# HG changeset patch
# User deepakjadmin
# Date 1443176340 14400
# Node ID 463a876ec2cf786715e90e1f1b0799da6c5aaefc

Uploaded

diff -r 000000000000 -r 463a876ec2cf carettest.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/carettest.xml	Fri Sep 25 06:19:00 2015 -0400
@@ -0,0 +1,23 @@
+<tool id="danmofdgk03dls" name="R 3.2.0 caret installation test" version="1.0.0">
+  <description>R version and installation test</description>
+<requirements>
+     <requirement type="set_environment">R_ROOT_DIR</requirement>
+    <requirement type="package" version="3.2.0">R</requirement>
+    <requirement type="package" version="1.0.0">caret-tools</requirement>
+</requirements>
+  <command>   	 GALAXY_ROOT_DIR=`pwd`; 
+  		 echo \$GALAXY_ROOT_DIR &gt; $log 2&gt;&amp;1;
+                 cd ../../../../;
+                 GALAXY_ROOT_DIR=`pwd`;
+                 echo \$GALAXY_ROOT_DIR &gt; $log 2&gt;&amp;1;
+                 \$R_ROOT_DIR/bin/Rscript \${GALAXY_ROOT_DIR}/tools/toop2/test.R $output  &gt; $log 2&gt;&amp;1
+   </command>
+  <outputs>
+    <data type="data" format="RData" name="output" label ="R-environment" />
+    <data format="txt" name="log" label ="packages loaded" />
+  </outputs>
+  <help>
+ 
+  </help>
+</tool>
+
diff -r 000000000000 -r 463a876ec2cf test.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test.R	Fri Sep 25 06:19:00 2015 -0400
@@ -0,0 +1,10 @@
+args <- commandArgs(T)
+arg1 <- args[1] ## Reae Input prediction file
+library("Rcpp")
+library("Hmisc")
+library("caret")
+library("randomForest")
+library("e1071")
+libray("pROC")
+asd <- sessionInfo()
+save(asd,file=arg1)
diff -r 000000000000 -r 463a876ec2cf tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Sep 25 06:19:00 2015 -0400
@@ -0,0 +1,292 @@
+<?xml version="1.0"?>
+<tool_dependency>
+   <package name="R" version="3.2.0">
+        <repository changeset_revision="d973c8e9b29e" name="package_r_3_2_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="caret-tools" version="1.0.0">
+        <install version="1.0">
+            <actions>
+		<action type="setup_r_environment">
+			<repository changeset_revision="d973c8e9b29e" name="package_r_3_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                          <package name="R" version="3.2.0" />
+                        </repository>
+				<!--package>https://bioarchive.galaxyproject.org/limma_3.25.3.tar.gz?raw=true</package>
+				<package>http://bioconductor.org/packages/release/bioc/src/contrib/edgeR_3.10.2.tar.gz?raw=true</package>
+				<package>https://cran.r-project.org/src/contrib/Rcpp_0.12.1.tar.gz?raw=true</package-->
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