Mercurial > repos > sblanck > smagexp

diff MetaMA.xml @ 9:328f4031e5d3 draft

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planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty
author sblanck
date Wed, 10 May 2017 08:12:48 -0400
parents 7f74250a083d
children c05f899d5dcd
line wrap: on
line diff
--- a/MetaMA.xml	Wed May 10 04:12:26 2017 -0400
+++ b/MetaMA.xml	Wed May 10 08:12:48 2017 -0400
@@ -1,29 +1,36 @@
 <tool id="metaMA" name="Microarray data meta-analysis" version="0.1.0">
-	<description>Perform meta-analysis thanks to metaMA.</description>
-	<requirements>
-	  <!--container type="docker">sblanck/smat</container-->
-	  <requirement type="package" version="0.1.0">r-smagexp</requirement>
-	</requirements>
-	<command>
-		<![CDATA[ 
-		Rscript 
-		${__tool_directory__}/MetaMA.R
-		--input $input
-       	--htmloutput $result_html 
-		--htmloutputpath $result_html.extra_files_path
-		--htmltemplate ${__tool_directory__}/MetaMa_tpl.html
-		]]>
+
+    <description>Perform meta-analysis thanks to metaMA.</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 
+        ${__tool_directory__}/MetaMA.R
+            --input $input
+            --htmloutput $result_html 
+            --htmloutputpath $result_html.extra_files_path
+            --htmltemplate ${__tool_directory__}/MetaMa_tpl.html
+        ]]>
 	</command>
-	
-	<inputs>
-		<param format="rdata" name="input" multiple="true" type="data" optional="false" label="rdata files" help="rdata files containing the results of the analysis to be used in the meta-analysis"/>
-	</inputs>
-		
-	<outputs>
-		<data format="html" name="result_html" label="Meta-analysis results"/>
-	</outputs>
+
+    <inputs>
+        <param format="rdata" name="input" multiple="true" type="data" optional="false" label="rdata files" help="rdata files containing the results of the analysis to be used in the meta-analysis"/>
+    </inputs>
 
-	<help>
+    <outputs>
+        <data format="html" name="result_html" label="Meta-analysis results"/>
+    </outputs>
+
+    <help>
 <![CDATA[ 
 **What it does**
 		
@@ -42,6 +49,6 @@
 		
 - Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database.
 ]]>
-	</help>
+    </help>
 
 </tool>