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comparison facets_analysis.R @ 3:d1914f4d9daf draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 64ac36125f04497dd51028f307e059fca9ec0503
author artbio
date Sun, 05 Oct 2025 00:55:34 +0000
parents 66a56502199d
children 3f62267c4be7
comparison
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2:66a56502199d 3:d1914f4d9daf
4 # This script serves as the backend for the Galaxy FACETS Analysis tool. 4 # This script serves as the backend for the Galaxy FACETS Analysis tool.
5 # It takes a SNP pileup file as input and performs allele-specific copy 5 # It takes a SNP pileup file as input and performs allele-specific copy
6 # number analysis using the R package 'facets'. 6 # number analysis using the R package 'facets'.
7 # ============================================================================== 7 # ==============================================================================
8 8
9 # --- 1. Load Libraries --- 9 # --- Load Libraries ---
10 suppressPackageStartupMessages(library(argparse)) 10 suppressPackageStartupMessages(library(argparse))
11 suppressPackageStartupMessages(library(facets)) 11 suppressPackageStartupMessages(library(facets))
12 12
13 # --- 2. Define and Parse Arguments --- 13 # --- Source the external plot_facets_enhanced function ---
14 # This finds the path of the currently running script and sources
15 # the R function file relative to it.
16 initial_opts <- commandArgs(trailingOnly = FALSE)
17 script_path <- dirname(sub("--file=", "", initial_opts[grep("--file=", initial_opts)]))
18 source(file.path(script_path, "plot_facets_enhanced-v22.R"))
19
20 # --- Define and Parse Arguments ---
14 21
15 # Create the parser 22 # Create the parser
16 parser <- ArgumentParser(description = "Run FACETS algorithm on a SNP pileup file.") 23 parser <- ArgumentParser(description = "Run FACETS algorithm on a SNP pileup file.")
17 24
18 # Define arguments 25 # Define arguments
33 type = "character", required = TRUE, 40 type = "character", required = TRUE,
34 help = "Path for the output summary file (TSV)." 41 help = "Path for the output summary file (TSV)."
35 ) 42 )
36 parser$add_argument("--output_plots", 43 parser$add_argument("--output_plots",
37 type = "character", required = TRUE, 44 type = "character", required = TRUE,
38 help = "Path for the output plots file (PDF)." 45 help = "Path for the main output plots file (PNG)."
39 ) 46 )
40 47 parser$add_argument("--output_spider",
48 type = "character", required = TRUE,
49 help = "Path for the diagnostic spider plot file (PNG)."
50 )
41 parser$add_argument("--cval", 51 parser$add_argument("--cval",
42 type = "double", default = 150, 52 type = "double", default = 150,
43 help = "Critical value for segmentation." 53 help = "Critical value for segmentation."
44 ) 54 )
45 parser$add_argument("--min_nhet", 55 parser$add_argument("--min_nhet",
54 type = "character", default = "hg38", 64 type = "character", default = "hg38",
55 choices = c("hg19", "hg38", "hg18", "mm9", "mm10"), 65 choices = c("hg19", "hg38", "hg18", "mm9", "mm10"),
56 help = "Genome build used for alignment." 66 help = "Genome build used for alignment."
57 ) 67 )
58 68
59 # --- 3. Main Analysis Function --- 69 # --- Main Analysis Function ---
60 main <- function(args) { 70 main <- function(args) {
61 # Set seed for reproducibility 71 # Set seed for reproducibility
62 set.seed(1965) 72 set.seed(1965)
63 73
64 # --- Read the data with readSnpMatrix() from facets --- 74 # --- Read the data with readSnpMatrix() from facets ---
102 args$gbuild 112 args$gbuild
103 ) 113 )
104 ) 114 )
105 write.table(summary_df, file = args$output_summary, sep = "\t", quote = FALSE, row.names = FALSE) 115 write.table(summary_df, file = args$output_summary, sep = "\t", quote = FALSE, row.names = FALSE)
106 116
107 # Generate the plots PDF 117 # Generate the plots PNG
108 pdf(file = args$output_plots, width = 12, height = 8) 118 png(file = args$output_plots, width = 12, height = 8, units = "in", res = 300)
109 plotSample(x = oo, emfit = fit, sname = args$sample_id) 119 plotSample(x = oo, emfit = fit, sname = args$sample_id)
120 plot_facets_enhanced(oo, emfit = fit, plot.type = "em", sname = args$sample_id)
121 dev.off()
122 png(file = args$output_spider, width = 8, height = 8, units = "in", res = 300)
123 logRlogORspider(oo$out, oo$dipLogR)
110 dev.off() 124 dev.off()
111 } 125 }
112 126
113 # --- 4. Execution Block --- 127 # --- Execution Block ---
114 if (!interactive()) { 128 if (!interactive()) {
115 args <- parser$parse_args() 129 args <- parser$parse_args()
116 main(args) 130 main(args)
117 } 131 }