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Commit message:
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added:
GRsetFromGEO/._.DS_Store GRsetFromGEO/GRsetFromGEO.R GRsetFromGEO/GRsetFromGEO.xml GRsetFromGEO/test-data/GenomicRatioSet.Rdata GRsetFromGEO/tool_dependencies.xml |
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removed:
getGRsetFromGEO/.Rapp.history getGRsetFromGEO/.Rhistory getGRsetFromGEO/._.DS_Store getGRsetFromGEO/getGRsetFromGEO.R getGRsetFromGEO/getGRsetFromGEO.xml getGRsetFromGEO/test-data/._.DS_Store getGRsetFromGEO/test-data/GEOdata.RData getGRsetFromGEO/tool_dependencies.xml |
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| diff -r 983651783ce9 -r 0631845b906d GRsetFromGEO/._.DS_Store |
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| Binary file GRsetFromGEO/._.DS_Store has changed |
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| 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 |
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| @@ -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) + + |
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| 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 |
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| @@ -0,0 +1,33 @@ +<tool id="GRset" name="GRsetFromGEO" version="1.16.2"> + <requirements> + <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement> +</requirements> +<stdio> + <exit_code range="1:" /> +</stdio> + <command> Rscript $__tool_directory__/GRsetFromGEO.R "$GSE" "$output" </command> + <inputs> + <param name="GSE" type="text" value="" label="Enter GSE ID." help="e.g. 'GSE51547'"/> + </inputs> + <outputs> + <data format="Rdata" name="output" label="GenomicRatioSet.Rdata"/> + </outputs> + <tests> + <test> + <param name="test"> + <element name="test-data"> + <collection type="data"> + <element name="GSE" value="GSE51547"/> + </collection> + </element> + </param> + <output format="Rdata" name="output" label="test-data/GenomicRatioSet.Rdata"/> + </test> + </tests> + <help> +Reading Illumina methylation array data from GEO. +</help> +<citations> +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. +</citations> +</tool> |
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| diff -r 983651783ce9 -r 0631845b906d GRsetFromGEO/test-data/GenomicRatioSet.Rdata |
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| Binary file GRsetFromGEO/test-data/GenomicRatioSet.Rdata has changed |
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| 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 |
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| b'@@ -0,0 +1,273 @@\n+<?xml version="1.0"?>\n+<tool_dependency>\n+ <install version="1.0">\n+ <actions>\n+ <action type="setup_r_environment">\n+ <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n+ <package name="R" version="3.2.1"/>\n+ </repository>\n+ <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n+ https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n+ </package>\n+ <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">\n+ https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz\n+ </package>\n+ <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">\n+ https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz\n+ </package>\n+ <package sha256sum="de6f46918b40bcf4f8c03442f2a0411f1796794e0e7b00770ed0aac56601833d">\n+ 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https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz\n+ </package>\n+ </action>\n+ </actions>\n+ </install>\n+ </tool_dependency>\n' |
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| 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 |
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| @@ -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 |
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| Binary file getGRsetFromGEO/._.DS_Store has changed |
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| 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) - |
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| 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 |
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| @@ -1,36 +0,0 @@ -<tool id="getGRsetFromGEO" name="getGRsetFromGEO" version="1.16.2"> - <description> - from GEO - </description> - <requirements> - <requirement type="package" version="3.2.1">R</requirement> - </requirements> -<stdio> - <exit_code range="1:" /> -</stdio> -<command> Rscript $__tool_directory__/getGRsetFromGEO.R "$GSE" "$output"</command> -<inputs> - <param type="text" name="GSE" value="" label="The GSE ID from GEO" help="e.g. 'GSE51547'"/> -</inputs> - <outputs> - <data format="rdata" name="output" label="GenomicRatioSetFromGEO"/> - </outputs> - <tests> - <test> - <param name="test"> - <element name="test-data"> - <collection type="data"> - <element name="GSE" value="GSE51547"/> - </collection> - </element> - </param> - <output format="rdata" name="output" label="test-data/GEOdata.RData"/> - </test> - </tests> - <help> -**Description** -</help> -<citations> -GEO -</citations> -</tool> |
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| diff -r 983651783ce9 -r 0631845b906d getGRsetFromGEO/test-data/._.DS_Store |
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| diff -r 983651783ce9 -r 0631845b906d getGRsetFromGEO/test-data/GEOdata.RData |
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| Binary file getGRsetFromGEO/test-data/GEOdata.RData has changed |
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| 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 |
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| b'@@ -1,267 +0,0 @@\n-<?xml version=\'1.0\' encoding=\'utf-8\'?>\n- <tool_dependency>\n- <actions>\n- <action type="setup_r_environment">\n- <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">\n- <package name="R" version="3.2.1" />\n- </repository>\n-\n- <package>http://bioconductor.org/packages/release/bioc/src/contrib/minfi_1.20.2.tar.gz</package>\n-\n- <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">\n- https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz\n- </package>\n- <package sha256sum="0d8069eb48e91f6f6d6a9148f4e2dc5026cabead15dd15fc343eff9cf33f538f">\n- https://depot.galaxyproject.org/software/labeling/labeling_0.3.tar.gz\n- </package>\n- <package sha256sum="762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881">\n- https://depot.galaxyproject.org/software/DO.db/DO.db_2.9.tar.gz\n- </package>\n- <package 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