diff cluster.tools/remove.tcga.normals.xml @ 3:563832f48c08 draft

Uploaded

--- a/cluster.tools/remove.tcga.normals.xml	Fri Mar 01 10:17:24 2013 -0500
+++ b/cluster.tools/remove.tcga.normals.xml	Fri Mar 01 19:51:25 2013 -0500
@@ -1,14 +1,24 @@
 <tool id="remove_tcga_normal_samples" name="Remove TGCA Normal Samples" force_history_refresh="True">
     <command interpreter="python">remove.tcga.normals.py
 -d $dataset
--o ${output}
-
-</command>
+-o ${output_tumor}
+-r ${return_normal_matrix}
+#if str($return_normal_matrix) == 'yes':
+-O ${output_normal}
+#end if
+    </command>
     <inputs>
-    	<param name="dataset" type="data" format='tabular' label="Matrix containing TCGA Normal Samples"/>
+      <param name="dataset" type="data" format='tabular' label="Matrix containing TCGA Normal Samples"/>
+      <param name="return_normal_matrix"  type='select'  display="radio" label="Return Normals in Separate File?" help="Specify whether or not to return a file containing the normals">
+	<option value="yes" selected='true' >Yes</option>
+	<option value="no">No</option>
+      </param>
     </inputs>
     <outputs>
-        <data format="tabular" name="output" label="Tumor Sample Matrix"/>
+      <data format="tabular" name="output_tumor" label="Tumor Sample Matrix"/>
+      <data format="tabular" name="output_normal" label="Normal Sample Matrix">
+	<filter>(return_normal_matrix)=="yes"</filter>
+      </data>
     </outputs>
 <help>
 .. class:: infomark