Mercurial > repos > s-kaufmann > synteny_mapper

diff visualization.xml @ 10:a6c5e5a41025 draft

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Uploaded
author s-kaufmann
date Fri, 15 Aug 2014 08:35:52 -0400
parents 8a4190457eb7
children 25ec18816c91
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--- a/visualization.xml	Wed Jul 30 08:23:49 2014 -0400
+++ b/visualization.xml	Fri Aug 15 08:35:52 2014 -0400
@@ -5,10 +5,12 @@
     <requirement type="set_environment">JAR_PATH</requirement>
     <requirement type="package" version="0.64">circos</requirement>
     <requirement type="set_environment">CIRCOS_SCRIPT_PATH</requirement>
+    <requirement type="package" version="3.0.1">R_3_0_1</requirement>
+    <requirement type="set_environment">R_PATH</requirement>
 </requirements>
 
   <command>
-	java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/visualization/SyntenyPlotterWrapper $syntenyRegion $mappingFile $syntenyFile $out_file1 \$CIRCOS_PATH \$CIRCOS_SCRIPT_PATH $out_file1.files_path
+	java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/visualization/SyntenyPlotterWrapper $syntenyRegion $mappingFile $syntenyFile $out_file1 \$CIRCOS_PATH \$CIRCOS_SCRIPT_PATH $out_file1.files_path $linear \$R_PATH
   </command>
 
 <inputs>
@@ -23,6 +25,10 @@
 			<filter type="sort_by" column="0" ref="syntenyFile"/>
 		</options>
 	</param>
+	<param name="linear" type="select" label="Linear">
+			<option value="false">Circular representation</option>
+			<option value="true">Linear representation</option>
+	</param>
 </inputs>
   <outputs>
     <data format="html" name="out_file1" label="Visualization of Mapping"/>