# HG changeset patch
# User deepakjadmin
# Date 1453490019 18000
# Node ID 8b939f621c64c341737b2671a16236f79221148b
Uploaded
diff -r 000000000000 -r 8b939f621c64 csv2rdatatrain.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/csv2rdatatrain.R Fri Jan 22 14:13:39 2016 -0500
@@ -0,0 +1,25 @@
+args <- commandArgs(TRUE)
+####source("/home/galaxy/galaxy-dist/tools/mpdstools/tool1/csv2rdatatrain2.R")
+
+csv2rdatatrain <- function(arg1,arg2){ file <- read.csv(arg1,row.names =1, header=T)
+ col <- ncol(file)
+ stopifnot(is.null(file) | col > 2 )
+
+ #cat("the Outcome column is not a factor vector.\n",file=stderr())
+ stopifnot(is.numeric(file[,col]))
+
+ # if(is.numeric(file[,col]) {
+ dataX <- file[,1:(col-1)]
+ dataY <- file[,col]
+ stopifnot(nrow(dataX) == length(dataY))
+ save(dataX,dataY,file=arg2)
+ # }else { cat("the Outcome column has less number of entry than number of compounds.please check input file.\n",file=stderr())
+ # }
+ }
+
+csv2rdatatrain(args[1],args[2])
+
+
+
+
+
diff -r 000000000000 -r 8b939f621c64 tool1reg.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool1reg.xml Fri Jan 22 14:13:39 2016 -0500
@@ -0,0 +1,39 @@
+
+
+This Tool Converts Input csv File into RData Which Is Further Used for Model Building
+
+
+
+ CARET_REG_TOOL1_PATH
+ R_ROOT_DIR
+ R
+
+ csv2rdatatrain.R $file1 $RData
+
+
+
+
+
+
+
+.. class:: infomark
+
+**Input "csv file" format must be as given below :**
+
+
+Name,feature1,feaure2,feature3,..,activity
+
+
+cpd1,623,0.4,3.4,..,Active
+
+cpd2,234,0.9,5.6,..,Inactive
+
+cpd3,567,0.5,3.14,..,Active
+
+cpd4,231,0.1,1.2,..,Inactive
+
+here "cpd" stands for name or id of a compound. It is rowname with no column header.
+
+
+
+
diff -r 000000000000 -r 8b939f621c64 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Jan 22 14:13:39 2016 -0500
@@ -0,0 +1,10 @@
+
+
+
+
+ $REPOSITORY_INSTALL_DIR
+
+
+
+
+