changeset 7:bea8435e1e79 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 6dc66b89f0792e4da40719ec83494a1fcee5e105"

--- a/probecoverage.r	Tue Jan 07 06:08:56 2020 -0500
+++ b/probecoverage.r	Thu Jun 03 23:59:31 2021 +0000
@@ -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()

--- a/probecoverage.xml	Tue Jan 07 06:08:56 2020 -0500
+++ b/probecoverage.xml	Thu Jun 03 23:59:31 2021 +0000
@@ -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" />