diff cluster.tools/heatmap.from.cluster.result.xml @ 3:563832f48c08 draft

Uploaded

--- a/cluster.tools/heatmap.from.cluster.result.xml	Fri Mar 01 10:17:24 2013 -0500
+++ b/cluster.tools/heatmap.from.cluster.result.xml	Fri Mar 01 19:51:25 2013 -0500
@@ -35,8 +35,8 @@
   <param format="rdata" name="dataset1" type="data" label="Clustering Classification" help="Cluster result file from CCPLUS, HAC, or PAM"/>
   <conditional name="plot_kms_cond">
     <param name="plot_kms" type='select' label="Plot Kaplan-Meiers Survival Plot as well (primary clustering ONLY)?" help="NOTE: this only works when the Image Format is PNG.  For a PDF of the KM plot, you can use the 'Generate Kaplan-Meiers Plot for Cluster Result' tool">
+      <option value="yes" >Yes</option>
       <option value="no" selected='true'>No</option>
-      <option value="yes" >Yes</option>
     </param>
     <when value='yes'>
       <param name="survial_data" type="data" format="tabular" label="Clinical Data" help="Specify the clinical data to use for the Kaplan-Meiers Plot (see help)"/>
@@ -50,8 +50,8 @@
   </conditional>
   <conditional name="cluster_second_direction_cond">
     <param name="cluster_second_direction" type="select" label="Cluster the second dimension? (e.g. rows if this is a sample cluster)"  help="Cluster the 2nd dimension of matrix in the cluster result (see help below)">
+      <option value="yes">Yes</option>
       <option value="no" selected="true">No</option>
-      <option value="yes">Yes</option>
       <option value="prev">Previous Cluster Result</option>
     </param>
     <when value="prev">
@@ -65,12 +65,12 @@
     </param>
   </conditional>
   <param name="output_treeview_format" type='select' display="radio" label="Output in TreeView format as well?" help="Specify whether or not to produce files for TreeView" >
+    <option value="yes" selected='true' >Yes</option>
     <option value="no">No</option>
-    <option value="yes" selected='true' >Yes</option>
   </param>
   <param name="reverse_rows"  type='select'  display="radio" label="Reverse Row-order (to make consistent w\TreeView Display)?" help="Specify whether or not to reverse Row-order (to make the heatmap consistent with output from TreeView (reversed otherwise)" >
+    <option value="yes">Yes</option>
     <option value="no" selected='true'>No</option>
-    <option value="yes">Yes</option>
   </param>
 </inputs>
 <outputs>