# 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
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+ Quality control and normalization of affymetrix expression data
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- r-smagexp
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- r-smagexp
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+ --rdataoutput $result_export_eset
+ --htmloutput $result_html
+ --htmloutputpath $result_html.files_path
+ --htmltemplate ${__tool_directory__}/AffyQCnormalization_tpl.html
+ ]]>
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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
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+ Perform gene expression analysis thanks to limma
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+ r-smagexp
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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 @@
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- GEOQuery wrapper
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+ GEOQuery wrapper
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+ r-smagexp
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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 @@
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- Quality control and normalization of a custom matrix expression data
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- r-smagexp
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+ Quality control and normalization of a custom matrix expression data
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+ r-smagexp
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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 @@
}
-
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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.
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- r-smagexp
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+ Perform meta-analysis thanks to metaMA.
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+ r-smagexp
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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
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+ perform meta-analysis thanks to metaRNAseq
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+ r-smagexp
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