# HG changeset patch # User sblanck # Date 1494418368 14400 # Node ID 328f4031e5d31d149a6cefb398f0e19ec5500265 # Parent 7f74250a083da9e2c26e98a708464e1cc93834c7 planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty diff -r 7f74250a083d -r 328f4031e5d3 AffyQCnormalization.xml --- a/AffyQCnormalization.xml Wed May 10 04:12:26 2017 -0400 +++ b/AffyQCnormalization.xml Wed May 10 08:12:48 2017 -0400 @@ -1,51 +1,45 @@ - Quality control and normalization of affymetrix expression data - - - - - + + Quality control and normalization of affymetrix expression data + - - r-smagexp - - - r-smagexp + + + + + + + + + - - - - - + --rdataoutput $result_export_eset + --htmloutput $result_html + --htmloutputpath $result_html.files_path + --htmltemplate ${__tool_directory__}/AffyQCnormalization_tpl.html + ]]> + - - - + + + + - - - - - - - - - + + - + + + + + + - + diff -r 7f74250a083d -r 328f4031e5d3 Analyse.xml --- a/Analyse.xml Wed May 10 04:12:26 2017 -0400 +++ b/Analyse.xml Wed May 10 08:12:48 2017 -0400 @@ -1,69 +1,60 @@ - Perform gene expression analysis thanks to limma - + + Perform gene expression analysis thanks to limma + + + r-smagexp + + + + - - - r-smagexp - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + diff -r 7f74250a083d -r 328f4031e5d3 GEOQuery.xml --- a/GEOQuery.xml Wed May 10 04:12:26 2017 -0400 +++ b/GEOQuery.xml Wed May 10 08:12:48 2017 -0400 @@ -1,41 +1,45 @@ - - GEOQuery wrapper - + + + GEOQuery wrapper + + + r-smagexp + + + + - - - - - - - - - - + + + + + + + + + + - + - - - - + + + + - + - - - + diff -r 7f74250a083d -r 328f4031e5d3 ImportDataFromMatrix.xml --- a/ImportDataFromMatrix.xml Wed May 10 04:12:26 2017 -0400 +++ b/ImportDataFromMatrix.xml Wed May 10 08:12:48 2017 -0400 @@ -1,42 +1,48 @@ - - Quality control and normalization of a custom matrix expression data - - - r-smagexp - - - - - - - - - - + + + Quality control and normalization of a custom matrix expression data + + + r-smagexp + + + + + + + + + + + + + + + - - - - + + + + - - - - + + + + - + - + diff -r 7f74250a083d -r 328f4031e5d3 MetaMA.R --- a/MetaMA.R Wed May 10 04:12:26 2017 -0400 +++ b/MetaMA.R Wed May 10 08:12:48 2017 -0400 @@ -1,44 +1,54 @@ -library(metaMA) -library(affy) -library(annaffy) -library(VennDiagram) -library(GEOquery) +#!/usr/bin/env Rscript +# 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") + +library("optparse") + +##### Read options +option_list=list( + make_option("--input",type="character",default="NULL",help="list of rdata objects containing eset objects"), + make_option("--htmloutput",type="character",default=NULL,help="Output html report"), + make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"), + make_option("--htmltemplate",type="character",default=NULL,help="html template)") +); -cargs<-commandArgs() -cargs<-cargs[(which(cargs=="--args")+1):length(cargs)] +opt_parser = OptionParser(option_list=option_list); +opt = parse_args(opt_parser); + +if(is.null(opt$input)){ + print_help(opt_parser) + stop("input required.", call.=FALSE) +} -nbargs=length(cargs) +#loading libraries + +suppressPackageStartupMessages(require(metaMA)) +suppressPackageStartupMessages(require(affy)) +suppressPackageStartupMessages(require(annaffy)) +suppressPackageStartupMessages(require(VennDiagram)) +suppressPackageStartupMessages(require(GEOquery)) + +listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) ) + rdataList=list() condition1List=list() condition2List=list() - -for (i in 1:(nbargs-5)) +for (input in listInput) { - Rdata=cargs[[i]] - #condition1=cargs[[i+1]] - #condition2=cargs[[i+2]] - load(Rdata) + load(input) rdataList=c(rdataList,(eset)) - #condition1List=c(condition1List,condition1) - #condition2List=c(condition2List,condition2) condition1List=c(condition1List,saveConditions[1]) condition2List=c(condition2List,saveConditions[2]) } -#tables<-cargs[[1]] -#tech<-cargs[[2]] -result.html<-cargs[[nbargs-4]] -result.path<-cargs[[nbargs-3]] -#result.venn<-cargs[[nbargs-3]] -result.template<-cargs[[nbargs-2]] - -#sink("/dev/null") -#dir.create(temp.files.path,recursive=TRUE) -#file.conn=file(diag.html,open="w") - -#writeLines(c(""),file.conn) +result.html<-htmloutput +result.path<-htmloutputpath +result.template<-htmltemplate showVenn<-function(res,file) { @@ -51,7 +61,6 @@ dev.off() } - library("org.Hs.eg.db") x <- org.Hs.egUNIGENE mapped_genes <- mappedkeys(x) @@ -107,8 +116,6 @@ } - - filterCondition<-function(gset,condition1, condition2){ selected=c(which((tolower(as.character(pData(gset)["source_name_ch1"][,1]))==condition1)), which(tolower(as.character(pData(gset)["source_name_ch1"][,1]))==condition2)) diff -r 7f74250a083d -r 328f4031e5d3 MetaMA.xml --- a/MetaMA.xml Wed May 10 04:12:26 2017 -0400 +++ b/MetaMA.xml Wed May 10 08:12:48 2017 -0400 @@ -1,29 +1,36 @@ - Perform meta-analysis thanks to metaMA. - - - r-smagexp - - - + + Perform meta-analysis thanks to metaMA. + + + r-smagexp + + + + + + + + + - - - - - - - - + + + + - + + + + + - + diff -r 7f74250a083d -r 328f4031e5d3 MetaRNAseq.xml --- a/MetaRNAseq.xml Wed May 10 04:12:26 2017 -0400 +++ b/MetaRNAseq.xml Wed May 10 08:12:48 2017 -0400 @@ -1,9 +1,16 @@ - perform meta-analysis thanks to metaRNAseq - + + perform meta-analysis thanks to metaRNAseq + + + r-smagexp + + + + + + + - +