# HG changeset patch
# User proteore
# Date 1588577376 14400
# Node ID ef723082fc547fe7784b92cd08ab7cd736d24359
# Parent  14c890ff105a5a8cf3f67cbfc6a59973a3140546
"planemo upload commit b061341e1157cccd90e33b945bc17705880b3e57"

diff -r 14c890ff105a -r ef723082fc54 Get_ms-ms_observations.R
--- a/Get_ms-ms_observations.R	Mon May 04 03:18:37 2020 -0400
+++ b/Get_ms-ms_observations.R	Mon May 04 03:29:36 2020 -0400
@@ -77,12 +77,9 @@
 }
 
 clean_ids <- function(ids){
-  
-  ids = gsub(" ","",ids)
-  ids = ids[which(ids!="")]
-  ids = ids[which(ids!="NA")]
-  ids = ids[!is.na(ids)]
- 
+  ids = gsub(" ",NA,ids)
+  ids = gsub("^$|^ $", NA, ids)
+  ids = gsub("NA",NA,ids)
   return(ids) 
 }
 
@@ -109,9 +106,6 @@
   args <- as.list(as.character(argsDF$V2))
   names(args) <- argsDF$V1
   
-  #save(args,file="/Users/David/work/ProteoRE/tools/Get_ms-ms_observations/args.Rda")
-  load("/Users/David/work/ProteoRE/tools/Get_ms-ms_observations/args.Rda")
-  
   # Extract input
   input_type = args$input_type
   if (input_type == "list") {
diff -r 14c890ff105a -r ef723082fc54 Get_ms-ms_observations.xml
--- a/Get_ms-ms_observations.xml	Mon May 04 03:18:37 2020 -0400
+++ b/Get_ms-ms_observations.xml	Mon May 04 03:29:36 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2020.01.23">
+<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2020.04.30">
     <description>[Human Peptide Atlas]</description>
     <requirements>
-        <requirement type="package" version="3.4.1">R</requirement>
+        <requirement type="package" version="3.6.1">r-base</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />