diff chipseeker.R @ 8:8bd92f2404dd draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"

--- a/chipseeker.R	Sat Apr 27 11:04:35 2019 -0400
+++ b/chipseeker.R	Fri Aug 27 10:49:39 2021 +0000
@@ -1,117 +1,140 @@
-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)
+  }
+)
 
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 
 suppressPackageStartupMessages({
-    library(ChIPseeker)
-    library(GenomicFeatures)
-    library(rtracklayer)
-    library(optparse)
+  library(ChIPseeker)
+  library(GenomicFeatures)
+  library(rtracklayer)
+  library(optparse)
+  library(ggupset)
 })
 
 option_list <- list(
-    make_option(c("-i","--infile"), type="character", help="Peaks file to be annotated"),
-    make_option(c("-H","--header"), type="logical", help="Peaks file contains header row"),
-    make_option(c("-G","--gtf"), type="character", help="GTF to create TxDb."),
-    make_option(c("-u","--upstream"), type="integer", help="TSS upstream region"),
-    make_option(c("-d","--downstream"), type="integer", help="TSS downstream region"),
-    make_option(c("-F","--flankgeneinfo"), type="logical", help="Add flanking gene info"),
-    make_option(c("-D","--flankgenedist"), type="integer", help="Flanking gene distance"),
-    make_option(c("-j","--ignoreUpstream"), type="logical", help="Ignore upstream"),
-    make_option(c("-k","--ignoreDownstream"), type="logical", help="Ignore downstream"),
-    make_option(c("-f","--format"), type="character", help="Output format (interval or tabular)."),
-    make_option(c("-p","--plots"), type="logical", help="PDF of plots."),
-    make_option(c("-r","--rdata"), type="logical", help="Output RData file.")
-  )
+  make_option(c("-i", "--infile"), type = "character", help = "Peaks file to be annotated"),
+  make_option(c("-H", "--header"), type = "logical", help = "Peaks file contains header row"),
+  make_option(c("-G", "--gtf"), type = "character", help = "GTF to create TxDb."),
+  make_option(c("-u", "--upstream"), type = "integer", help = "TSS upstream region"),
+  make_option(c("-d", "--downstream"), type = "integer", help = "TSS downstream region"),
+  make_option(c("-F", "--flankgeneinfo"), type = "logical", help = "Add flanking gene info"),
+  make_option(c("-D", "--flankgenedist"), type = "integer", help = "Flanking gene distance"),
+  make_option(c("-j", "--ignore_upstream"), type = "logical", help = "Ignore upstream"),
+  make_option(
+    c("-k", "--ignore_downstream"),
+    type = "logical",
+    help = "Ignore downstream"
+  ),
+  make_option(c("-f", "--format"), type = "character", help = "Output format (interval or tabular)."),
+  make_option(c("-p", "--plots"), type = "logical", help = "PDF of plots."),
+  make_option(c("-r", "--rdata"), type = "logical", help = "Output RData file.")
+)
 
-parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
-args = parse_args(parser)
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args <- parse_args(parser)
 
-peaks = args$infile
-gtf = args$gtf
-up = args$upstream
-down = args$downstream
-format = args$format
+peaks <- args$infile
+gtf <- args$gtf
+up <- args$upstream
+down <- args$downstream
+format <- args$format
 
 if (!is.null(args$flankgeneinfo)) {
-    flankgeneinfo <- TRUE
+  flankgeneinfo <- TRUE
 } else {
-    flankgeneinfo <- FALSE
+  flankgeneinfo <- FALSE
 }
 
-if (!is.null(args$ignoreUpstream)) {
-    ignoreUpstream <- TRUE
+if (!is.null(args$ignore_upstream)) {
+  ignore_upstream <- TRUE
 } else {
-    ignoreUpstream <- FALSE
+  ignore_upstream <- FALSE
 }
 
-if (!is.null(args$ignoreDownstream)) {
-    ignoreDownstream <- TRUE
+if (!is.null(args$ignore_downstream)) {
+  ignore_downstream <- TRUE
 } else {
-    ignoreDownstream <- FALSE
+  ignore_downstream <- FALSE
 }
 
 if (!is.null(args$header)) {
-    header <- TRUE
+  header <- TRUE
 } else {
-    header <- FALSE
+  header <- FALSE
 }
 
