diff cluster.tools/hclust.xml @ 8:a58527c632b7 draft

Uploaded

--- a/cluster.tools/hclust.xml	Mon Mar 04 04:11:28 2013 -0500
+++ b/cluster.tools/hclust.xml	Mon Mar 11 16:31:29 2013 -0400
@@ -5,8 +5,18 @@
 -n ${direction} 
 -m ${distance_metric} 
 -l ${linkage} 
+
+#if str($numk) != "-1":
 -k ${numk} 
--o ${rdata_output}
+#end if
+
+#if str($direction) == "rows":
+-o ${rdata_output_rows}
+#end if
+
+#if str($direction) == "cols":
+-o ${rdata_output_cols}
+#end if
 
 </command>
     <inputs>
@@ -41,11 +51,16 @@
 	  <option value="ward">Ward</option>
     	</param>
     	
-    	<param name="numk" type="integer" label="Number of Clusters" value="50" help="Specify the number of clusters to use"/>
+    	<param name="numk" type="integer" label="Number of Clusters" value="-1" help="Specify the number of clusters to use (-1 to use default. See help below)."/>
     	
     </inputs>
     <outputs>
-        <data format="rdata" name="rdata_output" label="Hierarchical Clustering Result (RData)"/>
+      <data format="rdata" name="rdata_output_rows" label="Hierarchical Clustering Results; Gene Clusters (RData)">
+        <filter>(direction)=="rows"</filter>
+      </data>
+      <data format="rdata" name="rdata_output_cols" label="Hierarchical Clustering Results; Sample Clusters (RData)">
+        <filter>(direction)=="cols"</filter>
+      </data>
     </outputs>
 <help>
 .. class:: infomark
@@ -92,7 +107,9 @@
          * McQuity
          * Ward
 
-- **Number of Clusters** Specify the number of clusters to use
+- **Number of Clusters** Specify the number of clusters to use.  If set to -1, default values will be used, with the default set as follows:
+        * if samples/columns are being clustered, the **default** is 5.
+        * if genes/rows are being clustered, the **default** is set to num_rows/30, e.g. if there are 600 row/genes in the matrix, the default will be 20 clusters.
 
 </help>
 </tool>