Mercurial > repos > proteore > proteore_pathview_mapping

changeset 7:b617d4bbebf8 draft

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planemo upload commit 41ba6f74dfad14f894dbe396fc765893b971b5ae-dirty
author proteore
date Mon, 27 Aug 2018 11:21:34 -0400
parents 059f17f98ab5
children 33c9bd75882a
files PathView.R Pathview.xml
diffstat 2 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/PathView.R	Fri Aug 24 08:51:20 2018 -0400
+++ b/PathView.R	Mon Aug 27 11:21:34 2018 -0400
@@ -63,9 +63,6 @@
     q(save="no")
   }
   
-  
-  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda")
-  #load("/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda")
   parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
   argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
   args <- as.list(as.character(argsDF$V2))
@@ -88,6 +85,10 @@
 
 #### hsa00010 -> 00010
 remove_kegg_prefix <- function(x){
+  x = gsub(":","",x)
+  if (substr(x,1,4) == 'path'){
+    x=substr(x,5,nchar(x))
+  }
   if (is.letter(substr(x,1,3))){
     x <- substr(x,4,nchar(x))
   }
@@ -121,7 +122,7 @@
 #read input file or list
 if (!is.null(args$input)){
   tab <- read_file(args$input,header)
-  tab <- tab[!apply(is.na(tab) | tab == "", 1, all),] #delete empty rows
+  tab <- data.frame(tab[which(tab[ncol]!=""),])
 } else {
   tab <- data.frame(id_list)
   ncol=1
--- a/Pathview.xml	Fri Aug 24 08:51:20 2018 -0400
+++ b/Pathview.xml	Mon Aug 27 11:21:34 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.08.22">
+<tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.08.27">
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
     </requirements>