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added:
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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removed:
getGEO/.Rhistory getGEO/._.DS_Store getGEO/getGEO.R getGEO/getGEO.xml getGEO/test-data/._.DS_Store getGEO/test-data/._input.csv getGEO/test-data/IlmnTable.txt getGEO/test-data/MetaTable.txt getGEO/test-data/gmTable.txt getGEO/test-data/input.csv getGEO/tool_dependencies.xml |
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| diff -r cbc8174bd361 -r 983651783ce9 getGEO/.Rhistory --- a/getGEO/.Rhistory Mon Mar 20 06:54:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -??options -options(warn = -1) -+options("download.file.method"="wget") -options("download.file.method"="wget") -options(warn = -1,"download.file.method"="wget") -??getPlatform -??getPlatform |
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| diff -r cbc8174bd361 -r 983651783ce9 getGEO/._.DS_Store |
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| Binary file getGEO/._.DS_Store has changed |
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| diff -r cbc8174bd361 -r 983651783ce9 getGEO/getGEO.R --- a/getGEO/getGEO.R Mon Mar 20 06:54:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,54 +0,0 @@ -require("BiocGenerics", quietly = TRUE) -require("data.table", quietly = TRUE) -require("GEOquery", quietly = TRUE) -require("rtracklayer", quietly = TRUE) -require("FDb.InfiniumMethylation.hg19", quietly = TRUE) - -options("download.file.method.GEOquery"="wget") -options(warn = -1) - -args <- commandArgs(trailingOnly = TRUE) -GSMTable = args[1] -protocol = args[2] -platform = args[3] -Data_Table = args[4] - -TAB = fread(GSMTable) - -if (is.null(TAB)) { - stop("Must specify input files") -} else { - GEODataTable <- getGEO(TAB$ID[1], getGPL = FALSE) - IlmnIDTable <- Table(GEODataTable) - MetaData <- data.frame(Meta(GEODataTable)) - - - write.table(MetaData, protocol, row.names = FALSE, sep = "\t") -} - -hm450.hg19 <- getPlatform() - -IlmnInfo <- - data.table( - IlmnID = names(hm450.hg19), - CHR = as.data.frame(hm450.hg19@seqnames)$value, - BP = as.numeric(hm450.hg19@elementMetadata$probeStart) - ) - - -write.table(IlmnInfo, platform, row.names = FALSE, sep = "\t") - - -if (length(TAB$ID) > 1) { - mysamples <- - do.call("data.table", lapply(TAB$ID[-1], function(x) - Table(getGEO(x, getGPL = FALSE))[, -1])) - - gmSet <- data.table(IlmnIDTable[, -1], mysamples) - -} else { - gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE)) -} - -write.table(gmSet, Data_Table, row.names = FALSE,quote=FALSE,sep="\t") - |
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| diff -r cbc8174bd361 -r 983651783ce9 getGEO/getGEO.xml --- a/getGEO/getGEO.xml Mon Mar 20 06:54:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,39 +0,0 @@ -<tool id="GEO" name="getGEO" version="1.16.2"> - <requirements> - <requirement type="package" version="3.2.1">R</requirement> - </requirements> -<stdio> - <exit_code range="1:" /> - </stdio> - <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$protocol" "$platform" "$Data_Table"</command> - <inputs> - <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable"> - <validator type="empty_field" message="This field is required."/> - </param> - </inputs> - <outputs> - <data format="txt" name="protocol" label="protocol.txt"/> - <data format="txt" name="platform" label="platform.txt"/> - <data format="txt" name="Data_Table" label="Data_Table.txt"/> - </outputs> - <tests> - <test> - <param name="test"> - <element name="test-data"> - <collection type="data"> - <element name="GSMTable" value="test-data/input.csv" /> - </collection> - </element> - </param> - <output format="txt" name="protocol" label="test-data/protocol.txt"/> - <output format="txt" name="platform" label="test-data/platform.txt"/> - <output format="txt" name="Data_Table" label="test-data/Data_Table.txt"/> - </test> - </tests> - <help> -**Description** -</help> -<citations> -GEO -</citations> -</tool> |
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| diff -r cbc8174bd361 -r 983651783ce9 getGEO/test-data/._.DS_Store |
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| Binary file getGEO/test-data/._.DS_Store has changed |
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| diff -r cbc8174bd361 -r 983651783ce9 getGEO/test-data/._input.csv |
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| Binary file getGEO/test-data/._input.csv has changed |
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| diff -r cbc8174bd361 -r 983651783ce9 getGEO/test-data/IlmnTable.txt --- a/getGEO/test-data/IlmnTable.txt Mon Mar 20 06:54:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,485578 +0,0 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| diff -r cbc8174bd361 -r 983651783ce9 getGEO/test-data/MetaTable.txt --- a/getGEO/test-data/MetaTable.txt Mon Mar 20 06:54:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -"channel_count","characteristics_ch1","contact_address","contact_city","contact_country","contact_department","contact_institute","contact_name","contact_zip.postal_code","data_processing","data_row_count","description","extract_protocol_ch1","geo_accession","hyb_protocol","label_ch1","label_protocol_ch1","last_update_date","molecule_ch1","organism_ch1","platform_id","scan_protocol","series_id","source_name_ch1","status","submission_date","supplementary_file","taxid_ch1","title","type" -"1","sample