Mercurial > repos > proteore > proteore_tissue_specific_expression_data
changeset 9:8e75580b7d39 draft
"planemo upload commit 2e48dad9436cb087acaea82977d76544b04344f7-dirty"
| author | proteore |
|---|---|
| date | Mon, 03 Feb 2020 09:55:02 +0000 |
| parents | 5dfe3d971bd2 |
| children | c13a9112a345 |
| files | Build_tissue-specific_expression_dataset.R Build_tissue-specific_expression_dataset.xml proteore_protein_atlas_rna_tissue.loc.sample |
| diffstat | 3 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/Build_tissue-specific_expression_dataset.R Mon Feb 03 09:12:42 2020 +0000 +++ b/Build_tissue-specific_expression_dataset.R Mon Feb 03 09:55:02 2020 +0000 @@ -17,6 +17,7 @@ select_HPARNAseq<-function(hpa_ref, sample) { HPA.rnaTissue = read.table(hpa_ref,header=TRUE,sep="\t",stringsAsFactors = FALSE) + names(HPA.rnaTissue) = sapply(names(HPA.rnaTissue), function(string) gsub('Sample','Tissue',string),USE.NAMES = F) res.rna <- subset(HPA.rnaTissue, Tissue%in%sample) if ("Unit" %in% names(res.rna)){ res.rna = subset(res.rna, select = -Unit) @@ -56,7 +57,6 @@ # Extract options data_source = args$data_source - names(data_source) = sapply(names(data_source), function(string) gsub('Sample','Tissue',string),USE.NAMES = F) hpa_ref = args$hpa_ref if (data_source == "IHC") { tissue = strsplit(args$tissue, ",")[[1]]
--- a/Build_tissue-specific_expression_dataset.xml Mon Feb 03 09:12:42 2020 +0000 +++ b/Build_tissue-specific_expression_dataset.xml Mon Feb 03 09:55:02 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2020.02.03.1"> +<tool id="retrieve_from_hpa" name="Build tissue-specific expression dataset" version="2020.02.03.2"> <description>[Human Protein Atlas]</description> <requirements> <requirement type="package" version="3.4.1">R</requirement>
--- a/proteore_protein_atlas_rna_tissue.loc.sample Mon Feb 03 09:12:42 2020 +0000 +++ b/proteore_protein_atlas_rna_tissue.loc.sample Mon Feb 03 09:55:02 2020 +0000 @@ -1,2 +1,2 @@ #<id> <release> <name> <tissue> <value> -9979818977 HPA_RNA_23-10-2018 HPA RNA 23/10/2018 HPA_rna_tissue tool-data/HPA_rna_tissue_23-10-2018.tsv +9979818977 HPA_RNA_23-10-2018 HPA rna tissue 23/10/2018 HPA_rna_tissue tool-data/HPA_rna_tissue_23-10-2018.tsv