Mercurial > repos > proteore > proteore_clusterprofiler

changeset 8:b29255864039 draft

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planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty
author proteore
date Fri, 21 Dec 2018 04:12:32 -0500
parents 4609346d8108
children 2f67202ffdb3
files GO-enrich.R cluster_profiler.xml
diffstat 2 files changed, 6 insertions(+), 5 deletions(-) [+]
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line diff
--- a/GO-enrich.R	Tue Dec 18 09:21:32 2018 -0500
+++ b/GO-enrich.R	Fri Dec 21 04:12:32 2018 -0500
@@ -152,13 +152,14 @@
   argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
   args <- as.list(as.character(argsDF$V2))
   names(args) <- argsDF$V1
+  
+  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
+  #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
+  
   plot = unlist(strsplit(args$plot,","))
   go_represent=str2bool(args$go_represent)
   go_enrich=str2bool(args$go_enrich)
   
-  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
-  #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
-  
   suppressMessages(library(args$species, character.only = TRUE, quietly = TRUE))
   
   # Extract OrgDb
@@ -232,7 +233,7 @@
         # Get file content
         universe_file = read_file(universe_filename, universe_header)
         # Extract Protein IDs list
-        universe <- sapply(universe_file[,universe_ncol], function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE)
+        universe <- unlist(sapply(universe_file[,universe_ncol], function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
       }
       universe_id_type = args$universe_id_type
       ##to initialize
--- a/cluster_profiler.xml	Tue Dec 18 09:21:32 2018 -0500
+++ b/cluster_profiler.xml	Fri Dec 21 04:12:32 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.18">
+<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.21">
     <description>(Human, Mouse, Rat)[clusterProfiler]</description>
     <requirements>
         <requirement type="package" version="3.4.1">R</requirement>