| Next changeset 1:cc96abdef027 (2017-06-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 5798bd978553dee97521c39920d263dd750e0755 |
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masigpro.R masigpro.xml test-data/Results.pdf test-data/control_1H.counts test-data/control_2H.counts test-data/control_3H.counts test-data/data_out.txt test-data/edesign_out.txt test-data/masigpro_out.tab test-data/treat_1H.counts test-data/treat_2H.counts test-data/treat_3H_1.counts test-data/treat_3H_2.counts |
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| 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 |
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| @@ -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 |
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| 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 |
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| b'@@ -0,0 +1,430 @@\n+<tool id="masigpro" name="maSigPro" version="1.49.0.0">\r\n+ <description>Significant Gene Expression Profile Differences in Time Course Gene Expression Data</description>\r\n+ <requirements>\r\n+ <requirement type="package" version="1.49.0">bioconductor-masigpro</requirement>\r\n+ <requirement type="package" version="1.3.2">r-optparse</requirement>\r\n+ <requirement type="package" version="4.4">sed</requirement>\r\n+ </requirements>\r\n+ <stdio>\r\n+ <regex match="Execution halted"\r\n+ source="both"\r\n+ level="fatal"\r\n+ description="Execution halted." />\r\n+ <regex match="Error in"\r\n+ source="both"\r\n+ level="fatal"\r\n+ description="An undefined error occurred, please check your input carefully and contact your administrator." />\r\n+ <regex match="Fatal error"\r\n+ source="both"\r\n+ level="fatal"\r\n+ description="An undefined error occurred, please check your input carefully and contact your administrator." />\r\n+ </stdio>\r\n+ <version_command>\r\n+ <![CDATA[\r\n+ echo $(R --version | grep version | grep -v GNU)", maSigPro version" $(R --vanilla --slave -e "library(maSigPro); cat(sessionInfo()\\$otherPkgs\\$maSigPro\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\r\n+ ]]>\r\n+ </version_command>\r\n+ <command>\r\n+ <![CDATA[\r\n+ #if str($source.source_selector) == "advanced":\r\n+ paste\r\n+ #set $start = True\r\n+ #set $header = \'\'\r\n+ #for $time in $source.rep_time:\r\n+ #for $file in $time.files:\r\n+ #if $start:\r\n+ <(cut -f1 $file)\r\n+ #set $start = False\r\n+ #end if\r\n+ #set $header += \' "\' + $file.name + \'"\'\r\n+ <(cut -f2 $file)\r\n+ #end for\r\n+ #end for\r\n+ > data && sed -i \'1i$header\' data &&\r\n+ #if $source.enable_output:\r\n+ ln -f data $data_out && ln -f $design_matrix $edesign_out &&\r\n+ #end if\r\n+ #set $data = \'data\'\r\n+ #set $edesign = $design_matrix\r\n+ #else:\r\n+ #set $data = $source.data\r\n+ #set $edesign = $source.edesign\r\n+ #end if\r\n+ Rscript \'${__tool_directory__}/masigpro.R\'\r\n+ -e \'$edesign\'\r\n+ -d \'$data\'\r\n+ -o \'$masigpro_out\'\r\n+ #if str($source.source_selector) == "defaults":\r\n+ --time_col $source.time_col\r\n+ --repl_col $source.repl_col\r\n+ #end if\r\n+ --degree $makeDesignMatrix.degree\r\n+ --qvalue $p_vector.qvalue\r\n+ --min_obs $p_vector.min_obs\r\n+ --step_method \'$Tfit.step_method\'\r\n+ --nvar_correction $Tfit.nvar_correction\r\n+ --alfa $Tfit.alfa\r\n+ --rsq $getSiggenes.rsq\r\n+ --vars \'$getSiggenes.vars\'\r\n+ --significant_intercept \'$getSiggenes.significant_intercept\'\r\n+ #if $pdf.pdf_selector:\r\n+ --cluster_data $pdf.seeGenes.clusterData\r\n+ -k $pdf.seeGenes.k\r\n+ --cluster_method $pdf.seeGenes.clustering.clusterMethod\r\n+ #if str($pdf.seeGenes.clustering.clusterMethod) == "hclust":\r\n+ --distance $pdf.seeGenes.clustering.distance\r\n+ --agglo_method $pdf.seeGenes.clustering.aggloMethod\r\n+ #end if\r\n+ #if str($pdf.seeGenes.clustering.clusterMethod) == "kmeans":\r\n+ --iter_max $pdf.seeGenes.clustering.iterMax\r\n+ #end if\r\n+ --color_mode $pdf.seeGenes.colorMode\r\n+ --show_fit $pdf.seeGenes.showFit\r\n+ --show_lines $pdf.seeGenes.showLines\r\n+ --cexlab $pdf.seeGenes.cexlab\r\n+ --legend $pdf.seeGenes.legend\r\n+ #end if\r\n+ ]]>\r\n+ </command>\r\n+ <configfiles>\r\n+<configfile name="design_matrix">#if str($source.source_selector) == "advanced":\r\n+#set $header = "Name Time Replicate"\r\n+#for $group in $source.rep_groups:\r\n+ #set $header = $header + \' \' + str($group.name)\r\n+#end for\r\n+$header\r\n+#set $c = len($source.rep_repl) + 1\r\n+#for $time in $source.rep_time:\r\n+ #for $file in $time.files:\r\n+ '..b' ((\r\n+ source[\'source_selector\'] == \'advanced\' and\r\n+ source[\'enable_output\'] == True\r\n+ ))\r\n+ </filter>\r\n+ </data>\r\n+ <data format="pdf" name="pdf_out" from_work_dir="Results.pdf" label="maSigPro Plot file on ${on_string}">\r\n+ <filter>\r\n+ ((\r\n+ pdf[\'pdf_selector\'] == True\r\n+ ))\r\n+ </filter>\r\n+ </data>\r\n+ </outputs>\r\n+ <tests>\r\n+ <test>\r\n+ <param name="source_selector" value="advanced" />\r\n+ <param name="enable_output" value="1" />\r\n+ <repeat name="rep_time">\r\n+ <param name="time" value="1" />\r\n+ <param name="files" value="control_1H.counts,treat_1H.counts" />\r\n+ </repeat>\r\n+ <repeat name="rep_time">\r\n+ <param name="time" value="2" />\r\n+ <param name="files" value="control_2H.counts,treat_2H.counts" />\r\n+ </repeat>\r\n+ <repeat name="rep_time">\r\n+ <param name="time" value="3" />\r\n+ <param name="files" value="control_3H.counts,treat_3H_1.counts,treat_3H_2.counts" />\r\n+ </repeat>\r\n+ <param name="replicates_selector" value="advanced" />\r\n+ <repeat name="rep_repl">\r\n+ <param name="files" value="treat_3H_1.counts,treat_3H_2.counts" />\r\n+ </repeat>\r\n+ <repeat name="rep_groups">\r\n+ <param name="name" value="Control" />\r\n+ <param name="files" value="control_1H.counts,control_2H.counts,control_3H.counts" />\r\n+ </repeat>\r\n+ <repeat name="rep_groups">\r\n+ <param name="name" value="Treatment" />\r\n+ <param name="files" value="treat_1H.counts,treat_2H.counts,treat_3H_1.counts,treat_3H_2.counts" />\r\n+ </repeat>\r\n+ <output name="masigpro_out" file="masigpro_out.tab" />\r\n+ <output name="data_out" file="data_out.txt" />\r\n+ <output name="edesign_out" file="edesign_out.txt" />\r\n+ <output name="pdf_out" file="Results.pdf" />\r\n+ </test>\r\n+ <test>\r\n+ <param name="source_selector" value="defaults" />\r\n+ <param name="edesign" value="edesign_out.txt" />\r\n+ <param name="data" value="data_out.txt" />\r\n+ <output name="masigpro_out" file="masigpro_out.tab" />\r\n+ <output name="pdf_out" file="Results.pdf" />\r\n+ </test>\r\n+ </tests>\r\n+ <help>\r\n+<![CDATA[\r\n+.. class:: infomark\r\n+\r\n+**What it does**\r\n+\r\n+maSigPro_ is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.\r\n+\r\n+**Inputs**\r\n+\r\n+The maSigPro wrapper has two options for input data:\r\n+\r\n+ - directly through two seperate text files containing the experiment design (edesign) and the data or\r\n+ - count tables generated from HTSeq-count. Count tables must be generated for each sample individually.\r\n+ \r\n+To set up an experimental design from seperate count files you first have to select which files belong to a certain time point.\r\n+Likewise you can specify which files are replicates. In a third step you have to create the experimental groups and select the related files.\r\n+For a more comfortable setup in future analysis you have the option to output the generated edesign and data files.\r\n+\r\n+**Output**\r\n+\r\n+maSigPro_ generates a summary file containing the list of significant genes. Additionally you can obtain a PDF file containing plots of profiles and groups that visualize the clustering analysis.\r\n+\r\n+.. _maSigPro: https://bioconductor.org/packages/release/bioc/html/maSigPro.html\r\n+]]>\r\n+ </help>\r\n+ <citations>\r\n+ <citation type="doi">10.1093/bioinformatics/btl056</citation>\r\n+ </citations>\r\n+</tool>\n\\ No newline at end of file\n' |
