# HG changeset patch # User iuc # Date 1494847743 14400 # Node ID c8c290f3ea7d3c71eca9e637f59e5e98719de71d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755 diff -r 000000000000 -r c8c290f3ea7d masigpro.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/masigpro.R Mon May 15 07:29:03 2017 -0400 @@ -0,0 +1,104 @@ +#!/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() \ No newline at end of file diff -r 000000000000 -r c8c290f3ea7d masigpro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/masigpro.xml Mon May 15 07:29:03 2017 -0400 @@ -0,0 +1,430 @@ + + Significant Gene Expression Profile Differences in Time Course Gene Expression Data + + bioconductor-masigpro + r-optparse + sed + + + + + + + + /dev/null | grep -v -i "WARNING: ") + ]]> + + + data && sed -i '1i$header' data && + #if $source.enable_output: + ln -f data $data_out && ln -f $design_matrix $edesign_out && + #end if + #set $data = 'data' + #set $edesign = $design_matrix + #else: + #set $data = $source.data + #set $edesign = $source.edesign + #end if + Rscript '${__tool_directory__}/masigpro.R' + -e '$edesign' + -d '$data' + -o '$masigpro_out' + #if str($source.source_selector) == "defaults": + --time_col $source.time_col + --repl_col $source.repl_col + #end if + --degree $makeDesignMatrix.degree + --qvalue $p_vector.qvalue + --min_obs $p_vector.min_obs + --step_method '$Tfit.step_method' + --nvar_correction $Tfit.nvar_correction + --alfa $Tfit.alfa + --rsq $getSiggenes.rsq + --vars '$getSiggenes.vars' + --significant_intercept '$getSiggenes.significant_intercept' + #if $pdf.pdf_selector: + --cluster_data $pdf.seeGenes.clusterData + -k $pdf.seeGenes.k + --cluster_method $pdf.seeGenes.clustering.clusterMethod + #if str($pdf.seeGenes.clustering.clusterMethod) == "hclust": + --distance $pdf.seeGenes.clustering.distance + --agglo_method $pdf.seeGenes.clustering.aggloMethod + #end if + #if str($pdf.seeGenes.clustering.clusterMethod) == "kmeans": + --iter_max $pdf.seeGenes.clustering.iterMax + #end if + --color_mode $pdf.seeGenes.colorMode + --show_fit $pdf.seeGenes.showFit + --show_lines $pdf.seeGenes.showLines + --cexlab $pdf.seeGenes.cexlab + --legend $pdf.seeGenes.legend + #end if + ]]> + + +#if str($source.source_selector) == "advanced": +#set $header = "Name Time Replicate" +#for $group in $source.rep_groups: + #set $header = $header + ' ' + str($group.name) +#end for +$header +#set $c = len($source.rep_repl) + 1 +#for $time in $source.rep_time: + #for $file in $time.files: + #set $is_repl = False + #for $i, $repl in enumerate($source.rep_repl): + #if str($file) in str($repl.files): + #set $r = $i + 1 + #set $is_repl = True + #end if + #end for + #if $is_repl == False: + #set $r = $c + #set $c += 1 + #end if + #set $line = '"' + str($file.name) + '" ' + str($time.time) + ' ' + str($r) + #for $group in $source.rep_groups: + #if str($file) in str($group.files): + #set $line += " 1" + #else + #set $line += " 0" + #end if + #end for +$line + #end for +#end for +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ +
+
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+ + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + (( + source['source_selector'] == 'advanced' and + source['enable_output'] == True + )) + + + + + (( + source['source_selector'] == 'advanced' and + source['enable_output'] == True + )) + + + + + (( + pdf['pdf_selector'] == True + )) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/btl056 + + \ No newline at end of file diff -r 000000000000 -r c8c290f3ea7d test-data/Results.pdf Binary file test-data/Results.pdf has changed diff -r 000000000000 -r c8c290f3ea7d test-data/control_1H.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/control_1H.counts Mon May 15 07:29:03 2017 -0400 @@ -0,0 +1,15682 @@ +FBgn0000003 0 +FBgn0000008 15 +FBgn0000014 0 +FBgn0000015 0 +FBgn0000017 1211 +FBgn0000018 92 +FBgn0000022 1 +FBgn0000024 0 +FBgn0000028 0 +FBgn0000032 233 +FBgn0000036 0 +FBgn0000037 2 +FBgn0000038 0 +FBgn0000039 0 +FBgn0000042 16320 +FBgn0000043 5625 +FBgn0000044 13 +FBgn0000045 1 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