Mercurial > repos > sblanck > smagexp

diff GEOQuery.xml @ 9:328f4031e5d3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty
author sblanck
date Wed, 10 May 2017 08:12:48 -0400
parents 7f74250a083d
children e5a94bc69bd6
line wrap: on
line diff
--- a/GEOQuery.xml	Wed May 10 04:12:26 2017 -0400
+++ b/GEOQuery.xml	Wed May 10 08:12:48 2017 -0400
@@ -1,41 +1,45 @@
-<tool id="GEOQuery" name="GEOQuery">
-	<description>GEOQuery wrapper</description>
-	<stdio>
+<tool id="GEOQuery" name="GEOQuery" version="0.1.0">
+
+    <description>GEOQuery wrapper</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>
-	<!--requirements>
-	  	<!container type="docker">sblanck/smagexp</container>
-		<requirement type="package" version="0.1.0">r-smagexp</requirement>
-	</requirements-->
-	<command>
-		<![CDATA[ 
-			Rscript --vanilla
-			${__tool_directory__}/GEOQuery.R 
-			--id ${GEOQueryID} 
-			--transformation ${transformation}
-			--data ${GEOQueryData} 
-			--rdata ${GEOQueryRData} 
-			--conditions ${conditions}
-		]]>
-	</command>
 
-	<inputs>
-		<param name="GEOQueryID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
-			<validator type="empty_field"/>
-		</param>
-	<param name="transformation" type="select" label="log2 transformation">
-			<option value="auto">auto</option>
+    <command>
+        <![CDATA[ 
+        Rscript --vanilla
+        ${__tool_directory__}/GEOQuery.R 
+            --id ${GEOQueryID} 
+            --transformation ${transformation}
+            --data ${GEOQueryData} 
+            --rdata ${GEOQueryRData} 
+            --conditions ${conditions}
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="GEOQueryID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
+            <validator type="empty_field"/>
+        </param>
+        <param name="transformation" type="select" label="log2 transformation">
+            <option value="auto">auto</option>
             <option value="yes">yes</option>
             <option value="no">no</option>
         </param>
-	</inputs>
+    </inputs>
 
-		<outputs>
-		<data format="tabular" name="GEOQueryData" label="GEOQuery Data of ${GEOQueryID}"/>
-		<data format="cond" name="conditions" label="conditions of ${GEOQueryID}"/>
-        <data format="rdata" name="GEOQueryRData" label="GEOQuery RData of ${GEOQueryID}"/>		
+    <outputs>
+        <data format="tabular" name="GEOQueryData" label="GEOQuery Data of ${GEOQueryID}"/>
+        <data format="cond" name="conditions" label="conditions of ${GEOQueryID}"/>
+        <data format="rdata" name="GEOQueryRData" label="GEOQuery RData of ${GEOQueryID}"/>
 	</outputs>
-	<help>
+    <help>
 <![CDATA[ 
 **What it does**     	
 
@@ -61,8 +65,6 @@
 - Condition (.cond) file summarizing conditions of the experiment
 - Tabular (.txt) file containing expression data for each sample
 ]]> 		
-
-	</help>
-
+    </help>
 
 </tool>