| Previous changeset 43:39b78c48d064 (2013-07-05) Next changeset 45:6b0981ab063e (2014-08-14) |
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Commit message:
Deleted selected files |
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removed:
RnBeadsGalaxy.R install.rnbeads.R rnbeads.xml rnbeads_galaxy_wrapper.sh rnbeads_repos.txt.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 39b78c48d064 -r 51c4548d56ed RnBeadsGalaxy.R --- a/RnBeadsGalaxy.R Fri Jul 05 17:39:25 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,211 +0,0 @@ -#msg.file<-file("RnBeads.messages.out", open="w") -#sink(file=msg.file) - - -## add the RnBeads dependencies if we are on a cloud share-instance -if("Rsitelibrary" %in% list.files("/mnt")){ - - .libPaths("/mnt/galaxy/Rsitelibrary") - - -} - -if(!'wordcloud' %in% rownames(installed.packages())){ - install.packages('wordcloud',repos='http://cran.us.r-project.org') -} - -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\t<option value=\"True\">True</option>\n\t\t\t<option value=\"False\">False</option>" - 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<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\">\n%s\n\t\t</param>\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<param name=\"%s\" type=\"%s\" label=\"%s\" value=\"%s\"/>\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 |
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| diff -r 39b78c48d064 -r 51c4548d56ed install.rnbeads.R --- a/install.rnbeads.R Fri Jul 05 17:39:25 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -source("http://rnbeads.mpi-inf.mpg.de/install.R") \ No newline at end of file |
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| diff -r 39b78c48d064 -r 51c4548d56ed rnbeads.xml --- a/rnbeads.xml Fri Jul 05 17:39:25 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,506 +0,0 @@\n-<?xml version="0.9"?>\r\n-<tool id="rnbeads" name="RnBeads" version="0.9">\r\n- <description>Performs RnBeads analysis for the selected set of </description>\r\n- <requirements>\r\n- <requirement type="set_environment" version="1.0">R_SCRIPTS_PATH</requirement>\r\n- <requirement type="package" version="3.0.0">R</requirement>\r\n- </requirements>\r\n- <command interpreter="bash">rnbeads_galaxy_wrapper.sh\r\n- \t\t--report-dir="$html_file.extra_files_path"\r\n- \t--output-file="$html_file"\r\n- #if str( $inputDataSelector.dataType ) == "idats" \r\n- \t--pheno="$inputDataSelector.sampleAnnotations"\r\n- #end if\r\n- #if str( $inputDataSelector.dataType ) != "idats"\r\n- \t#pass\r\n- #else if str( $inputDataSelector.idatSelector.idatSource ) == "history"\r\n- \t--data-type="idatFiles"\r\n- \t#set $idatList=""\r\n- \t#for $input_file in $inputDataSelector.idatSelector.idatSeries:\r\n- \t\t#set $idatList+=str( $input_file.idatFile )\r\n- \t\t#set $idatList+=","\t\t\t\t\r\n- \t#end for\r\n- \t--idat-files="$idatList"\r\n- #else:\r\n- \t\t--data-type="idatDir"\r\n- \t\t--idat-dir="$inputDataSelector.idatSelector.idatRepo.fields.path"\r\n- #end if\r\n- #if str( $inputDataSelector.dataType ) == "gsreport"\r\n- \t--data-type="GS.report"\r\n- \t--gs-report="$inputDataSelector.gsReportFile"\r\n- #end if\r\n- #if str( $inputDataSelector.dataType ) == "geo"\r\n- \t--data-type="GEO"\r\n- \t--geo-series=$inputDataSelector.geoSeries\r\n- #end if\r\n- #if str( $inputDataSelector.dataType ) == "tables"\r\n- --data-type="data.files"\r\n- --pheno="$inputDataSelector.sampleAnnotations"\r\n- #end if\r\n- #if str( $inputDataSelector.dataType ) == "tables"\r\n- \t--data-type="data.files"\r\n- \t--pheno="$inputDataSelector.sampleAnnotations"\r\n- \t--betas="$inputDataSelector.betaTable"\r\n- \t--pvals="$inputDataSelector.pvalTable"\r\n- #end if\r\n- #if str( $inputDataSelector.dataType ) == "bed"\r\n- --data-type="bed.dir"\r\n- \t--pheno="$inputDataSelector.sampleAnnotations"\r\n- #set $bedList=""\r\n- \t#for $input_file in $inputDataSelector.bedSeries:\r\n- \t\t#set $bedList+=str( $input_file.bedFile )\r\n- \t\t#set $bedList+=","\t\t\t\t\r\n- \t#end for\r\n- \t--bed-files="$bedList"\r\n- #end if\r\n- #if str( $options.optionSet ) == "full"\r\n-\t\t#if str( $options.analysisName ) != ""\r\n-\t\t\t--analysis-name="$options.analysisName" \r\n-\t\t#end if\r\n-\t\t#if str( $options.logging ) == "True"\r\n-\t\t\t--logging\r\n-\t\t#end if\r\n-\t\t#if str( $options.email ) != ""\r\n-\t\t\t--email="$options.email" \r\n-\t\t#end if\r\n-\t\t#if str( $options.assembly ) != ""\r\n-\t\t\t--assembly="$options.assembly" \r\n-\t\t#end if\r\n-\t\t#if str( $options.columnsPairing ) != ""\r\n-\t\t\t--columns-pairing="$options.columnsPairing" \r\n-\t\t#end if\r\n-\t\t#if str( $options.analyzeSites ) == "True"\r\n-\t\t\t--analyze-sites\r\n-\t\t#end if\r\n-\t\t#if str( $options.regionTypes ) != ""\r\n-\t\t\t--region-types="$options.regionTypes" \r\n-\t\t#end if\r\n-\t\t#if str( $options.identifiersColumn ) != ""\r\n-\t\t\t--identifiers-column="$options.identifiersColumn" \r\n-\t\t#end if\r\n-\t\t#if str( $options.pointsCategory ) != ""\r\n-\t\t\t--points-category="$options.pointsCategory" \r\n-\t\t#end if\r\n-\t\t#if str( $options.colorsCategory ) != ""\r\n-\t\t\t--colors-category="$options.colorsCategory" \r\n-\t\t#end if\r\n-\t\t#if str( $options.colorsGradient ) != ""\r\n-\t\t\t--colors-gradient="$options.colorsGradient" \r\n-\t\t#end if\r\n-\t\t#if str( $options.minGroupSize ) != ""\r\n-\t\t\t--min-group-size="$options.minGroupSize" \r\n-\t\t#end if\r\n-\t\t#if str( $options.maxGroupCount ) != ""\r\n-\t\t\t--max-group-count="$options.maxGroupCount" \r\n-\t\t#end if\r\n-\t\t#if str( $options.gzLargeFiles ) == "True"\r\n-\t\t\t--gz-large-files\r\n-\t\t#end if\r\n-\t\t#if str( $options.strandSpecific ) == "True"\r\n-\t\t\t--strand-specific\r\n-\t\t#end if\r\n-\t\t#if str( $options.replicateIdColumn ) != ""\r\n-\t\t\t--replicate-id-column="$options.replicateIdColumn" \r\n-\t\t#end if\r\n-\t\t#if str( $options.loadingNormalization ) == "True"\r\n-\t\t\t--loading-normalization\r\n-\t\t#en'..b'xt" label="batch.correlation.permutations, integer" value="10000"/>\r\n-\t\t\t<param name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n-\t\t\t<param name="profiles" type="select" label="profiles, logical" value="1">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n-\t\t\t<param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n-\t\t\t<param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n-\t\t\t<param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n-\t\t\t<param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/>\r\n-\t\t\t<param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n-\t\t\t<param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/>\r\n-\t\t\t<param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>\r\n-\t\t\t<param name="differential" type="select" label="differential, logical" value="1">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n-\t\t\t<param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>\r\n-\t\t\t<param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>\r\n-\t\t\t<param name="differentialComparisonColumnsAllPairwise" type="text" label="differential.comparison.columns.all.pairwise, integer vector" value=""/>\r\n-\t\t\t<param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n-\t\t\t<param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/>\r\n-\t\t\t<param name="exportToBed" type="select" label="export.to.bed, logical" value="1">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n-\t\t\t<param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n-\t\t\t<param name="exportTypes" type="text" label="export.types, character vector" value="sites"/>\r\n-\t\t\t<param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>\r\n-\t\t\t<param name="loggingMemory" type="select" label="logging.memory, logical" value="0">\r\n-\t\t\t\t<option value="True">True</option>\r\n-\t\t\t\t<option value="False">False</option>\r\n-\t\t\t</param>\r\n- \t\t</when>\r\n- </conditional>\r\n- </inputs>\r\n- \r\n- <outputs>\r\n-\t<data format="html" name="html_file" label="index.html" />\r\n- </outputs>\r\n-\r\n- <!--\r\n- <tests>\r\n- <test>\r\n- <param name="input" value="fa_gc_content_input.fa"/>\r\n- <output name="out_file1" file="fa_gc_content_output.txt"/>\r\n- </test>\r\n- </tests> -->\r\n-\r\n- <help>\r\n-\tRnBeads 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.\r\n- </help>\r\n-\r\n-</tool>\n\\ No newline at end of file\n' |
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| diff -r 39b78c48d064 -r 51c4548d56ed rnbeads_galaxy_wrapper.sh --- a/rnbeads_galaxy_wrapper.sh Fri Jul 05 17:39:25 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 "<html><body>" >> $outfile - echo "<a href=\"index.html\">RnBeads report</a>" >> $outfile - echo "<br/><br/>Output was generated during the execution:<br/>" >> $outfile - echo "<pre>" >> outfile - cat /tmp/rnbeads_${random_hash}.stdout |sed -e "s/$/<br\/>/g" >> $outfile - echo "</pre>" >> outfile - echo "</p>" >> $outfile - echo "</body></html>" >> $outfile - exit 0 -fi \ No newline at end of file |
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| diff -r 39b78c48d064 -r 51c4548d56ed rnbeads_repos.txt.sample --- a/rnbeads_repos.txt.sample Fri Jul 05 17:39:25 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -repo1 Repository1 /data/iscan/idats \ No newline at end of file |
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| diff -r 39b78c48d064 -r 51c4548d56ed tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Fri Jul 05 17:39:25 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<tables> - <table name="rnbeads_repos" comment_char="#"> - <columns>id, name, value</columns> - <file path="tool-data/rnbeads_repos.txt" /> - </table> -</tables> \ No newline at end of file |
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| diff -r 39b78c48d064 -r 51c4548d56ed tool_dependencies.xml --- a/tool_dependencies.xml Fri Jul 05 17:39:25 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,22 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="1.0"> - <environment_variable name="R_SCRIPTS_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> - <package name="R" version="3.0.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://CRAN.R-project.org/src/base/R-3/R-3.0.0.tar.gz</action> - <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-x=no</action> - <action type="shell_command">make</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - <action type="shell_command">R --no-save <<< "install.packages("getopt"); source('http://rnbeads.mpi-inf.mpg.de')"</action> - </actions> - </install> - <readme> - You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. - </readme> - </package> -</tool_dependency> \ No newline at end of file |