Mercurial > repos > proteore > proteore_expression_rnaseq_abbased

comparison add_expression_HPA.R @ 14:778f7281ccba draft

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"planemo upload commit 58e072579a4be282c00b54ebb88fbc59e189a7ed-dirty"
author proteore
date Thu, 23 Jan 2020 11:10:19 +0000
parents 8ee4cfdc1a92
children 64681d9836e7
comparison
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13:8ee4cfdc1a92 14:778f7281ccba
156 main = function() { 156 main = function() {
157 157
158 args = get_args() 158 args = get_args()
159 159
160 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda") 160 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
161 #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda") 161 load("/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
162 162
163 inputtype = args$inputtype 163 inputtype = args$inputtype
164 if (inputtype == "copypaste") { 164 if (inputtype == "copypaste") {
165 ids = strsplit(args$input, "[ \t\n]+")[[1]] 165 ids = strsplit(args$input, "[ \t\n]+")[[1]]
166 } else if (inputtype == "tabfile") { 166 } else if (inputtype == "tabfile") {
188 output = args$output 188 output = args$output
189 options = strsplit(args$select, ",")[[1]] 189 options = strsplit(args$select, ",")[[1]]
190 if (tail(unlist(strsplit(args$atlas,"/")),1) == "HPA_full_atlas_23-10-2018.tsv"){ 190 if (tail(unlist(strsplit(args$atlas,"/")),1) == "HPA_full_atlas_23-10-2018.tsv"){
191 options = convert_to_previous_header(options) 191 options = convert_to_previous_header(options)
192 } else { 192 } else {
193 options[which(options != 'TPM max in non-specific')] 193 options = options[which(options != 'TPM max in non-specific')]
194 } 194 }
195 res = add_expression(ids, protein_atlas, options) 195 res = add_expression(ids, protein_atlas, options)
196 196
197 # Write output 197 # Write output
198 if (is.null(res)) { 198 if (is.null(res)) {