# HG changeset patch
# User pavlo-lutsik
# Date 1373051658 14400
# Node ID 05220e275e4b3285ca3b4551968d19537fcf68d0
# Parent 450c8ff1d11a76772733029a4a79627a98bd1b75
Deleted selected files
diff -r 450c8ff1d11a -r 05220e275e4b RnBeadsGalaxy.R
--- a/RnBeadsGalaxy.R Fri Jul 05 09:08:41 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,198 +0,0 @@
-#msg.file<-file("RnBeads.messages.out", open="w")
-#sink(file=msg.file)
-
-suppressWarnings(suppressPackageStartupMessages(library(RnBeads)))
-suppressWarnings(suppressPackageStartupMessages(library(getopt)))
-
-#all.opts<-names(rnb.options())
-opt.class<-RnBeads:::OPTION.TYPES[-28]
-all.opts<-names(opt.class)
-#all.opts<-paste("--", all.opts, sep="")
-#all.opts<-gsub("\\.([a-z])", "\\U\\1", all.opts, perl=TRUE)
-all.opts<-gsub("\\.","-", all.opts)
-#opt.class<-sapply(rnb.options(), class)
-
-rnb.opt.spec<-data.frame(
- Long=all.opts,
- Short=as.character(1:length(all.opts)),
- Mask=c(1,2)[as.integer((opt.class=="logical"))+1],
- Type=opt.class)
-
-### automated xml file preparation
-xml.strings<-apply(rnb.opt.spec,1, function(row){
-
- opt.lab<-gsub("-", ".", row[1])
- opt.def.val<-rnb.getOption(opt.lab)
- opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
- tf.opt<-"\t\t\tTrue \n\t\t\tFalse "
- opt.lab<-paste(opt.lab, gsub("\\."," ", row[4]), sep=", ")
- if(row[4]=="logical"){
- opt.type<-'select'
- if(!is.null(opt.def.val) && opt.def.val)
- opt.def.val<-"1" else
- opt.def.val<-"0"
- string<-sprintf("\t\t \n%s\n\t\t\n", opt.name, opt.type, opt.lab, opt.def.val, tf.opt)
- }else{
- opt.type<-'text'
- if(!is.null(opt.def.val) && opt.def.val!="")
- opt.def.val<-paste(opt.def.val, collapse=",") else
- opt.def.val<-""
- string<-sprintf("\t\t \n", opt.name, opt.type, opt.lab, opt.def.val)
- }
- string
- })
-
-cat(xml.strings, sep="", file="automated.settings.xml.txt")
-
-opt.def.strings<-apply(rnb.opt.spec,1, function(row){
-
- opt.name<-gsub("-([0-9a-z])", "\\U\\1", row[1], perl=TRUE)
- opt.long<-row[1]
- opt.short<-row[2]
-
- if(row[4]=="logical"){
- def.string<-sprintf("#if str( $options.%s ) == \"True\"\n\t--%s\n#end if\n", opt.name, opt.long)
- }else{
- def.string<-sprintf("#if str( $options.%s ) != \"\"\n\t--%s=\"$options.%s\" \n#end if\n", opt.name, opt.long, opt.name)
- }
- def.string
-
- })
-cat(opt.def.strings, sep="", file="automated.option.assignments.txt")
-
-
-rnb.opt.spec$Type<-gsub("\\.vector", "", rnb.opt.spec$Type)
-rnb.opt.spec$Type<-gsub("numeric", "double", rnb.opt.spec$Type)
-rnb.opt.spec<-rbind(data.frame(
- Long=c("data-type", "pheno", "idat-dir","idat-files","bed-files", "gs-report", "geo-series", "betas", "pvals","output-file", "report-dir"),
- Short=c("d","s","a","i","f","g","e","b","p","r","o"),
- Mask=c(1,2,2,2,2,2,2,2,2,1,1),
- Type=c("character","character","character","character","character","character","character","character","character","character", "character")),
- rnb.opt.spec)
-
-opts<-getopt(as.matrix(rnb.opt.spec))
-#opts<-getopt(as.matrix(rnb.opt.spec), opt=list("--data-type=idats","--report-dir=dir", "--idats=file1\tfile2"))
-print(opts)
-
-if(opts[["data-type"]]=="idatDir"){
-
- data.source<-list()
- data.type<-"idat.dir"
- data.source[["idat.dir"]]<-opts[["idat-dir"]]
- data.source[["sample.sheet"]]<-opts[["pheno"]]
-
-}else if(opts[["data-type"]]=="idatFiles"){
-
- data.type<-"idat.dir"
- file.string<-gsub(" ","", opts[["idat-files"]])
- files<-strsplit(file.string, ",")[[1]]
- files<-files[files!=""]
- bed.dir<-sprintf("%s_beds",opts[["report-dir"]])
- dir.create(bed.dir)
- file.copy(files, bed.dir)
- for(dat.file in list.files(bed.dir, full.names = TRUE)){
- file.rename(dat.file, gsub("\\.dat", ".bed", dat.file))
- }
- data.source<-list()
- data.source[["bed.dir"]]<-bed.dir
- data.source[["sample.sheet"]]<-opts[["pheno"]]
