diff ImportDataFromMatrix.xml @ 8:7f74250a083d draft

planemo upload

--- a/ImportDataFromMatrix.xml	Wed Apr 12 03:47:05 2017 -0400
+++ b/ImportDataFromMatrix.xml	Wed May 10 04:12:26 2017 -0400
@@ -4,18 +4,18 @@
 	  	<!--container type="docker">sblanck/smagexp</container-->
 		<requirement type="package" version="0.1.0">r-smagexp</requirement>		
 	</requirements>
-	<command interpreter="python">
+	<command>
 		<![CDATA[ 
-		stderr_wrapper.py Rscript 
+		Rscript --vanilla 
 		${__tool_directory__}/ImportDataFromMatrix.R
-		    $input
-			$normalization
-			$conditions
-			$annotations
-			$result_export_eset
-       		$result_html
-			$result_html.files_path
-		${__tool_directory__}/ImportDataFromMatrix_tpl.html
+		    --input $input
+			--normalization $normalization
+			--conditions $conditions
+			--annotations $annotations
+			--rdataoutput $result_export_eset
+       		--htmloutput $result_html
+			--htmloutputpath $result_html.files_path
+			--htmltemplate ${__tool_directory__}/ImportDataFromMatrix_tpl.html
 		]]>		
 		</command>
 		
@@ -49,6 +49,7 @@
 Header of input tabular text file
 ::
 
+
 ""	"GSM80460"	"GSM80461"	"GSM80462"	"GSM80463"	"GSM80464"
 "1007_s_at"	-0.0513991525066443	0.306845500314283	0.0854246562526777	-0.142417044615852	0.0854246562526777
 "1053_at"	-0.187707155126729	-0.488026018218199	-0.282789700980404	0.160920188181103	0.989865622866287
@@ -62,7 +63,6 @@
 The .cond file should look like this 
 ::
 
- Sample ID 	Condition			Description
  GSM80460	series of 16 tumors	GSM80460 OSCE-2T SERIES OF 16 TUMORS
  GSM80461	series of 16 tumors	GSM80461 OSCE-4T Series of 16 Tumors
  GSM80462	series of 16 tumors	GSM80462 OSCE-6T Series of 16 Tumors