diff ImportDataFromMatrix.xml @ 9:328f4031e5d3 draft

planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty

--- a/ImportDataFromMatrix.xml	Wed May 10 04:12:26 2017 -0400
+++ b/ImportDataFromMatrix.xml	Wed May 10 08:12:48 2017 -0400
@@ -1,42 +1,48 @@
-<tool id="importMatrixData" name="Import custom data">
-	<description>Quality control and normalization of a custom matrix expression data</description>
-	<requirements>
-	  	<!--container type="docker">sblanck/smagexp</container-->
-		<requirement type="package" version="0.1.0">r-smagexp</requirement>		
-	</requirements>
-	<command>
-		<![CDATA[ 
-		Rscript --vanilla 
-		${__tool_directory__}/ImportDataFromMatrix.R
-		    --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>
-		
-	
-	<inputs>
-		<param name="input" type="data" format="tabular" label="Input data" help="Input data"/>
-		<param name="normalization" type="select" label="Preprocessing/normalization">
-    		<option value="quantile">quantile normalization + log2</option>
+<tool id="importMatrixData" name="Import custom data" version="0.1.0">
+
+    <description>Quality control and normalization of a custom matrix expression data</description>
+
+    <requirements>
+        <requirement type="package" version="0.1.0">r-smagexp</requirement>		
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <regex match="Warning" source="both" level="warning"/>
+    </stdio>
+
+    <command>
+        <![CDATA[ 
+        Rscript --vanilla 
+        ${__tool_directory__}/ImportDataFromMatrix.R
+            --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>
+
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Input data" help="Input data"/>
+        <param name="normalization" type="select" label="Preprocessing/normalization">
+            <option value="quantile">quantile normalization + log2</option>
             <option value="log2">log2 only</option>
             <option value="none">none</option>
-		</param>
-		<param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the input file"/>
-		<param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>		
-	</inputs>
+        </param>
+        <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the input file"/>
+        <param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>		
+    </inputs>
 
-	<outputs>
-		<data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>		
-		<data format="html" name="result_html" label="QC result"/>
-	</outputs>
+    <outputs>
+        <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>		
+        <data format="html" name="result_html" label="QC result"/>
+    </outputs>
 
-	<help>
+    <help>
 <![CDATA[ 
 **What it does**
 		     	
@@ -74,6 +80,6 @@
 	- Bboxplots and MA plots 
 	- Rdata object containing the data for further analysis.
 ]]>
-	</help>
+    </help>
 
 </tool>