# HG changeset patch
# User sblanck
# Date 1491983110 14400
# Node ID 5d25fe2fcab2a988347c7684503f8d8e14ecc4bc
# Parent  2c9e44ff68dc3d49480a6f42ddbbf4cfb7be9554
use optparse

diff -r 2c9e44ff68dc -r 5d25fe2fcab2 Analyse.xml
--- a/Analyse.xml	Wed Apr 12 03:44:54 2017 -0400
+++ b/Analyse.xml	Wed Apr 12 03:45:10 2017 -0400
@@ -1,25 +1,26 @@
 <tool id="LimmaAnalyse" name="Limma analysis" version="0.3.0">
 	<description>Perform gene expression analysis thanks to limma</description>
+	<stdio>
+        <exit_code range="1:" />
+    </stdio>
 	<requirements>
 	  	<!--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
 		${__tool_directory__}/Analyse.R
-		   	"${rdataset}"
-			"${conditions}"
-		 	"${selectCondition1}"
-			"${condition1}"
-		    "${selectCondition2}"
-			"${condition2}"
-			"${nbresult}"
-       		$result_export_eset
-       		$result_html 
-			$result_html.files_path
-			$result_tabular
-		${__tool_directory__}/Analyse_tpl.html
+		   	--rdatainput ${rdataset}
+			--conditions ${conditions}
+		 	--selectcondition1 "${selectCondition1}"
+		    --selectcondition2 "${selectCondition2}"
+			--nbresult ${nbresult}
+       		--rdataoutput ${result_export_eset}
+       		--htmloutput $result_html 
+			--htmloutputpath $result_html.files_path
+			--tabularoutput $result_tabular
+			--htmltemplate ${__tool_directory__}/Analyse_tpl.html
 		]]>
 	</command>
 	
@@ -33,13 +34,13 @@
     		<filter type="unique_value" column="1"/>
 		</options>
 		</param>
-		<param name="condition1" type="select" display="checkboxes" label="Condition 1" multiple="true">
+		<!--param name="condition1" type="select" display="checkboxes" label="Condition 1" multiple="true">
 			<options from_dataset="conditions">
     		<column name="name" index="2"/>
     		<column name="value" index="0"/>
 			<filter  type="param_value" ref="selectCondition1" column="1"/>
 		</options>
-		</param>	
+		</param-->	
 		<param name="selectCondition2" type="select" label="condition 2">
 			<options from_dataset="conditions">
     		<column name="name" index="1"/>
@@ -47,13 +48,13 @@
 			<filter type="unique_value" column="1"/>    		
 		</options>
 		</param>	
-		<param name="condition2" type="select" display="checkboxes" label="Condition 2" multiple="true">
+		<!--param name="condition2" type="select" display="checkboxes" label="Condition 2" multiple="true">
 			<options from_dataset="conditions">
     		<column name="name" index="2"/>
     		<column name="value" index="0"/>
 			<filter  type="param_value" ref="selectCondition2" column="1"/>
 		</options>
-		</param>	
+		</param-->	
 		<param name="nbresult" type="integer" value="1000" min="1" label="number of top genes" help="Number of genes to be displayed in result datatable"/>
 	</inputs>
 	<outputs>
@@ -74,7 +75,7 @@
 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