diff cluster.tools/extract.cons.cluster.from.result.xml @ 0:0decf3fd54bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/extract.cons.cluster.from.result.xml	Thu Feb 28 01:45:39 2013 -0500
@@ -0,0 +1,47 @@
+<tool id="extract_cons_cluster_from_result" name="Extract Clustering from ConsensusCluster Results (choice of K)" force_history_refresh="True">
+    <command interpreter="python">extract.cons.cluster.from.result.py
+-r ${results_file}
+-k ${k_select}
+
+#if str($out_format.format) == 'rdata':
+-d ${output_rdata}
+#end if
+#if str($out_format.format) == 'tabular':
+-o ${output_tab}
+#end if
+
+</command>
+    <inputs>
+    	<param name="results_file" type="data" format="rdata" label="Consensus Clustering Results File" help="Specify the result from a consensus clustering run (RData format)"/>
+    	<param name="k_select" type="integer" label="Choice of K" value="4" help="Specify the choice of K to extract from the clustering result"/>
+	<conditional name="out_format" >
+	  <param name="format" type="select" label="Select Output Format" help="Specify the output format (RData file or tab-delimited" >
+	    <option value="rdata" selected='true' >RData</option>
+	    <option value="tabular">Tab-delimited</option>
+	  </param>
+	</conditional>
+    </inputs>
+    <outputs>
+        <data format="rdata" name="output_rdata" label="CCPlus cluster RData file" >
+	  <filter>(out_format['format']=="rdata")</filter>
+	</data>
+        <data format="tabular" name="output_tab" label="Tabbed File" >
+	  <filter>(out_format['format']=="tabular")</filter>
+	</data>
+    </outputs>
+<help>
+
+.. class:: infomark
+     
+**Retrieves a class assignment for a user-specified choice of K, from a specified Consensus Clustering result**
+
+**Parameters**
+ - **Consensus Clustering Results File** Specify the result from a consensus clustering run (**MUST BE THE RData** outuput)
+
+ - **Choice of K** Specify the choice of K to extract from the clustering result
+
+ - **Select Output Format**  Specify the output format (Choice of):
+         * RData file 
+         * Tab-delimited
+</help>
+</tool>