diff AffyQCnormalization.xml @ 9:328f4031e5d3 draft

planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty

--- a/AffyQCnormalization.xml	Wed May 10 04:12:26 2017 -0400
+++ b/AffyQCnormalization.xml	Wed May 10 08:12:48 2017 -0400
@@ -1,51 +1,45 @@
 <tool id="QCnormalization" name="QCnormalization" version="0.1.0">
-	<description>Quality control and normalization of affymetrix expression data</description>
-	<stdio>
-        <exit_code range="1:" />
-        
-		<regex match="Warning"
-           source="both"
-           level="warning"
-		/>
-     </stdio>
+
+    <description>Quality control and normalization of affymetrix expression data</description>
+
     <requirements>
-	  <!--container type="docker">sblanck/smat</container-->
-	  <requirement type="package" version="0.1.0">r-smagexp</requirement>
-	</requirements>
-	<command>
-		<![CDATA[
-		Rscript 
-		${__tool_directory__}/AffyQCnormalization.R
-	    	--input "#for $input in $inputs# $input;$input.name, #end for#"
+        <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 
+        ${__tool_directory__}/AffyQCnormalization.R
+            --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>
-	
-		<inputs>
-	
-		<param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
+            --rdataoutput $result_export_eset
+            --htmloutput $result_html
+            --htmloutputpath $result_html.files_path
+            --htmltemplate ${__tool_directory__}/AffyQCnormalization_tpl.html
+        ]]>
+     </command>
 
-		<param name="normalization" type="select" label="Preprocessing/normalization">
-		
-    		<option value="rma">rma (backgroung correction + quantile normalization + log2)</option>
+    <inputs>
+        <param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
+        <param name="normalization" type="select" label="Preprocessing/normalization">
+            <option value="rma">rma (backgroung correction + quantile normalization + log2)</option>
             <option value="quantile">quantile normalization + log2</option>
             <option value="background">background correction + log2</option>
             <option value="log2">log2 only</option>
-           
-		
-		</param>
-		
-	</inputs>
-	<outputs>
-		<data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>		
-		<data format="html" name="result_html" label="QC result"/>
-	</outputs>
+        </param>
+    </inputs>
 
-	<help>
+    <outputs>
+        <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>		
+        <data format="html" name="result_html" label="QC result"/>
+    </outputs>
+
+    <help>
 <![CDATA[
 		**What it does** 
 		    	
@@ -62,6 +56,6 @@
 - Rdata object containing the normalized data for further analysis
   		
 ]]>
-</help>
+    </help>
 
 </tool>