedtools') { - cumul <- function(x,y) sum(Table[,y]/(Table$end-Table$start) > x)/length(Table$chromosome) +if (args$method == "bedtools") { + cumul <- function(x, y) sum(table[, y] / (table$end - table$start) > x) / length(table$chromosome) } else { - cumul <- function(x,y) sum(Table[,y] > x)/length(Table$chromosome) + cumul <- function(x, y) sum(table[, y] > x) / length(table$chromosome) } -scaleFUN <- function(x) sprintf("%.3f", x) +scale_fun <- function(x) sprintf("%.3f", x) ## end of function ## let's do a dataframe before plotting -if (args$method == 'bedtools') { - maxdepth <- trunc(max(Table[,5:length(Table)]/(Table$end-Table$start))) + 20 +if (args$method == "bedtools") { + maxdepth <- trunc(max(table[, 5:length(table)] / (table$end - table$start))) + 20 } else { - maxdepth <- trunc(max(Table[,5:length(Table)])) + 20 + maxdepth <- trunc(max(table[, 5:length(table)])) + 20 } graphpoints <- data.frame(1:maxdepth) i <- 5 -for (colonne in colnames(Table)[5:length(colnames(Table))]) { +for (colonne in colnames(table)[5:length(colnames(table))]) { graphpoints <- cbind(graphpoints, mapply(cumul, 1:maxdepth, rep(i, maxdepth))) i <- i + 1 } -colnames(graphpoints) <- c("Depth", colnames(Table)[5:length(Table)]) -maxfrac = max(graphpoints[,2:length(graphpoints)]) +colnames(graphpoints) <- c("Depth", colnames(table)[5:length(table)]) +maxfrac <- max(graphpoints[, 2:length(graphpoints)]) -graphpoints <- melt(graphpoints, id.vars="Depth", variable.name="Samples", value.name="sample_value") +graphpoints <- melt(graphpoints, id.vars = "Depth", variable.name = "Samples", value.name = "sample_value") ## GRAPHS -pdf(file=args$output) -ggplot(data=graphpoints, aes(x=Depth, y=sample_value, colour=Samples)) + - geom_line(size=1) + - scale_x_continuous(trans='log2', breaks = 2^(seq(0,log(maxdepth, 2)))) + - scale_y_continuous(breaks = seq(0, maxfrac, by=maxfrac/10), labels=scaleFUN) + - labs(x=args$xlab, y=args$ylab, title=args$title) + - theme(legend.position="top", legend.title=element_blank(), legend.text=element_text(colour="blue", size=7)) - - -## facet_wrap(~Samples, ncol=2) +pdf(file = args$output) +ggplot(data = graphpoints, aes(x = Depth, y = sample_value, colour = Samples)) + + geom_line(size = 1) + + scale_x_continuous(trans = "log2", breaks = 2 ^ (seq(0, log(maxdepth, 2)))) + + scale_y_continuous(breaks = seq(0, maxfrac, by = maxfrac / 10), labels = scale_fun) + + labs(x = args$xlab, y = args$ylab, title = args$title) + + theme(legend.position = "top", legend.title = element_blank(), + legend.text = element_text(colour = "blue", size = 7)) -devname=dev.off() - +devname <- dev.off() |
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| diff -r 7c4feda2d9c7 -r bea8435e1e79 probecoverage.xml --- a/probecoverage.xml Tue Jan 07 06:08:56 2020 -0500 +++ b/probecoverage.xml Thu Jun 03 23:59:31 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="probecoverage" name="Probe Coverage" version="0.6.0"> +<tool id="probecoverage" name="Probe Coverage" version="0.7.0"> <description></description> <requirements> <requirement type="package" version="1.10=h9402c20_2">samtools</requirement> @@ -6,7 +6,7 @@ <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement> <requirement type="package" version="3.2.1=r36h6115d3f_0">r-ggplot2</requirement> <requirement type="package" version="1.17.3=py37h95a1406_0">numpy</requirement> - <requirement type="package" version="0.15.3=py37hbcae180_3">pysam</requirement> + <requirement type="package" version="0.16.0.1">pysam</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> |