| Next changeset 1:d4c4069367d7 (2013-04-17) |
|
Commit message:
First commit |
|
added:
RnBeadsGalaxy.R install.rnbeads.R rnbeads.xml rnbeads_galaxy_wrapper.sh rnbeads_repos.txt.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| b |
| diff -r 000000000000 -r d1d0d07a8af4 RnBeadsGalaxy.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RnBeadsGalaxy.R Wed Apr 17 07:44:04 2013 -0400 |
| [ |
| @@ -0,0 +1,154 @@ +library(RnBeads) +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="C:\\Users\\User\\workspace\\RnBeads\\Supplement\\galaxy\\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="C:\\Users\\User\\workspace\\RnBeads\\Supplement\\galaxy\\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","report-dir"), + Short=c("d","s","a","i","f","g","e","b","p","r"), + Mask=c(1,2,2,2,2,2,2,2,2,1), + Type=c("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" + files<-strsplit(opts[["idat-files"]], "\t")[[1]] + idat.dir<-mkdir(file.path(opts[["report-dir"]], "idats")) + file.copy(as.list(files), idat.dir) + data.source<-list() + data.source[["idat.dir"]]<-idat.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"]]=="beds"){ + + data.type<-"idat.dir" + files<-strsplit(opts[["bed-files"]], "\t")[[1]] + bed.dir<-mkdir(file.path(opts[["report-dir"]], "beds")) + file.copy(as.list(files), bed.dir) + data.source<-list() + data.source[["bed.dir"]]<-bed.dir + data.source[["sample.sheet"]]<-opts[["pheno"]] + +} + +dump<-sapply(names(opt.class), function(on){ + getopname<-gsub("\\.","-",on) + if(getoptname %in% names(opts)){ + if(opt.class[on]=="logical"){ + rnb.options(on=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,",")) + } + rnb.options(on=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,",")) + } + rnb.options(on=ov) + } + } +}) + + +rnb.run.analysis(data.source=data.source, dir.report=opts[["report-dir"]], data.type=data.type) + |
| b |
| diff -r 000000000000 -r d1d0d07a8af4 install.rnbeads.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/install.rnbeads.R Wed Apr 17 07:44:04 2013 -0400 |
| b |
| @@ -0,0 +1,1 @@ +source("http://rnbeads.mpi-inf.mpg.de/install.R") \ No newline at end of file |
| b |
| diff -r 000000000000 -r d1d0d07a8af4 rnbeads.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnbeads.xml Wed Apr 17 07:44:04 2013 -0400 |
| b |
| b'@@ -0,0 +1,495 @@\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="0.9">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+ #if str( $inputDataSelector.dataType ) == "idat" \r\n+ \t--data-type="idat.dir"\r\n+ \t--pheno="$inputDataSelector.sampleAnnotations"\r\n+ \t#if str( $idatSelector.idatSelector.idatSource ) == "history"\r\n+ \t--idat-files =="\r\n+ \t\t#for $input_files in $inputDataSelector.input_series:\r\n+ \t\t\t${input_files.input_files}\\t\t\t\t\t\r\n+ \t\t#end for\r\n+ \t"\r\n+ \t#else:\r\n+ \t\t--idat-files == "$idatRepo"\r\n+ \t#end if\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+ --beds =="\r\n+ \t#for $input_files in $inputDataSelector.input_series:\r\n+ \t\t\t${input_files.input_files}\\t\t\t\t\t\r\n+ \t\t#end for\r\n+ #end if\r\n+ \t--report-dir="$html_file.files_path"\r\n+ #if str( $options.optionSet ) == "full"\r\n+\t\t\t\t#if str( $options.analysisName ) != ""\r\n+\t\t\t\t\t--analysis-name = "$options.analysisName" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.logging ) == "True"\r\n+\t\t\t\t\t--logging\r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.email ) != ""\r\n+\t\t\t\t\t--email = "$options.email" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.assembly ) != ""\r\n+\t\t\t\t\t--assembly = "$options.assembly" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.analyzeSites ) == "True"\r\n+\t\t\t\t\t--analyze-sites\r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.regionTypes ) != ""\r\n+\t\t\t\t\t--region-types = "$options.regionTypes" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.identifiersColumn ) != ""\r\n+\t\t\t\t\t--identifiers-column = "$options.identifiersColumn" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.pointsCategory ) != ""\r\n+\t\t\t\t\t--points-category = "$options.pointsCategory" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.colorsCategory ) != ""\r\n+\t\t\t\t\t--colors-category = "$options.colorsCategory" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.colorsGradient ) != ""\r\n+\t\t\t\t\t--colors-gradient = "$options.colorsGradient" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.minGroupSize ) != ""\r\n+\t\t\t\t\t--min-group-size = "$options.minGroupSize" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.maxGroupCount ) != ""\r\n+\t\t\t\t\t--max-group-count = "$options.maxGroupCount" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.gzLargeFiles ) == "True"\r\n+\t\t\t\t\t--gz-large-files\r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.strandSpecific ) == "True"\r\n+\t\t\t\t\t--strand-specific\r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.replicateIdColumn ) != ""\r\n+\t\t\t\t\t--replicate-id-column = "$options.replicateIdColumn" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.loadingNormalization ) == "True"\r\n+\t\t\t\t\t--loading-normalization\r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.loadingDefaultDataType ) != ""\r\n+\t\t\t\t\t--loading-default-data-type = "$options.loadingDefaultDataType" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.loadingTableSeparator ) != ""\r\n+\t\t\t\t\t--loading-table-separator = "$options.loadingTableSeparator" \r\n+\t\t\t\t#end if\r\n+\t\t\t\t#if str( $options.loadingBedStyle'..b'name="batchCorrelationQc" type="select" label="batch.correlation.qc, logical" value="1">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="profiles" type="select" label="profiles, logical" value="1">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="profilesBetaDistribution" type="select" label="profiles.beta.distribution, logical" value="1">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="profilesIntersample" type="select" label="profiles.intersample, logical" value="1">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="profilesDeviationPlots" type="select" label="profiles.deviation.plots, logical" value="0">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="profilesColumns" type="text" label="profiles.columns, integer vector" value=""/>\r\n+\t\t\t\t<param name="profilesClustering" type="select" label="profiles.clustering, logical" value="1">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="profilesClusteringTopProbes" type="text" label="profiles.clustering.top.probes, integer vector" value="1000"/>\r\n+\t\t\t\t<param name="regionProfilesTypes" type="text" label="region.profiles.types, character vector" value="genes,promoters,cpgislands"/>\r\n+\t\t\t\t<param name="differential" type="select" label="differential, logical" value="1">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="differentialPermutations" type="text" label="differential.permutations, integer" value="0"/>\r\n+\t\t\t\t<param name="differentialComparisonColumns" type="text" label="differential.comparison.columns, integer vector" value=""/>\r\n+\t\t\t\t<param name="differentialEnrichment" type="select" label="differential.enrichment, logical" value="0">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="exportToUcsc" type="text" label="export.to.ucsc, character vector" value="bigBed,bigWig"/>\r\n+\t\t\t\t<param name="exportToBed" type="select" label="export.to.bed, logical" value="1">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="exportToCsv" type="select" label="export.to.csv, logical" value="0">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="exportTypes" type="text" label="export.types, character vector" value=""/>\r\n+\t\t\t\t<param name="colors3Gradient" type="text" label="colors.3.gradient, character vector" value="#832424,#FFFFFF,#3A3A98"/>\r\n+\t\t\t\t<param name="loggingMemory" type="select" label="logging.memory, logical" value="0">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+\t\t\t\t<param name="usePstoimg" type="select" label="use.pstoimg, logical" value="0">\r\n+\t\t\t\t\t<option value="True">True</option>\r\n+\t\t\t\t\t<option value="False">False</option>\r\n+\t\t\t\t</param>\r\n+ \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' |
| b |
| diff -r 000000000000 -r d1d0d07a8af4 rnbeads_galaxy_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnbeads_galaxy_wrapper.sh Wed Apr 17 07:44:04 2013 -0400 |
| b |
| @@ -0,0 +1,4 @@ +#!/bin/bash + +#Rscript --slave $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* +Rscript --slave \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $* \ No newline at end of file |
| b |
| diff -r 000000000000 -r d1d0d07a8af4 rnbeads_repos.txt.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnbeads_repos.txt.sample Wed Apr 17 07:44:04 2013 -0400 |
| b |
| @@ -0,0 +1,1 @@ +repo1 Repository1 /data/iscan/idats \ No newline at end of file |
| b |
| diff -r 000000000000 -r d1d0d07a8af4 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Apr 17 07:44:04 2013 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="rnbeads_repos" comment_char="#"> + <columns>id, name, value</columns> + <file path="tool-data/rnbeads_repos.txt" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r 000000000000 -r d1d0d07a8af4 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Apr 17 07:44:04 2013 -0400 |
| b |
| @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="0.9"> + <environment_variable name="R_SCRIPTS_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> + <package name="R" version="3.0.0"> + <install version="0.9"> + <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 <<< "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 |