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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 68db09d2e2a4 -r 945690943560 RnBeadsGalaxy.R --- a/RnBeadsGalaxy.R Thu Apr 18 07:38:46 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,154 +0,0 @@ -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="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","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){ - getoptname<-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) - |
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| diff -r 68db09d2e2a4 -r 945690943560 install.rnbeads.R --- a/install.rnbeads.R Thu Apr 18 07:38:46 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 68db09d2e2a4 -r 945690943560 rnbeads.xml --- a/rnbeads.xml Thu Apr 18 07:38:46 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,495 +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="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' |
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| diff -r 68db09d2e2a4 -r 945690943560 rnbeads_galaxy_wrapper.sh --- a/rnbeads_galaxy_wrapper.sh Thu Apr 18 07:38:46 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -#!/bin/bash - -Rscript --slave $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > RnBeads.out -#Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $* -exit 0 \ No newline at end of file |
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| diff -r 68db09d2e2a4 -r 945690943560 rnbeads_repos.txt.sample --- a/rnbeads_repos.txt.sample Thu Apr 18 07:38:46 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -repo1 Repository1 /data/iscan/idats \ No newline at end of file |
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| diff -r 68db09d2e2a4 -r 945690943560 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu Apr 18 07:38:46 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<tables> - <table name="rnbeads_repos" comment_char="#"> - <columns>id, name, value</columns> - <file path="tool-data/rnbeads_repos.txt" /> - </table> -</tables> \ No newline at end of file |
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| diff -r 68db09d2e2a4 -r 945690943560 tool_dependencies.xml --- a/tool_dependencies.xml Thu Apr 18 07:38:46 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,22 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="0.9"> - <environment_variable name="R_SCRIPTS_PATH" action="set_to">$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 <<< "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 |