changeset 0:874a905405db draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/csv2rdatatrain.R	Fri Jan 22 03:19:46 2016 -0500
@@ -0,0 +1,29 @@
+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.factor(file[,col]))
+
+  if(levels(file[,col])[1] != ""){
+    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])
+
+
+
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool1V2.xml	Fri Jan 22 03:19:46 2016 -0500
@@ -0,0 +1,39 @@
+<tool id="AdsmkdqaddodfdalV2" name="Prepare input file">
+<description>
+This Tool Converts Input csv File into RData Which Is Further Used for Model Building
+ </description>
+ <!--command interpreter="bash">step1.sh $file1 $output1 </command-->
+ <requirements>
+       <requirement type="set_environment">CARET_TOOL1_PATH</requirement>
+     <requirement type="set_environment">R_ROOT_DIR</requirement>
+    <requirement type="package" version="3.2.0">R</requirement>
+    </requirements>
+ <command interpreter="Rscript">csv2rdatatrain.R $file1 $RData </command>
+ <inputs>
+ <param format="csv" name="file1" type="data" label="Select file containing training data" help="CSV format" />
+ </inputs>
+ <outputs>
+ <data format="RData" name="RData" label="Input RData" />
+ </outputs>
+<help>
+.. class:: infomark
+
+**Input "csv file" format must be as given below :**
+
+
+"",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.     
+
+
+</help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jan 22 03:19:46 2016 -0500
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tool_dependency>
+
+<set_environment version="1.0">
+        <environment_variable name="CARET_TOOL1_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>   
+        </set_environment>
+   
+</tool_dependency>