changeset 1:51e37d436e76 draft

Uploaded

--- a/R_test.R	Tue Oct 28 06:25:06 2014 -0400
+++ b/R_test.R	Tue Oct 28 06:38:53 2014 -0400
@@ -1,16 +1,33 @@
 systemUser <- system("whoami",T)
 rVersion <- R.version.string
 
-cat( "Starting R_test\n" )	
+cat( "-----\n starting\n-----\n")
 cat( rVersion, "\n" )
 cat( systemUser, "\n" )
 
-#qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
+cmdLineArgs <- commandArgs(TRUE)
+config      <- cmdLineArgs[1]
+source(config) ## retrieves variables
 
+png( pngFile )
+	plot( 1,1, main="PNG test" )
+dev.off()
+## -----
+## check loading of packages
+## -----
 packs <- c()
 for ( pack in packs ){
 	catMsg( c("Loading ", pack) )
 	library( pack )
 }
 
+## -----
+## get package versions
+## -----
+#qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
+cat( "-----\n session info\n-----\n")
+sessionInfo()
+
+
+## -----
 q(status=0)

--- a/R_test.xml	Tue Oct 28 06:25:06 2014 -0400
+++ b/R_test.xml	Tue Oct 28 06:38:53 2014 -0400
@@ -11,26 +11,29 @@
   </command>
 
   <stdio>
-    <!-- Anything higher than 0 means the R script didnt finish (correctly) -->
-    <!-- Because different R packages deal with err/warn differently unable to waterproof this -->
     <exit_code range="1:" level="fatal" description="R script didnt finish correctly, check log" />
   </stdio>
   
   <inputs>
     
-    <!-- Job name: must contain non-whitespace chars -->
     <param name="jobName" type="text" optional="false" label="Analysis/ouput name" help="Supply a name for the outputs to remind you what they contain" value="TEST">
       <validator type="empty_field" />
       <validator type="regex" message="This field should contain some non-whitespace character">.*\S</validator>
     </param>
 
   </inputs>
+  
+  <configfiles>
+    <configfile name="qdnaseq_cfg">
+"${jobName}"  -> outputName
+"${htmlFile}" -> htmlFile
+"${pngFile}"  -> pngFile
+    </configfile>
+  </configfiles>
 
   <outputs>
-
-    <!-- main output is a html report -->
-    <!-- ...but there can be more outputs using the id of the htmlFile output -->
-    <data format="html" name="htmlFile" label="rTest: ${jobName}" />
+    <data format="html" name="htmlFile" label="rTestHTML: ${jobName}" />
+    <data format="png" name="pngFile" label="rTestPNG: ${jobName}" />
 
   </outputs>
 
@@ -39,7 +42,7 @@
 
 **Introduction**
 
-This is just a tiny package to test R install
+This is just a tiny package to test R dependecies
   </help>
 
 </tool>