# HG changeset patch
# User proteore
# Date 1544691581 18000
# Node ID cfcc7a780991152de4c1f005fa60abc6bdca4830
# Parent 6fc8d303bcf130d58aaba5ed0bbe48a474e08041
planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
diff -r 6fc8d303bcf1 -r cfcc7a780991 Build_tissue-specific_expression_dataset.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Build_tissue-specific_expression_dataset.R Thu Dec 13 03:59:41 2018 -0500
@@ -0,0 +1,76 @@
+
+
+select_HPAimmunohisto<-function(hpa_ref, tissue, level, reliability) {
+ HPA.normal = read.table(hpa_ref,header=TRUE,sep="\t",stringsAsFactors = FALSE)
+ if (tissue == "tissue") {
+ tissue <- unique(HPA.normal$Tissue)
+ }
+ if (level == "level") {
+ level <- unique(HPA.normal$Level)
+ }
+ if (reliability == "reliability") {
+ reliability <- unique(HPA.normal$Reliability)
+ }
+ res.imm <- subset(HPA.normal, Tissue%in%tissue & Level%in%level & Reliability%in%reliability)
+ return(res.imm)
+}
+
+
+
+select_HPARNAseq<-function(hpa_ref, sample) {
+ HPA.rnaTissue = read.table(hpa_ref,header=TRUE,sep="\t",stringsAsFactors = FALSE)
+ res.rna <- subset(HPA.rnaTissue, Sample%in%sample, select = -c(Unit))
+ colnames(res.rna)[which(colnames(res.rna) == 'Value')] <- 'Value (TPM unit)'
+ return(res.rna)
+}
+
+main <- function() {
+ args <- commandArgs(TRUE)
+ if(length(args)<1) {
+ args <- c("--help")
+ }
+
+ # Help section
+ if("--help" %in% args) {
+ cat("Selection and Annotation HPA
+ Arguments:
+ --data_source: immuno/rnaseq
+ --hpe_ref: path to reference file normal_tissue.tsv/rna_tissue.tsv)
+ if immuno:
+ --tissue: list of tissues
+ --level: Not detected, Low, Medium, High
+ --reliability: Supported, Approved, Enhanced, Uncertain
+ if rnaseq:
+ --sample: Sample tissues
+ --output: output filename \n")
+ q(save="no")
+ }
+
+ # Parse arguments
+ parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
+ argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
+ args <- as.list(as.character(argsDF$V2))
+ names(args) <- argsDF$V1
+
+ # Extract options
+ data_source = args$data_source
+ hpa_ref = args$hpa_ref
+ if (data_source == "immuno") {
+ tissue = strsplit(args$tissue, ",")[[1]]
+ level = strsplit(args$level, ",")[[1]]
+ reliability = strsplit(args$reliability, ",")[[1]]
+ # Calculation
+ res = select_HPAimmunohisto(hpa_ref, tissue, level, reliability)
+ }
+ else if (data_source == "rnaseq") {
+ sample = strsplit(args$sample, ",")[[1]]
+ # Calculation
+ res = select_HPARNAseq(hpa_ref, sample)
+ }
+
+ # Write output
+ output = args$output
+ write.table(res, output, sep = "\t", quote = FALSE, row.names = FALSE)
+}
+
+main()
diff -r 6fc8d303bcf1 -r cfcc7a780991 Build_tissue-specific_expression_dataset.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/Build_tissue-specific_expression_dataset.xml Thu Dec 13 03:59:41 2018 -0500
@@ -0,0 +1,210 @@
+
+[Human Protein Atlas](no input required)
+
+ R
+
+
+
+
+
+ $__tool_directory__/Build_tissue-specific_expression_dataset.R
+ --data_source="$input.data_source"
+ #if $input.data_source == "immuno"
+ --hpa_ref="$__tool_directory__/normal_tissue.tsv"
+ --tissue="$input.normal_tissue"
+ --level="$input.level"
+ --reliability="$input.reliability"
+ #else if $input.data_source == "rnaseq"
+ --hpa_ref="$__tool_directory__/rna_tissue.tsv"
+ --sample="$input.sample"
+ #end if
+ --output="$output"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 6fc8d303bcf1 -r cfcc7a780991 RetrieveFromHPA.R
--- a/RetrieveFromHPA.R Mon Nov 12 11:19:38 2018 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-
-
-select_HPAimmunohisto<-function(hpa_ref, tissue, level, reliability) {
- HPA.normal = read.table(hpa_ref,header=TRUE,sep="\t",stringsAsFactors = FALSE)
- if (tissue == "tissue") {
- tissue <- unique(HPA.normal$Tissue)
- }
- if (level == "level") {
- level <- unique(HPA.normal$Level)
- }
- if (reliability == "reliability") {
- reliability <- unique(HPA.normal$Reliability)
- }
- res.imm <- subset(HPA.normal, Tissue%in%tissue & Level%in%level & Reliability%in%reliability)
- return(res.imm)
-}
-
-
-
-select_HPARNAseq<-function(hpa_ref, sample) {
- HPA.rnaTissue = read.table(hpa_ref,header=TRUE,sep="\t",stringsAsFactors = FALSE)
- res.rna <- subset(HPA.rnaTissue, Sample%in%sample, select = -c(Unit))
- colnames(res.rna)[which(colnames(res.rna) == 'Value')] <- 'Value (TPM unit)'
- return(res.rna)
-}
-
-main <- function() {
- args <- commandArgs(TRUE)
- if(length(args)<1) {
- args <- c("--help")
- }
-
- # Help section
- if("--help" %in% args) {
- cat("Selection and Annotation HPA
- Arguments:
- --data_source: immuno/rnaseq
- --hpe_ref: path to reference file normal_tissue.tsv/rna_tissue.tsv)
- if immuno:
- --tissue: list of tissues
- --level: Not detected, Low, Medium, High
- --reliability: Supported, Approved, Enhanced, Uncertain
- if rnaseq:
- --sample: Sample tissues
- --output: output filename \n")
- q(save="no")
- }
-
- # Parse arguments
- parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
- argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
- args <- as.list(as.character(argsDF$V2))
- names(args) <- argsDF$V1
-
- # Extract options
- data_source = args$data_source
- hpa_ref = args$hpa_ref
- if (data_source == "immuno") {
- tissue = strsplit(args$tissue, ",")[[1]]
- level = strsplit(args$level, ",")[[1]]
- reliability = strsplit(args$reliability, ",")[[1]]
- # Calculation
- res = select_HPAimmunohisto(hpa_ref, tissue, level, reliability)
- }
- else if (data_source == "rnaseq") {
- sample = strsplit(args$sample, ",")[[1]]
- # Calculation
- res = select_HPARNAseq(hpa_ref, sample)
- }
-
- # Write output
- output = args$output
- write.table(res, output, sep = "\t", quote = FALSE, row.names = FALSE)
-}
-
-main()
diff -r 6fc8d303bcf1 -r cfcc7a780991 retrieve_from_hpa.xml
--- a/retrieve_from_hpa.xml Mon Nov 12 11:19:38 2018 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,210 +0,0 @@
-
-(no input required)
-
- R
-
-
-
-
-
- $__tool_directory__/RetrieveFromHPA.R
- --data_source="$input.data_source"
- #if $input.data_source == "immuno"
- --hpa_ref="$__tool_directory__/normal_tissue.tsv"
- --tissue="$input.normal_tissue"
- --level="$input.level"
- --reliability="$input.reliability"
- #else if $input.data_source == "rnaseq"
- --hpa_ref="$__tool_directory__/rna_tissue.tsv"
- --sample="$input.sample"
- #end if
- --output="$output"
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-