# HG changeset patch
# User proteore
# Date 1588255582 0
# Node ID 03f3d7d3acfc912cbc8b299227f388613aee7a37
# Parent  82cec53a3123aa86c1aafa3ba38f22152e947c23
"planemo upload commit 9a871575622a1318adc64dad63fa5e3a9d2a19fd-dirty"

diff -r 82cec53a3123 -r 03f3d7d3acfc Get_ms-ms_observations.R
--- a/Get_ms-ms_observations.R	Thu Jun 27 04:16:06 2019 -0400
+++ b/Get_ms-ms_observations.R	Thu Apr 30 14:06:22 2020 +0000
@@ -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="/home/dchristiany/proteore_project/ProteoRE/tools/Get_ms-ms_observations/args.Rda")
-  #load("/home/dchristiany/proteore_project/ProteoRE/tools/Get_ms-ms_observations/args.Rda")
-  
   # Extract input
   input_type = args$input_type
   if (input_type == "list") {
diff -r 82cec53a3123 -r 03f3d7d3acfc Get_ms-ms_observations.xml
--- a/Get_ms-ms_observations.xml	Thu Jun 27 04:16:06 2019 -0400
+++ b/Get_ms-ms_observations.xml	Thu Apr 30 14:06:22 2020 +0000
@@ -1,7 +1,7 @@
-<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.06.27">
-    <description>[Peptide Atlas]</description>
+<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:" />