-
-
-}else if(opts[["data-type"]]=="GS.report"){
-
- data.type<-"GS.report"
- data.source<-opts[["gs-report"]]
-
-}else if(opts[["data-type"]]=="GEO"){
-
- data.type<-"GEO"
- data.source<-opts[["geo-series"]]
-
-}else if(opts[["data-type"]]=="data.files"){
-
- data.type<-"GEO"
- data.source<-opts[["geo-series"]]
-
-}else if(opts[["data-type"]]=="data.files"){
-
- data.type<-"data.files"
- data.source<-c(opts[["pheno"]], opts[["betas"]])
- if(!is.null(opts[["pvals"]]))
- data.source<-c(data.source, opts[["pvals"]])
-
-}else if(opts[["data-type"]]=="bed.dir"){
-
- data.type<-"bed.dir"
- file.string<-gsub(" ","", opts[["bed-files"]])
- files<-strsplit(file.string, ",")[[1]]
- files<-files[files!=""]
- bed.dir<-sprintf("%s_beds",opts[["report-dir"]])
- dir.create(bed.dir)
- file.copy(files, bed.dir)
- for(dat.file in list.files(bed.dir, full.names = TRUE)){
- file.rename(dat.file, gsub("\\.dat", ".bed", dat.file))
- }
- data.source<-list()
- data.source[["bed.dir"]]<-bed.dir
-
- logger.start(fname="NA")
- sample.sheet<-rnb.read.annotation(opts[["pheno"]])
- logger.close()
- if(length(files) < nrow(sample.sheet))
- stop("Not all bed files are present")
-
- cn<-colnames(sample.sheet)
- dat.files<-sapply(strsplit(files, "\\/"), function(el) el[length(el)])
- sample.sheet<-cbind(sample.sheet, gsub("\\.dat", ".bed", dat.files))
- colnames(sample.sheet)<-c(cn, "BED_files")
- data.source[["sample.sheet"]]<-sample.sheet
-}
-
-if("logging" %in% names(opts)){ # TODO create a cleaner way of checking whether the full options set was supplied
-
- dump<-sapply(names(opt.class), function(on){
- getoptname<-gsub("-", "\\.","-",on)
- if(getoptname %in% names(opts)){
- if(opt.class[on]=="logical"){
- ov<-TRUE
- }else if(opt.class %in% c("character","character.vector")){
- ov<-opts[[getoptname]]
- ov<-gsub("\"", "", ov)
- if(opt.class=="character.vector"){
- ov<-as.character(strsplit(ov,","))
- }
-
- }else if(opt.class %in% c("integer","numeric","integer.vector","numeric.vector")){
- ov<-opts[[getoptname]]
- ov<-gsub("\"", "", ov)
- if(opt.class %in% c("integer.vector","numeric.vector")){
- ov<-as.character(strsplit(ov,","))
- }
- }
- eval(parse(text=sprintf("rnb.options(%s=ov)",on)))
- }
- })
-
- logical.opts<-names(opt.class[opt.class=="logical"])
- logical.opts.false<-logical.opts[!logical.opts %in% gsub("-",".",names(opts))]
-
-
- dump<-sapply(logical.opts.false, function(on){
- eval(parse(text=sprintf("rnb.options(%s=FALSE)",on)))
- })
-}
-
-print(rnb.options())
-
-#report.out.dir<-sprintf("%s_rnbReport", tempdir())
-report.out.dir<-opts[["report-dir"]]
-print("Starting RnBeads with the following inputs:")
-print(data.source)
-print(report.out.dir)
-print(data.type)
-rnb.run.analysis(data.source=data.source, dir.report=report.out.dir, data.type=data.type)
-
-
-#sink(file=NULL)
-#flush(msg.file)
-#close(msg.file)
\ No newline at end of file
diff -r 450c8ff1d11a -r 05220e275e4b install.rnbeads.R
--- a/install.rnbeads.R Fri Jul 05 09:08:41 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-source("http://rnbeads.mpi-inf.mpg.de/install.R")
\ No newline at end of file
diff -r 450c8ff1d11a -r 05220e275e4b rnbeads.xml
--- a/rnbeads.xml Fri Jul 05 09:08:41 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,506 +0,0 @@
-
-
- Performs RnBeads analysis for the selected set of
-
- R_SCRIPTS_PATH
- R
-
- rnbeads_galaxy_wrapper.sh
- --report-dir="$html_file.extra_files_path"
- --output-file="$html_file"
- #if str( $inputDataSelector.dataType ) == "idats"
- --pheno="$inputDataSelector.sampleAnnotations"
- #end if
- #if str( $inputDataSelector.dataType ) != "idats"
- #pass
- #else if str( $inputDataSelector.idatSelector.idatSource ) == "history"
- --data-type="idatFiles"
- #set $idatList=""
- #for $input_file in $inputDataSelector.idatSelector.idatSeries:
- #set $idatList+=str( $input_file.idatFile )
- #set $idatList+=","
- #end for
- --idat-files="$idatList"
- #else:
- --data-type="idatDir"
- --idat-dir="$inputDataSelector.idatSelector.idatRepo.fields.path"
- #end if
- #if str( $inputDataSelector.dataType ) == "gsreport"
- --data-type="GS.report"
- --gs-report="$inputDataSelector.gsReportFile"
- #end if
- #if str( $inputDataSelector.dataType ) == "geo"
- --data-type="GEO"
- --geo-series=$inputDataSelector.geoSeries
- #end if
- #if str( $inputDataSelector.dataType ) == "tables"
- --data-type="data.files"
- --pheno="$inputDataSelector.sampleAnnotations"
- #end if
- #if str( $inputDataSelector.dataType ) == "tables"
- --data-type="data.files"
- --pheno="$inputDataSelector.sampleAnnotations"
- --betas="$inputDataSelector.betaTable"
- --pvals="$inputDataSelector.pvalTable"
- #end if
- #if str( $inputDataSelector.dataType ) == "bed"
- --data-type="bed.dir"
- --pheno="$inputDataSelector.sampleAnnotations"
- #set $bedList=""
- #for $input_file in $inputDataSelector.bedSeries:
- #set $bedList+=str( $input_file.bedFile )
- #set $bedList+=","
- #end for
- --bed-files="$bedList"
- #end if
- #if str( $options.optionSet ) == "full"
- #if str( $options.analysisName ) != ""
- --analysis-name="$options.analysisName"
- #end if
- #if str( $options.logging ) == "True"
- --logging
- #end if
- #if str( $options.email ) != ""
- --email="$options.email"
- #end if
- #if str( $options.assembly ) != ""
- --assembly="$options.assembly"
- #end if
- #if str( $options.columnsPairing ) != ""
- --columns-pairing="$options.columnsPairing"
- #end if
- #if str( $options.analyzeSites ) == "True"
- --analyze-sites
- #end if
- #if str( $options.regionTypes ) != ""
- --region-types="$options.regionTypes"
- #end if
- #if str( $options.identifiersColumn ) != ""
- --identifiers-column="$options.identifiersColumn"
- #end if
- #if str( $options.pointsCategory ) != ""
- --points-category="$options.pointsCategory"
- #end if
- #if str( $options.colorsCategory ) != ""
- --colors-category="$options.colorsCategory"
- #end if
- #if str( $options.colorsGradient ) != ""
- --colors-gradient="$options.colorsGradient"
- #end if
- #if str( $options.minGroupSize ) != ""
- --min-group-size="$options.minGroupSize"
- #end if
- #if str( $options.maxGroupCount ) != ""
- --max-group-count="$options.maxGroupCount"
- #end if
- #if str( $options.gzLargeFiles ) == "True"
- --gz-large-files
- #end if
- #if str( $options.strandSpecific ) == "True"
- --strand-specific
- #end if
- #if str( $options.replicateIdColumn ) != ""
- --replicate-id-column="$options.replicateIdColumn"
- #end if
- #if str( $options.loadingNormalization ) == "True"
- --loading-normalization
- #end if
- #if str( $options.loadingDefaultDataType ) != ""
- --loading-default-data-type="$options.loadingDefaultDataType"
- #end if
- #if str( $options.loadingTableSeparator ) != ""
- --loading-table-separator="$options.loadingTableSeparator"
- #end if
- #if str( $options.loadingBedStyle ) != ""
- --loading-bed-style="$options.loadingBedStyle"
- #end if
- #if str( $options.loadingBedColumns ) != ""
- --loading-bed-columns="$options.loadingBedColumns"
- #end if
- #if str( $options.loadingBedFrameShift ) != ""
- --loading-bed-frame-shift="$options.loadingBedFrameShift"
- #end if
- #if str( $options.normalizationMethod ) != ""
- --normalization-method="$options.normalizationMethod"
- #end if
- #if str( $options.normalizationBackgroundMethod ) != ""
- --normalization-background-method="$options.normalizationBackgroundMethod"
- #end if
- #if str( $options.qc ) == "True"
- --qc
- #end if
- #if str( $options.qcBoxplots ) == "True"
- --qc-boxplots
- #end if
- #if str( $options.qcBarplots ) == "True"
- --qc-barplots
- #end if
