Mercurial > repos > proteore > proteore_expression_rnaseq_abbased
changeset 10:07858c6dbbff draft
"planemo upload commit 330a2527c7e20c4d189a0f1b7a184a8c4610b4b6-dirty"
| author | proteore |
|---|---|
| date | Wed, 22 Jan 2020 15:26:11 +0000 |
| parents | 28d51adf8292 |
| children | 4c27466a4e15 |
| files | add_expression_HPA.R add_expression_data.xml |
| diffstat | 2 files changed, 4 insertions(+), 9 deletions(-) [+] |
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--- a/add_expression_HPA.R Wed Jan 22 15:20:35 2020 +0000 +++ b/add_expression_HPA.R Wed Jan 22 15:26:11 2020 +0000 @@ -1,11 +1,7 @@ # Read file and return file content as data.frame read_file <- function(path,header){ - file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE) - if (inherits(file,"try-error")){ - stop("File not found !") - }else{ - return(file) - } + file <- read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F) + return(file) } #convert a string to boolean @@ -175,8 +171,7 @@ check_ensembl_geneids(ids) # Read protein atlas - protein_atlas = args$atlas - protein_atlas = read_file(protein_atlas, T) + protein_atlas = read_file(args$atlas, T) # Add expression output = args$output
--- a/add_expression_data.xml Wed Jan 22 15:20:35 2020 +0000 +++ b/add_expression_data.xml Wed Jan 22 15:26:11 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="rna_abbased_data" name="Add expression data" version="2020.01.22.2"> +<tool id="rna_abbased_data" name="Add expression data" version="2020.01.22.3"> <description> (RNAseq or Immuno-assays)[Human Protein Atlas] </description> <requirements>