-peaks <- readPeakFile(peaks, header=header)
+peaks <- readPeakFile(peaks, header = header)
 
 # Make TxDb from GTF
-txdb <- makeTxDbFromGFF(gtf, format="gtf")
+txdb <- makeTxDbFromGFF(gtf, format = "gtf")
 
 # Annotate peaks
-peakAnno <-  annotatePeak(peaks, TxDb=txdb,
-    tssRegion=c(-up, down),
-    addFlankGeneInfo=flankgeneinfo,
-    flankDistance=args$flankgenedist,
-    ignoreUpstream=ignoreUpstream,
-    ignoreDownstream=ignoreDownstream)
+peak_anno <-  annotatePeak(
+  peaks,
+  TxDb = txdb,
+  tssRegion = c(-up, down),
+  addFlankGeneInfo = flankgeneinfo,
+  flankDistance = args$flankgenedist,
+  ignoreUpstream = ignore_upstream,
+  ignoreDownstream = ignore_downstream
+)
 
 # Add gene name
-features <- import(gtf, format="gtf")
+features <- import(gtf, format = "gtf")
 ann <- unique(mcols(features)[, c("gene_id", "gene_name")])
-res <- as.data.frame(peakAnno)
-res <- merge(res, ann, by.x="geneId", by.y="gene_id")
+res <- as.data.frame(peak_anno)
+res <- merge(res, ann, by.x = "geneId", by.y = "gene_id")
 names(res)[names(res) == "gene_name"] <- "geneName"
 
 #Extract metadata cols, 1st is geneId, rest should be from col 7 to end
 metacols <- res[, c(7:ncol(res), 1)]
 # Convert from 1-based to 0-based format
 if (format == "interval") {
-    metacols <- apply(as.data.frame(metacols), 1, function(col) paste(col, collapse="|"))
-    resout <- data.frame(res$seqnames,
-                    res$start - 1,
-                    res$end,
-                    metacols)
-    colnames(resout)[1:4] <- c("Chrom", "Start", "End", "Comment")
+  metacols <-
+    apply(as.data.frame(metacols), 1, function(col)
+      paste(col, collapse = "|"))
+  resout <- data.frame(res$seqnames,
+                       res$start - 1,
+                       res$end,
+                       metacols)
+  colnames(resout)[1:4] <- c("Chrom", "Start", "End", "Comment")
 } else {
-    resout <- data.frame(res$seqnames,
-                    res$start - 1,
-                    res$end,
-                    metacols)
-    colnames(resout)[1:3] <- c("Chrom", "Start", "End")
+  resout <- data.frame(res$seqnames,
+                       res$start - 1,
+                       res$end,
+                       metacols)
+  colnames(resout)[1:3] <- c("Chrom", "Start", "End")
 }
-write.table(resout, file="out.tab", sep="\t", row.names=FALSE, quote=FALSE)
+write.table(
+  resout,
+  file = "out.tab",
+  sep = "\t",
+  row.names = FALSE,
+  quote = FALSE
+)
 
 if (!is.null(args$plots)) {
-    pdf("out.pdf", width=14)
-    plotAnnoPie(peakAnno)
-    p1 <- plotAnnoBar(peakAnno)
-    print(p1)
-    vennpie(peakAnno)
-    upsetplot(peakAnno)
-    p2 <- plotDistToTSS(peakAnno, title="Distribution of transcription factor-binding loci\nrelative to TSS")
-    print(p2)
-    dev.off()
-    rm(p1, p2)
+  pdf("out.pdf", width = 14)
+  plotAnnoPie(peak_anno)
+  p1 <- plotAnnoBar(peak_anno)
+  print(p1)
+  vennpie(peak_anno)
+  upsetplot(peak_anno)
+  p2 <-
+    plotDistToTSS(peak_anno, title = "Distribution of transcription factor-binding loci\nrelative to TSS")
+  print(p2)
+  dev.off()
+  rm(p1, p2)
 }
 
 ## Output RData file
 
 if (!is.null(args$rdata)) {
   save.image(file = "ChIPseeker_analysis.RData")
-}
\ No newline at end of file
+}