- #if str( $options.qcSnpHeatmap ) == "True"
- --qc-snp-heatmap
- #end if
- #if str( $options.qcSnpHeatmap ) == "True"
- --qc-snp-heatmap
- #end if
- #if str( $options.qcSnpBoxplot ) == "True"
- --qc-snp-boxplot
- #end if
- #if str( $options.qcSnpBarplot ) == "True"
- --qc-snp-barplot
- #end if
- #if str( $options.qcSampleBatchSize ) != ""
- --qc-sample-batch-size="$options.qcSampleBatchSize"
- #end if
- #if str( $options.filteringContextRemoval ) != ""
- --filtering-context-removal="$options.filteringContextRemoval"
- #end if
- #if str( $options.filteringSnp ) == "True"
- --filtering-snp
- #end if
- #if str( $options.filteringSnpFrequency ) != ""
- --filtering-snp-frequency="$options.filteringSnpFrequency"
- #end if
- #if str( $options.filteringSnpAccepted ) != ""
- --filtering-snp-accepted="$options.filteringSnpAccepted"
- #end if
- #if str( $options.filteringSexChromosomesRemoval ) == "True"
- --filtering-sex-chromosomes-removal
- #end if
- #if str( $options.filteringMissingValueQuantile ) != ""
- --filtering-missing-value-quantile="$options.filteringMissingValueQuantile"
- #end if
- #if str( $options.filteringCoverageThreshold ) != ""
- --filtering-coverage-threshold="$options.filteringCoverageThreshold"
- #end if
- #if str( $options.filteringLowCoverageMasking ) == "True"
- --filtering-low-coverage-masking
- #end if
- #if str( $options.filteringHighCoverageOutliers ) == "True"
- --filtering-high-coverage-outliers
- #end if
- #if str( $options.filteringGreedycut ) == "True"
- --filtering-greedycut
- #end if
- #if str( $options.filteringGreedycutPvalueThreshold ) != ""
- --filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold"
- #end if
- #if str( $options.filteringGreedycutRcTies ) != ""
- --filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies"
- #end if
- #if str( $options.filteringDeviationThreshold ) != ""
- --filtering-deviation-threshold="$options.filteringDeviationThreshold"
- #end if
- #if str( $options.batch ) == "True"
- --batch
- #end if
- #if str( $options.batchDreductionColumns ) != ""
- --batch-dreduction-columns="$options.batchDreductionColumns"
- #end if
- #if str( $options.batchPrincipalComponents ) != ""
- --batch-principal-components="$options.batchPrincipalComponents"
- #end if
- #if str( $options.batchCorrelationColumns ) != ""
- --batch-correlation-columns="$options.batchCorrelationColumns"
- #end if
- #if str( $options.batchCorrelationPvalueThreshold ) != ""
- --batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold"
- #end if
- #if str( $options.batchCorrelationPermutations ) != ""
- --batch-correlation-permutations="$options.batchCorrelationPermutations"
- #end if
- #if str( $options.batchCorrelationQc ) == "True"
- --batch-correlation-qc
- #end if
- #if str( $options.profiles ) == "True"
- --profiles
- #end if
- #if str( $options.profilesBetaDistribution ) == "True"
- --profiles-beta-distribution
- #end if
- #if str( $options.profilesIntersample ) == "True"
- --profiles-intersample
- #end if
- #if str( $options.profilesDeviationPlots ) == "True"
- --profiles-deviation-plots
- #end if
- #if str( $options.profilesColumns ) != ""
- --profiles-columns="$options.profilesColumns"
- #end if
- #if str( $options.profilesClustering ) == "True"
- --profiles-clustering
- #end if
- #if str( $options.profilesClusteringTopProbes ) != ""
- --profiles-clustering-top-probes="$options.profilesClusteringTopProbes"
- #end if
- #if str( $options.regionProfilesTypes ) != ""
- --region-profiles-types="$options.regionProfilesTypes"
- #end if
- #if str( $options.differential ) == "True"
- --differential
- #end if
- #if str( $options.differentialPermutations ) != ""
- --differential-permutations="$options.differentialPermutations"
- #end if
- #if str( $options.differentialComparisonColumns ) != ""
