Mercurial > repos > proteore > proteore_go_terms_enrich_comparison

changeset 22:c4eacadcff2d draft

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planemo upload commit c9d70181a2b587e53dcc4b5885b74b625def6b8c
author proteore
date Mon, 18 Nov 2019 14:34:04 +0000
parents 82f7c56f575d
children cb5f8b6f86bd
files GO_terms_enrich_comparison.R GO_terms_enrich_comparison.xml
diffstat 2 files changed, 16 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/GO_terms_enrich_comparison.R	Thu Nov 14 16:25:59 2019 +0000
+++ b/GO_terms_enrich_comparison.R	Mon Nov 18 14:34:04 2019 +0000
@@ -26,6 +26,7 @@
   
   ## Collect arguments
   args <- commandArgs(TRUE)
+  #value = character vector of length=nb of arguments
   
   ## Default setting when no arguments passed
   if(length(args) < 1) {
@@ -273,11 +274,20 @@
   #to get the args of the command line
   args=get_args()  
 
+  #saved
   l<-list()
   for(i in 1:args$nb){
     ids<-get_ids(args$input, args$inputtype, args$header, args$column) 
     l[[i]]<-ids
   }
+  #saved
+
+  for(i in 1:args$nb){
+
+    
+
+  }
+
   
   ont = strsplit(args$ont, ",")[[1]] 
   org=args$org
--- a/GO_terms_enrich_comparison.xml	Thu Nov 14 16:25:59 2019 +0000
+++ b/GO_terms_enrich_comparison.xml	Mon Nov 18 14:34:04 2019 +0000
@@ -1,4 +1,4 @@
-<tool id="go_terms_enrich_comparison" name="GO terms enrich comparison " version="2019.11.14.12">
+<tool id="go_terms_enrich_comparison" name="GO terms enrich comparison " version="2019.11.14.13">
     <description>(Human, Mouse, Rat)[clusterProfiler]</description>
     <requirements>
         <requirement type="package">R</requirement>
@@ -15,15 +15,15 @@
 
         --nb=$len($lists)
 
-        #for $list in $lists
+        #for $index, $list in enumerate($lists)
         		    
-		    #if $list.input.ids == "file"
-		        --input="$list.input.file" --name="$list.list_name" --inputtype="file" --header="$list.input.header" --column="$list.input.ncol" 
+            #if $list.input.ids == "file"
+		        --input.$index="$list.input.file" --name="$list.list_name" --inputtype="file" --header="$list.input.header" --column="$list.input.ncol" 
             #else
-                --input="$list.input.txt" --name="$list.list_name" --inputtype="text" 
+                --input.$index="$list.input.txt" --name="$list.list_name" --inputtype="text" 
  		    #end if
             
-        #end for 
+        #end for
 
         --org="$species"
         --ont="$ontology"