# HG changeset patch # User testtool # Date 1492000185 14400 # Node ID 0631845b906d8421dedf07c60af358b610d8c19b # Parent 983651783ce95140f9ce0d89e70ad10a7104459a Uploaded diff -r 983651783ce9 -r 0631845b906d GRsetFromGEO/._.DS_Store Binary file GRsetFromGEO/._.DS_Store has changed diff -r 983651783ce9 -r 0631845b906d GRsetFromGEO/GRsetFromGEO.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO/GRsetFromGEO.R Wed Apr 12 08:29:45 2017 -0400 @@ -0,0 +1,14 @@ +require("minfi", quietly = TRUE) + +options(warn = -1) +options("download.file.method"="wget") + +args <- commandArgs(trailingOnly = TRUE) +GSE = args[1] +output = args[2] + +GRset <- getGenomicRatioSetFromGEO(GSE) + +save(GRset,file = output) + + diff -r 983651783ce9 -r 0631845b906d GRsetFromGEO/GRsetFromGEO.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO/GRsetFromGEO.xml Wed Apr 12 08:29:45 2017 -0400 @@ -0,0 +1,33 @@ + + + R + + + + + Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" + + + + + + + + + + + + + + + + + + + +Reading Illumina methylation array data from GEO. + + +Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369. + + diff -r 983651783ce9 -r 0631845b906d GRsetFromGEO/test-data/GenomicRatioSet.Rdata Binary file GRsetFromGEO/test-data/GenomicRatioSet.Rdata has changed diff -r 983651783ce9 -r 0631845b906d GRsetFromGEO/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GRsetFromGEO/tool_dependencies.xml Wed Apr 12 08:29:45 2017 -0400 @@ -0,0 +1,273 @@ + + + + + + + + + + https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz + + + https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz + + + https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz + + + https://bioarchive.galaxyproject.org/fgsea_1.1.2.tar.gz + + + https://bioarchive.galaxyproject.org/GOSemSim_2.1.2.tar.gz + + + https://depot.galaxyproject.org/software/igraph/igraph_1.0.1.tar.gz + + + https://bioarchive.galaxyproject.org/qvalue_2.7.0.tar.gz + + + https://depot.galaxyproject.org/software/reshape2/reshape2_1.4.2.tar.gz + + + https://depot.galaxyproject.org/software/scales/scales_0.4.1.tar.gz + + + https://bioarchive.galaxyproject.org/biomaRt_2.31.3.tar.gz + + + https://depot.galaxyproject.org/software/gtable/gtable_0.2.0.tar.gz + + + https://depot.galaxyproject.org/software/tibble/tibble_1.2.tar.gz + + + https://depot.galaxyproject.org/software/lazyeval/lazyeval_0.2.0.tar.gz + + + https://depot.galaxyproject.org/software/gdata/gdata_2.17.0.tar.gz + + + https://depot.galaxyproject.org/software/caTools/caTools_1.17.1.tar.gz + + + https://depot.galaxyproject.org/software/assertthat/assertthat_0.1.tar.gz + + + https://depot.galaxyproject.org/software/R6/R6_2.2.0.tar.gz + + + https://depot.galaxyproject.org/software/BH/BH_1.62.0-1.tar.gz + + + https://depot.galaxyproject.org/software/gridExtra/gridExtra_2.2.1.tar.gz + + + https://bioarchive.galaxyproject.org/DOSE_3.1.2.tar.gz + + + https://bioarchive.galaxyproject.org/GenomeInfoDb_1.11.6.tar.gz + + + https://bioarchive.galaxyproject.org/BiocGenerics_0.21.1.tar.gz + + + https://bioarchive.galaxyproject.org/S4Vectors_0.13.5.tar.gz + + + https://bioarchive.galaxyproject.org/IRanges_2.9.14.tar.gz + + + https://bioarchive.galaxyproject.org/GenomicRanges_1.27.16.tar.gz + + + https://bioarchive.galaxyproject.org/GenomicFeatures_1.27.4.tar.gz + + + https://depot.galaxyproject.org/software/ggplot2/ggplot2_2.2.0.tar.gz + + + https://depot.galaxyproject.org/software/gplots/gplots_3.0.1.tar.gz + + + https://depot.galaxyproject.org/software/gridBase/gridBase_0.4-7.tar.gz + + + https://depot.galaxyproject.org/software/gtools/gtools_3.5.0.tar.gz + + + https://depot.galaxyproject.org/software/plotrix/plotrix_3.6-3.tar.gz + + + https://depot.galaxyproject.org/software/dplyr/dplyr_0.5.0.tar.gz + + + https://depot.galaxyproject.org/software/TxDb.Hsapiens.UCSC.hg19.knownGene/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz + + + https://depot.galaxyproject.org/software/UpSetR/UpSetR_1.3.1.tar.gz + + + https://depot.galaxyproject.org/software/httpuv/httpuv_1.3.3.tar.gz + + + https://depot.galaxyproject.org/software/htmltools/htmltools_0.3.5.tar.gz + + + https://depot.galaxyproject.org/software/sourcetools/sourcetools_0.1.5.tar.gz + + + https://depot.galaxyproject.org/software/shiny/shiny_0.14.2.tar.gz + + + https://depot.galaxyproject.org/software/jsonlite/jsonlite_1.1.tar.gz + + + https://depot.galaxyproject.org/software/mime/mime_0.5.tar.gz + + + https://depot.galaxyproject.org/software/curl/curl_2.3.tar.gz + + + https://depot.galaxyproject.org/software/openssl/openssl_0.9.5.tar.gz + + + https://bioarchive.galaxyproject.org/interactiveDisplayBase_1.13.0.tar.gz + + + https://depot.galaxyproject.org/software/httr/httr_1.2.1.tar.gz + + + https://depot.galaxyproject.org/software/yaml/yaml_2.1.14.tar.gz + + + https://bioarchive.galaxyproject.org/AnnotationHub_2.7.8.tar.gz + + + https://depot.galaxyproject.org/software/ade4/ade4_1.7-4.tar.gz + + + https://depot.galaxyproject.org/software/segmented/segmented_0.5-1.4.tar.gz + + + https://depot.galaxyproject.org/software/VennDiagram/VennDiagram_1.6.17.tar.gz + + + https://bioarchive.galaxyproject.org/BSgenome_1.43.1.tar.gz + + + https://depot.galaxyproject.org/software/matrixStats/matrixStats_0.51.0.tar.gz + + + https://bioarchive.galaxyproject.org/limma_3.31.6.tar.gz + + + https://bioarchive.galaxyproject.org/multtest_2.31.0.tar.gz + + + https://bioarchive.galaxyproject.org/RBGL_1.51.0.tar.gz + + + https://bioarchive.galaxyproject.org/graph_1.53.0.tar.gz + + + https://bioarchive.galaxyproject.org/regioneR_1.7.0.tar.gz + + + https://bioarchive.galaxyproject.org/ProtGenerics_1.7.0.tar.gz + + + https://bioarchive.galaxyproject.org/ensembldb_1.99.7.tar.gz + + + https://depot.galaxyproject.org/software/seqinr/seqinr_3.3-3.tar.gz + + + https://depot.galaxyproject.org/software/idr/idr_1.2.tar.gz + + + https://bioarchive.galaxyproject.org/ChIPpeakAnno_3.9.3.tar.gz + + + https://depot.galaxyproject.org/software/locfit/locfit_1.5-9.1.tar.gz + + + https://depot.galaxyproject.org/software/doRNG/doRNG_1.6.tar.gz + + + https://depot.galaxyproject.org/software/base64/base64_2.0.tar.gz + + + https://depot.galaxyproject.org/software/beanplot/beanplot_1.2.tar.gz + + + https://depot.galaxyproject.org/software/nor1mix/nor1mix_1.2-2.tar.gz + + + https://bioarchive.galaxyproject.org/siggenes_1.49.0.tar.gz + + + https://bioarchive.galaxyproject.org/preprocessCore_1.37.0.tar.gz + + + https://bioarchive.galaxyproject.org/illuminaio_0.17.0.tar.gz + + + https://depot.galaxyproject.org/software/mclust/mclust_5.2.tar.gz + + + https://bioarchive.galaxyproject.org/genefilter_1.57.0.tar.gz + + + https://depot.galaxyproject.org/software/reshape/reshape_0.8.6.tar.gz + + + https://depot.galaxyproject.org/software/quadprog/quadprog_1.5-5.tar.gz + + + https://bioarchive.galaxyproject.org/GEOquery_2.41.0.tar.gz + + + https://bioarchive.galaxyproject.org/Biobase_2.35.0.tar.gz + + + https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.4.0.tar.gz + + + https://depot.galaxyproject.org/software/data.table/data.table_1.10.0.tar.gz + + + https://depot.galaxyproject.org/software/GO.db/GO.db_3.4.0.tar.gz + + + https://depot.galaxyproject.org/software/NMF/NMF_0.20.6.tar.gz + + + https://depot.galaxyproject.org/software/colorspace/colorspace_1.3-1.tar.gz + + + https://depot.galaxyproject.org/software/dichromat/dichromat_2.0-0.tar.gz + + + https://depot.galaxyproject.org/software/fastmatch/fastmatch_1.0-4.tar.gz + + + https://depot.galaxyproject.org/software/irlba/irlba_2.1.2.tar.gz + + + https://depot.galaxyproject.org/software/pkgmaker/pkgmaker_0.22.tar.gz + + + https://depot.galaxyproject.org/software/registry/registry_0.3.tar.gz + + + https://depot.galaxyproject.org/software/rngtools/rngtools_1.2.4.tar.gz + + + https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz + + + + + diff -r 983651783ce9 -r 0631845b906d getGRsetFromGEO/.Rapp.history diff -r 983651783ce9 -r 0631845b906d getGRsetFromGEO/.Rhistory --- a/getGRsetFromGEO/.Rhistory Wed Mar 22 09:01:06 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,138 +0,0 @@ -TAB <- read.csv("input.csv") -mysamples <- lapply(TAB$ID,function(x)getGEO(x)) -input <- function(TAB) { if(is(TAB, "csv")){ -TAB <- read.csv("input.csv")} -else{ -print("error in data file") -}} -input() -TAB <- read.csv("input.csv")} -TAB <- read.csv("input.csv") -test_func <- function( -clusterSize=2, -cutoff=0.2, -platform_id='HM450', -genome_id='hg19') -{ -args = commandArgs(trailingOnly=TRUE) -methyl_file = args[1] -ChiPseq_file = args[2] -output_file = args[3] -options(warn=-1) -TAB=read.csv(methyl_file) -ChiPseq=import(ChiPseq_file) -if(is.null(TAB)){ -stop("Must specify input files") -}else{ -mysamples <- lapply(TAB$ID,function(x) getGEO(x)) -} -wrappedFunction <- function(test_func) -s0 <- lapply(mysamples,Table) -id_ref<-lapply(s0,function(x)x$ID_REF) -if(length(unique(id_ref)) != 1) { -stop("Error different ID_REF for samples") -} else if (is.null((unlist(unique(id_ref))))) { -stop("NO GSM data avaliable") -} else { -values<-do.call("cbind",lapply(s0,function(x)x$VALUE)) -colnames(values)=TAB$ID -rownames(values)=id_ref[[1]] -cg <- rownames(values) -probe <- c(cg) -hm450.hg19 <- getPlatform(platform=platform_id, genome=genome_id) -probe.info <- hm450.hg19[probe] -f <- data.table(probe=names(probe.info),CHR=as.data.frame(probe.info@seqnames)$value, -BP=as.numeric(probe.info@elementMetadata$probeStart)) -designMatrix <- model.matrix(~ TAB$Phenotype) -DMR <- bumphunter(values, design = designMatrix, -pos=f$BP,cutoff=cutoff,chr=f$CHR) -MAT <- DMR$table[which(DMR$table$L>=clusterSize),] -METH <- GRanges(seqnames=MAT$chr, -ranges=IRanges -(start=MAT$start, -end=MAT$end), -value_pos=MAT$value) -peaks<-findOverlapsOfPeaks(probe.info,ChiPseq,maxgap=5000) -p <- peaks$peaklist$`probe.info///ChiPseq` -peakAnno <- annotatePeak(p, file=peakAnno) -output_file <- annotatePeak(p, file=output_file) -}} -test_func <- function( -clusterSize=2, -cutoff=0.2, -platform_id='HM450', -genome_id='hg19') -{ -args = commandArgs(trailingOnly=TRUE) -methyl_file = args[1] -ChiPseq_file = args[2] -output_file = args[3] -options(warn=-1) -TAB=read.csv(methyl_file) -ChiPseq=import(ChiPseq_file) -if(is.null(TAB)){ -stop("Must specify input files") -}else{ -mysamples <- lapply(TAB$ID,function(x) getGEO(x)) -} -wrappedFunction <- function(test_func) -s0 <- lapply(mysamples,Table) -id_ref<-lapply(s0,function(x)x$ID_REF) -if(length(unique(id_ref)) != 1) { -stop("Error different ID_REF for samples") -} else if (is.null((unlist(unique(id_ref))))) { -stop("NO GSM data avaliable") -} else { -values<-do.call("cbind",lapply(s0,function(x)x$VALUE)) -colnames(values)=TAB$ID -rownames(values)=id_ref[[1]] -cg <- rownames(values) -probe <- c(cg) -hm450.hg19 <- getPlatform(platform=platform_id, genome=genome_id) -probe.info <- hm450.hg19[probe] -f <- data.table(probe=names(probe.info),CHR=as.data.frame(probe.info@seqnames)$value, -BP=as.numeric(probe.info@elementMetadata$probeStart)) -designMatrix <- model.matrix(~ TAB$Phenotype) -DMR <- bumphunter(values, design = designMatrix, -pos=f$BP,cutoff=cutoff,chr=f$CHR) -MAT <- DMR$table[which(DMR$table$L>=clusterSize),] -METH <- GRanges(seqnames=MAT$chr, -ranges=IRanges -(start=MAT$start, -end=MAT$end), -value_pos=MAT$value) -peaks<-findOverlapsOfPeaks(probe.info,ChiPseq,maxgap=5000) -p <- peaks$peaklist$`probe.info///ChiPseq` -peakAnno <- annotatePeak(p, file=peakAnno) -output_file <- annotatePeak(p, file=output_file) -}} -) -a<-c(3.2,3.7,3.6,3.9,3.7,3.5,3.8,4,3.5) -a<-c(3.2,3.7,3.6,3.9,3.7,3.5,3.8,4,3.5) -b<-c(2.9,2.7,2,6,2.7,2.5,2.5,3.2,3.1,3.3,2.8) -a-b -file<-read.csv("~/Documents/SS2.csv") -head(file) -e -file -t.test(file$WBT,file$WBA) -t.test(file$WBT,file$WBA,paired=TRUE) -mysamples <- lapply(TAB$ID,function(x) TablegetGEO(x)) -require("GEOquery",quietly = TRUE) -require("BiocGenerics",quietly = TRUE) -args <- commandArgs(trailingOnly = TRUE) -csv_file = args[1] -#csv_file <- ("test-data/input.csv") -TAB=read.csv(csv_file) -if(is.null(TAB)){ -stop("Must specify input files") -}else{ -mysamples <- lapply(TAB$ID,function(x) TablegetGEO(x)) -} -csv_file <- ("test-data/input.csv") -TAB=read.csv(csv_file) -TAB -csv_file<-("test-data/input.csv") -TAB = read.csv(csv_file) -TAB -??bumphunter diff -r 983651783ce9 -r 0631845b906d getGRsetFromGEO/._.DS_Store Binary file getGRsetFromGEO/._.DS_Store has changed diff -r 983651783ce9 -r 0631845b906d getGRsetFromGEO/getGRsetFromGEO.R --- a/getGRsetFromGEO/getGRsetFromGEO.R Wed Mar 22 09:01:06 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -require("minfi", quietly = TRUE) - -options(warn = -1) -options("download.file.method"="wget") - -args <- commandArgs(trailingOnly = TRUE) - -GSE = args[1] #GSE51547 -output = args[2] #output <- ("GEOdata.txt") - -GEO <- getGenomicRatioSetFromGEO(GSE) - -save(GEO, ascii=TRUE, file=output) - diff -r 983651783ce9 -r 0631845b906d getGRsetFromGEO/getGRsetFromGEO.xml --- a/getGRsetFromGEO/getGRsetFromGEO.xml Wed Mar 22 09:01:06 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ - - - from GEO - - - R - - - - - Rscript $__tool_directory__/getGRsetFromGEO.R "$GSE" "$output" - - - - - - - - - - - - - - - - - - - -**Description** - - -GEO - - diff -r 983651783ce9 -r 0631845b906d getGRsetFromGEO/test-data/._.DS_Store Binary file getGRsetFromGEO/test-data/._.DS_Store has changed diff -r 983651783ce9 -r 0631845b906d getGRsetFromGEO/test-data/GEOdata.RData Binary file getGRsetFromGEO/test-data/GEOdata.RData has changed diff -r 983651783ce9 -r 0631845b906d getGRsetFromGEO/tool_dependencies.xml --- a/getGRsetFromGEO/tool_dependencies.xml Wed Mar 22 09:01:06 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,267 +0,0 @@ - - - - - - - - - http://bioconductor.org/packages/release/bioc/src/contrib/minfi_1.20.2.tar.gz - - - https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz - - - https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz - - - https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz - - - https://bioarchive.galaxyproject.org/fgsea_1.1.2.tar.gz - - - https://bioarchive.galaxyproject.org/GOSemSim_2.1.2.tar.gz - - - https://depot.galaxyproject.org/software/igraph/igraph_1.0.1.tar.gz - - - https://bioarchive.galaxyproject.org/qvalue_2.7.0.tar.gz - - - https://depot.galaxyproject.org/software/reshape2/reshape2_1.4.2.tar.gz - - - https://depot.galaxyproject.org/software/scales/scales_0.4.1.tar.gz - - - https://bioarchive.galaxyproject.org/biomaRt_2.31.3.tar.gz - - - https://depot.galaxyproject.org/software/gtable/gtable_0.2.0.tar.gz - - - https://depot.galaxyproject.org/software/tibble/tibble_1.2.tar.gz - - - 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