type: melanoma cell line","Barngatan 2B","Lund","Sweden","Dept of Oncology","Lund University","Martin,,Lauss","22185","Raw intensities for methylated (M) and unmethylated (U) signal were extracted from Illumina’s GenomeStudio. Beta-values were calculated as M/(M+U). A total of 496 missing values (melanomas) were imputed using k-nearest neighbor imputation (k=10). For each sample we performed a peak-based correction of Illumina I and II chemical assays. For both assays we smoothed the beta values (Epanechnikov smoothing kernel) to estimate unmethylated and methylated peaks, respectively; and the unmethylated peak was moved to 0 and the methylated peak to 1 using linear scaling, with beta-values in between stretched accordingly. Beta-values below 0 were set back to 0 and values above 1 were set to 1.","485577","melanoma cell line","Genomic DNA was extracted from the biopsies using QIAamp DNA Mini Kit (Qiagen). A total of 500 ng of DNA were used for bisulfite treatment, using the EZ DNA Methylation Kit (Zymo). We hybridized 200 ng in 4 μl to the Infinium Human Methylation450 BeadChip array.","GSM1247787","Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol","Cy5 and Cy3","Standard Illumina Protocol","May 17 2015","genomic DNA","Homo sapiens","GPL13534","Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting","GSE51547","SKMEL3","Public on May 17 2015","Oct 22 2013","NONE","9606","genomic DNA from Sample SKMEL3","genomic" |
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| diff -r cbc8174bd361 -r 983651783ce9 getGEO/test-data/gmTable.txt --- a/getGEO/test-data/gmTable.txt Mon Mar 20 06:54:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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|
| b |
| diff -r cbc8174bd361 -r 983651783ce9 getGEO/test-data/input.csv --- a/getGEO/test-data/input.csv Mon Mar 20 06:54:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -ID,Phenotype -GSM1247787,melanoma -GSM1247784,melanoma -GSM1247733,healthy |
| b |
| diff -r cbc8174bd361 -r 983651783ce9 getGEO/tool_dependencies.xml --- a/getGEO/tool_dependencies.xml Mon Mar 20 06:54:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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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 cbc8174bd361 -r 983651783ce9 getGRsetFromGEO/.Rhistory --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGRsetFromGEO/.Rhistory Wed Mar 22 09:01:06 2017 -0400 |
| [ |
| @@ -0,0 +1,138 @@ +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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| diff -r cbc8174bd361 -r 983651783ce9 getGRsetFromGEO/._.DS_Store |
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| Binary file getGRsetFromGEO/._.DS_Store has changed |
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| diff -r cbc8174bd361 -r 983651783ce9 getGRsetFromGEO/getGRsetFromGEO.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGRsetFromGEO/getGRsetFromGEO.R Wed Mar 22 09:01:06 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] #GSE51547 +output = args[2] #output <- ("GEOdata.txt") + +GEO <- getGenomicRatioSetFromGEO(GSE) + +save(GEO, ascii=TRUE, file=output) + |
| b |
| diff -r cbc8174bd361 -r 983651783ce9 getGRsetFromGEO/getGRsetFromGEO.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGRsetFromGEO/getGRsetFromGEO.xml Wed Mar 22 09:01:06 2017 -0400 |
| b |
| @@ -0,0 +1,36 @@ +<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 cbc8174bd361 -r 983651783ce9 getGRsetFromGEO/test-data/._.DS_Store |
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| Binary file getGRsetFromGEO/test-data/._.DS_Store has changed |
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| diff -r cbc8174bd361 -r 983651783ce9 getGRsetFromGEO/test-data/GEOdata.RData |
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| Binary file getGRsetFromGEO/test-data/GEOdata.RData has changed |
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| diff -r cbc8174bd361 -r 983651783ce9 getGRsetFromGEO/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/getGRsetFromGEO/tool_dependencies.xml Wed Mar 22 09:01:06 2017 -0400 |
| b |
| b'@@ -0,0 +1,267 @@\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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https://depot.galaxyproject.org/software/reshape/reshape_0.8.6.tar.gz\n+ </package>\n+ <package sha256sum="d999620688354c283de5bb305203f5db70271b4dfdc23577cae8c2ba94c9e349">\n+ https://depot.galaxyproject.org/software/quadprog/quadprog_1.5-5.tar.gz\n+ </package>\n+ <package sha256sum="cd26dbd60b2e2060541c4bb579ec1e0f6c262501431460b096b5fef323204432">\n+ https://bioarchive.galaxyproject.org/GEOquery_2.41.0.tar.gz\n+ </package>\n+ <package sha256sum="bee70645c7cc88250761092762a9d293b4644f311047baecf49fde766d3059bc">\n+ https://bioarchive.galaxyproject.org/Biobase_2.35.0.tar.gz\n+ </package>\n+ <package sha256sum="c6133611cc991dfc17410d06a9ddcc6dcff0153bceffdf7d5a9b7dc42f31afa6">\n+ https://depot.galaxyproject.org/software/org.Hs.eg.db/org.Hs.eg.db_3.4.0.tar.gz\n+ </package>\n+ <package sha256sum="cf61732ef9b38ecb6579055d1cd145198ad23a5a9ae4378f94a1494e6c56c884">\n+ https://depot.galaxyproject.org/software/data.table/data.table_1.10.0.tar.gz\n+ </package>\n+ <package 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