Mercurial > repos > iuc > masigpro
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755
author | iuc |
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date | Mon, 15 May 2017 07:29:03 -0400 |
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children | cc96abdef027 |
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#!/usr/bin/env Rscript # A command-line interface to maSigPro for use with Galaxy # written by Clemens Blank. # Thanks to Bjoern Gruening and Michael Love for their DESeq2 # wrapper as a basis to build upon. # setup R error handling to go to stderr 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("maSigPro") library("optparse") library("mclust") }) options(stringAsFactors = FALSE, useFancyQuotes = FALSE) args <- commandArgs(trailingOnly = TRUE) # specify our desired options in a list # by default OptionParser will add an help option equivalent to # make_option(c("-h", "--help"), action="store_true", default=FALSE, # help="Show this help message and exit") option_list <- list( make_option(c("-q", "--quiet"), action="store_false", dest="verbose", help="Print little output"), make_option(c("-e", "--edesign"), type="character"), make_option(c("-d", "--data"), type="character"), make_option(c("-o", "--outfile"), type="character"), make_option("--degree", type="integer", default=1), make_option("--time_col", type="integer", default=1), make_option("--repl_col", type="integer", default=2), make_option("--qvalue", type="double", default=0.05), make_option("--min_obs", type="integer", default=6), make_option("--step_method", type="character", default="backward"), make_option("--nvar_correction", type="logical", default=FALSE), make_option("--alfa", type="double", default=0.05), make_option("--rsq", type="double", default=0.7), make_option("--vars", type="character", default="groups"), make_option("--significant_intercept", type="character", default="dummy"), make_option("--cluster_data", type="integer", default=1), make_option(c("-k", "--k"), type="integer", default=9), make_option("--cluster_method", type="character", default="hclust"), make_option("--distance", type="character", default="cor"), make_option("--agglo_method", type="character", default="ward.D"), make_option("--iter_max", type="integer", default=500), make_option("--color_mode", type="character", default="rainbow"), make_option("--show_fit", type="logical", default=TRUE), make_option("--show_lines", type="logical", default=TRUE), make_option("--cexlab", type="double", default=0.8), make_option("--legend", type="logical", default=TRUE) ) # get command line options, if help option encountered print help and exit, # otherwise if options not found on command line then set defaults opt <- parse_args(OptionParser(option_list=option_list)) # enforce the following required arguments if (is.null(opt$edesign)) { cat("'edesign' is required\n") q(status=1) } if (is.null(opt$data)) { cat("'data' is required\n") q(status=1) } if (is.null(opt$outfile)) { cat("'outfile' is required\n") q(status=1) } verbose <- if (is.null(opt$quiet)) { TRUE } else { FALSE } edesign <- as.matrix(read.table(opt$edesign, header=TRUE, row.names = 1)) data <- read.table(opt$data, header=TRUE) results <- maSigPro(data, edesign, degree = opt$degree, time.col = opt$time_col, repl.col = opt$repl_col, Q = opt$qvalue, min.obs = opt$min_obs, step.method = opt$step_method, nvar.correction = opt$nvar_correction, alfa = opt$alfa, rsq = opt$rsq, vars = opt$vars, significant.intercept = opt$significant_intercept, cluster.data = opt$cluster_data, k = opt$k, cluster.method = opt$cluster_method, distance = opt$distance, agglo.method = opt$agglo_method, iter.max = opt$iter_max, color.mode = opt$color_mode, show.fit = opt$show_fit, show.lines = opt$show_lines, cexlab = opt$cexlab, legend = opt$legend) filename <- opt$outfile write.table((results$summary), file=filename, sep="\t", quote=FALSE, row.names=FALSE, col.names=TRUE) cat("Session information:\n\n") sessionInfo()