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| 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 |
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|
| b |
| diff -r 000000000000 -r c8c290f3ea7d test-data/control_2H.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/control_2H.counts Mon May 15 07:29:03 2017 -0400 |
| b |
| b'@@ -0,0 +1,15682 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|
| b |
| diff -r 000000000000 -r c8c290f3ea7d test-data/control_3H.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/control_3H.counts Mon May 15 07:29:03 2017 -0400 |
| b |
| b'@@ -0,0 +1,15682 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|
| b |
| diff -r 000000000000 -r c8c290f3ea7d test-data/data_out.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data_out.txt Mon May 15 07:29:03 2017 -0400 |
| b |
| b'@@ -0,0 +1,15683 @@\n+"control_1H.counts" "treat_1H.counts" "control_2H.counts" "treat_2H.counts" "control_3H.counts" "treat_3H_1.counts" 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|
| b |
| diff -r 000000000000 -r c8c290f3ea7d test-data/edesign_out.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/edesign_out.txt Mon May 15 07:29:03 2017 -0400 |
| b |
| @@ -0,0 +1,8 @@ +Name Time Replicate Control Treatment +"control_1H.counts" 1 2 1 0 +"treat_1H.counts" 1 3 0 1 +"control_2H.counts" 2 4 1 0 +"treat_2H.counts" 2 5 0 1 +"control_3H.counts" 3 6 1 0 +"treat_3H_1.counts" 3 1 0 1 +"treat_3H_2.counts" 3 1 0 1 |
| b |
| diff -r 000000000000 -r c8c290f3ea7d test-data/masigpro_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masigpro_out.tab Mon May 15 07:29:03 2017 -0400 |
| b |
| @@ -0,0 +1,35 @@ +Control TreatmentvsControl +FBgn0003358 FBgn0001112 +FBgn0004188 FBgn0003358 +FBgn0029723 FBgn0004188 +FBgn0030449 FBgn0013276 +FBgn0030769 FBgn0020299 +FBgn0032180 FBgn0020639 +FBgn0032860 FBgn0029723 +FBgn0033834 FBgn0029817 +FBgn0036494 FBgn0030449 +FBgn0041336 FBgn0030769 +FBgn0041337 FBgn0030952 +FBgn0050239 FBgn0031082 +FBgn0263626 FBgn0031945 +FBgn0264482 FBgn0032180 + FBgn0032860 + FBgn0032913 + FBgn0033640 + FBgn0033834 + FBgn0034197 + FBgn0034459 + FBgn0036494 + FBgn0038163 + FBgn0038468 + FBgn0039373 + FBgn0041336 + FBgn0041337 + FBgn0045479 + FBgn0047338 + FBgn0050239 + FBgn0261613 + FBgn0262146 + FBgn0263084 + FBgn0263626 + FBgn0264482 |
| b |
| diff -r 000000000000 -r c8c290f3ea7d test-data/treat_1H.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treat_1H.counts Mon May 15 07:29:03 2017 -0400 |
| b |
| b'@@ -0,0 +1,15682 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|
| b |
| diff -r 000000000000 -r c8c290f3ea7d test-data/treat_2H.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treat_2H.counts Mon May 15 07:29:03 2017 -0400 |
| b |
| b'@@ -0,0 +1,15682 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|
| b |
| diff -r 000000000000 -r c8c290f3ea7d test-data/treat_3H_1.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treat_3H_1.counts Mon May 15 07:29:03 2017 -0400 |
| b |
| b'@@ -0,0 +1,15682 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|
| b |
| diff -r 000000000000 -r c8c290f3ea7d test-data/treat_3H_2.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/treat_3H_2.counts Mon May 15 07:29:03 2017 -0400 |
| b |
| b'@@ -0,0 +1,15682 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|