changeset 0:49d7eb9e1092 draft default tip

planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/csv2rdata.R	Thu May 31 11:40:01 2018 -0400
@@ -0,0 +1,28 @@
+args <- commandArgs(TRUE)
+
+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/csv2rdata.xml	Thu May 31 11:40:01 2018 -0400
@@ -0,0 +1,51 @@
+<tool id="csv2rdata" name="Prepare input file" version="1.0">
+    <description>
+         Converts input csv file into RData format
+    </description>
+
+    <requirements>
+        <requirement type="package" version="3.2.1">R</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+
+    <command interpreter="Rscript">csv2rdata.R $file1 $RData </command>
+
+    <inputs>
+	    <param name="file1" type="data" format="csv"  label="Select file containing training data" help="CSV format" />
+    </inputs>
+
+    <outputs>
+	    <data name="RData" format="rdata" label="Input.rdata" />
+    </outputs>
+
+    <tests>
+	<test>
+           <param  name="file1" value="non_redundant.csv" />
+           <output name="RData" file="desc.rdata" compare="sim_size" delta="50000" />
+        </test>
+    </tests>
+
+    <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	Thu May 31 11:40:01 2018 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+   <package name="R" version="3.2.1">
+          <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu/" />
+   </package>
+</tool_dependency>