- --differential-comparison-columns="$options.differentialComparisonColumns"
- #end if
- #if str( $options.differentialComparisonColumnsAllPairwise ) != ""
- --differential-comparison-columns-all-pairwise="$options.differentialComparisonColumnsAllPairwise"
- #end if
- #if str( $options.differentialEnrichment ) == "True"
- --differential-enrichment
- #end if
- #if str( $options.exportToUcsc ) != ""
- --export-to-ucsc="$options.exportToUcsc"
- #end if
- #if str( $options.exportToBed ) == "True"
- --export-to-bed
- #end if
- #if str( $options.exportToCsv ) == "True"
- --export-to-csv
- #end if
- #if str( $options.exportTypes ) != ""
- --export-types="$options.exportTypes"
- #end if
- #if str( $options.colors3Gradient ) != ""
- --colors-3-gradient="$options.colors3Gradient"
- #end if
- #if str( $options.loggingMemory ) == "True"
- --logging-memory
- #end if
- #end if
-
-
-
-
- Tabular data
- IDAT files
- GenomeStudio report
- Gene Expression Omnibus series
- BED files
-
-
-
-
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-
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- Select from history
- Repository on the server
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- Default options
- Full option set
-
-
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- RnBeads is an R-package for comprehensive analysis of Illumina Infinium HumanMethylation450 BeadChip data. It extends previous approaches for this type of data analysis by high throughput capabilities, as well as presenting results in a comprehensive, highly interpretable fashion.
-
-
-
\ No newline at end of file
diff -r 450c8ff1d11a -r 05220e275e4b rnbeads_galaxy_wrapper.sh
--- a/rnbeads_galaxy_wrapper.sh Fri Jul 05 09:08:41 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-#!/bin/bash
-random_hash=`tr -dc "[:alpha:]" < /dev/urandom | head -c 8`
-Rscript --no-save $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > /tmp/rnbeads_${random_hash}.stdout 2>/tmp/rnbeads_${random_hash}.stderr
-#Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $*
-outfile=`echo $* | cut -d\ -f2 | sed -e "s/--output-file=//g"`
-echo $outfile
-#outdir=`echo $* | sed -e "s/.*--report-dir=\(.*\)[[:blank:]].*/\1/g"`
-
-
-errl=`cat /tmp/rnbeads_${random_hash}.stderr | grep -e "[E|e]rror" | wc -l`
-if [ "$errl" -gt 0 ]
-then
- cat /tmp/rnbeads_${random_hash}.stdout >&2
- #cat $outdir/analysis.log >&2
- cat /tmp/rnbeads_${random_hash}.stderr >&2
- exit 3
-else
- echo "
" >> $outfile
- echo "RnBeads report " >> $outfile
- echo " Output was generated during the execution: " >> $outfile
- echo "" >> outfile
- cat /tmp/rnbeads_${random_hash}.stdout |sed -e "s/$/ /g" >> $outfile
- echo " " >> outfile
- echo "" >> $outfile
- echo "" >> $outfile
- exit 0
-fi
\ No newline at end of file
diff -r 450c8ff1d11a -r 05220e275e4b rnbeads_repos.txt.sample
--- a/rnbeads_repos.txt.sample Fri Jul 05 09:08:41 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-repo1 Repository1 /data/iscan/idats
\ No newline at end of file
diff -r 450c8ff1d11a -r 05220e275e4b tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Fri Jul 05 09:08:41 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
-
-
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diff -r 450c8ff1d11a -r 05220e275e4b tool_dependencies.xml
--- a/tool_dependencies.xml Fri Jul 05 09:08:41 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-
-
-
- $REPOSITORY_INSTALL_DIR
-
-
-
-
- http://CRAN.R-project.org/src/base/R-3/R-3.0.0.tar.gz
- ./configure --prefix=$INSTALL_DIR --with-x=no
- make
-
- $INSTALL_DIR/bin
-
- R --no-save <<< "install.packages("getopt"); source('http://rnbeads.mpi-inf.mpg.de')"
-
-
-
- You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.
-
-
-
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