diff AffyQCnormalization.xml @ 8:7f74250a083d draft

planemo upload

--- a/AffyQCnormalization.xml	Wed Apr 12 03:47:05 2017 -0400
+++ b/AffyQCnormalization.xml	Wed May 10 04:12:26 2017 -0400
@@ -1,22 +1,27 @@
 <tool id="QCnormalization" name="QCnormalization" version="0.1.0">
 	<description>Quality control and normalization of affymetrix expression data</description>
-	<requirements>
+	<stdio>
+        <exit_code range="1:" />
+        
+		<regex match="Warning"
+           source="both"
+           level="warning"
+		/>
+     </stdio>
+    <requirements>
 	  <!--container type="docker">sblanck/smat</container-->
 	  <requirement type="package" version="0.1.0">r-smagexp</requirement>
 	</requirements>
-	<command interpreter="python">
+	<command>
 		<![CDATA[
-		stderr_wrapper.py Rscript 
+		Rscript 
 		${__tool_directory__}/AffyQCnormalization.R
-		   	#for $input in $inputs
-                "${input}"
-			    "${input.name}"
-     		#end for
-			"${normalization}"
-			$result_export_eset
-       		$result_html
-			$result_html.files_path
-		/${__tool_directory__}/AffyQCnormalization_tpl.html
+	    	--input "#for $input in $inputs# $input;$input.name, #end for#"
+            --normalization ${normalization}
+			--rdataoutput $result_export_eset
+       		--htmloutput $result_html
+			--htmloutputpath $result_html.files_path
+		    --htmltemplate ${__tool_directory__}/AffyQCnormalization_tpl.html
 		]]>
 		</command>