diff cluster.tools/select.k.from.consensus.cluster.xml @ 0:0decf3fd54bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/select.k.from.consensus.cluster.xml	Thu Feb 28 01:45:39 2013 -0500
@@ -0,0 +1,70 @@
+<tool id="select_consensus_k" name="Select Consensus Clustering K" force_history_refresh="True">
+    <command interpreter="python">select.k.from.consensus.cluster.py
+-r ${cc_results}
+-c ${change_min}
+-m $metric_cond.metric
+-h $report 
+-p ${report.files_path}
+#if str($metric_cond.metric) == 'survival':
+-s $metric_cond.survival
+-e $metric_cond.mode
+#end if
+-o ${cluster_class}
+    </command>
+    <inputs>
+        <param name="cc_results" type="data" format="rdata" label="Consensus Clustering Results File" help="Specify the result from a consensus clustering run (see help below)"/>
+	<conditional name="metric_cond">
+	  <param name="metric" type="select" label="Change Metric" help="Specify the choice of 'change' metric to use">
+            <option value="difference">Difference</option>       
+            <option value="silhouette">silhouette</option>
+            <option value="survival">survival</option>
+	  </param>
+	  <when value="survival">
+	    <param name="survival" type="data" label="Clinical Data" optional="true" help="Specify Clinical data to use"/>
+	    <param name="mode" type="select" label="Survival Report Mode" help="Mode to use when performing Log-Rank tests">
+	      <option value="all">All</option>
+	      <option value="one">One</option>
+	      <option value="both">Both</option>
+	    </param>    
+	  </when>
+	</conditional>
+	<param name="change_min" type="float" label="Minimum relative change (AUC; pivot point for search)" value="0.1" help="Specify threshold to determine the minimum relative change"/>
+
+    </inputs>
+    <outputs>
+        <data format="rdata" name="cluster_class" label="Select K from Consensus Clustering Report (RData)"/>
+        <data format="html" name="report" label="Select K from Consensus Clustering Report (HTML)"/>        
+    </outputs>
+<help>
+.. class:: infomark
+     
+**Select an choice of K from consensus clustering result**
+
+----
+
+**Parameters**
+
+- **Consensus Clustering Results File** Specify the result from a consensus clustering run (**MUST BE THE RDATA** outuput)
+
+- **Change Metric** Specify the choice of 'change' metric to use.  Choice of:
+
+         * Difference (relative difference in AUC between different choices of K)
+         * Silhouette (Max average silhouette width - search anchored by 'Change Min')
+         * Survival (Min p-value from Log-rank tests - search anchored by 'Change Min') **NOTE: WE DISCOURAGE USING THIS METRIC.**
+
+- **Change Min** Threshold to determine the minimum relative change that's used to decide the choice of K
+
+
+- **IF 'SURVIVAL' IS THE CHANGE METRIC, the following become available:**
+
+- **Clinical Data** Specify Clinical data to use for performing the Log-Rank tests if 'Survival' is the metric 
+        *  **(MUST SPECIFY A PROPERLY FORMATTED CLINICAL DATA FILE** - See the "Format Raw TCGA sample IDs")
+
+- **Clinical Report Mode** Mode to use when performing Log-Rank tests.  Choice of:
+
+         * All - All clusters versus each other
+         * One - One cluster versus a meta-cluster composed of the others.  Search performed exhaustively.
+         * Both - Perform both all-v-all and and one-v-others test; select the choice of K that gives the best
+
+</help>
+</tool>