Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

changeset 13:8ee4cfdc1a92 draft

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"planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
author proteore
date Thu, 23 Jan 2020 11:02:34 +0000
parents f8d3a8a2f2e5
children 778f7281ccba
files add_expression_HPA.R add_expression_data.xml
diffstat 2 files changed, 8 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/add_expression_HPA.R	Thu Jan 23 10:44:39 2020 +0000
+++ b/add_expression_HPA.R	Thu Jan 23 11:02:34 2020 +0000
@@ -147,8 +147,8 @@
 }
 
 convert_to_previous_header <- function(options){
-    header = c('Gene','description','Evidence','Antibody','RNA tissue specificity','Reliability (IH)','Reliability (IF)','Subcellular location','RNA tissue specific NX')
-    names(header) = c('Gene','description','Evidence','Antibody','RNA tissue category','Reliability (IH)','Reliability (IF)','Subcellular location','RNA TS TPM')
+    header = c('Gene','description','Evidence','Antibody','RNA tissue specificity','Reliability (IH)','Reliability (IF)','Subcellular location','RNA tissue specific NX','TPM max in non-specific')
+    names(header) = c('Gene','description','Evidence','Antibody','RNA tissue category','Reliability (IH)','Reliability (IF)','Subcellular location','RNA TS TPM','TPM max in non-specific')
     options = names(header[which(header %in% options)])
     return(options)
 }
@@ -187,7 +187,11 @@
   # Add expression
   output = args$output
   options = strsplit(args$select, ",")[[1]]
-  if (tail(unlist(strsplit(args$atlas,"/")),1) == "HPA_full_atlas_23-10-2018.tsv"){ options = convert_to_previous_header(options)}
+  if (tail(unlist(strsplit(args$atlas,"/")),1) == "HPA_full_atlas_23-10-2018.tsv"){ 
+      options = convert_to_previous_header(options)
+  } else {
+      options[which(options != 'TPM max in non-specific')]
+      }
   res = add_expression(ids, protein_atlas, options)
   
   # Write output
--- a/add_expression_data.xml	Thu Jan 23 10:44:39 2020 +0000
+++ b/add_expression_data.xml	Thu Jan 23 11:02:34 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="rna_abbased_data" name="Add expression data" version="2020.01.23">
+<tool id="rna_abbased_data" name="Add expression data" version="2020.01.23.1">
 <description> (RNAseq or Immuno-assays)[Human Protein Atlas]
 </description>
 <requirements>