diff MetaRNAseq.xml @ 14:e5a94bc69bd6 draft

planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160

--- a/MetaRNAseq.xml	Thu May 11 11:08:05 2017 -0400
+++ b/MetaRNAseq.xml	Tue May 16 01:53:32 2017 -0400
@@ -11,32 +11,34 @@
         <regex match="Warning" source="both" level="warning"/>
     </stdio>
 
-	<command interpreter="python">
-		<![CDATA[ 	
-		stderr_wrapper.py Rscript 
-		${__tool_directory__}/MetaRNASeq.R 
-		#for $currentInput in $inputList
-        	"${currentInput}"
-			"${currentInput.name}"	
-		 #end for	
-			$top_table 
-			$diagnostic_html 
-			"$diagnostic_html.files_path"
-		${__tool_directory__}/MetaRNASeq_tpl.html
-	]]>	
-	</command>
+    <command>
+
+    <![CDATA[ 	
+        Rscript 
+        ${__tool_directory__}/MetaRNASeq.R 
+            --input "#for $input in $inputs# $input;$input.name, #end for#"
+            --result $top_table
+            --htmloutput $result_html 
+            --htmloutputpath $result_html.extra_files_path
+            --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html	
+    ]]>	
+    </command>
 
-	<inputs>
-		<param format="tabular" name="inputList" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/>
-	</inputs>
+    <inputs>
+        <param format="tabular" name="inputList" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/>
+    </inputs>
 
-	<outputs>
-		<data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
-		<data format="html" name="diagnostic_html" label="Charts for ${tool.name} on ${on_string}"/>
-	</outputs>
+    <outputs>
+        <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
+        <data format="html" name="diagnostic_html" label="Charts for ${tool.name} on ${on_string}"/>
+    </outputs>
+    
+    <tests>
+        
+    </tests>
 
-	<help>
-		
-	</help>
+    <help>
+
+    </help>
 
 </tool>