diff cluster.tools/normalize.matrix.xml @ 0:0decf3fd54bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/normalize.matrix.xml	Thu Feb 28 01:45:39 2013 -0500
@@ -0,0 +1,74 @@
+<tool id="normalize_matrix" name="Normalize Matrix" force_history_refresh="True">
+    <command interpreter="python">normalize.matrix.py
+-d $dataset 
+-r ${center_rows} 
+-c ${center_cols} 
+-R ${var_adj_rows} 
+-C ${var_adj_cols} 
+-o ${output}
+
+</command>
+    <inputs>
+    	<param name="dataset" type="data" format='tabular' label="Data Set" help="Matrix to be normalized (tab-delimited format)"/>
+    	<param name="center_rows" type="select" label="Center Rows" help="Centering Method for Rows">
+    		<option value="none">No Centering</option>
+    		<option value="mean">Mean</option>
+    		<option value="median" selected="true">Median</option>
+    	</param>
+    	
+    	<param name="center_cols" type="select" label="Center Columns" help="Centering Method for Columns" >
+    		<option value="none" selected="true">No Centering</option>
+    		<option value="mean">Mean</option>
+    		<option value="median">Median</option>
+    	</param>
+    	
+    	<param name="var_adj_rows" type="select" label="Variance Adjustment for Rows" help="Variance Adjustment Method for Rows" >
+    		<option value="none" selected="true">No Adjustment</option>
+    		<option value="mad">Median Absolute Deviation</option>
+    		<option value="sd">Standard Deviation</option>
+    	</param>
+    	<param name="var_adj_cols" type="select" label="Variance Adjustment for Columns" help="Variance Adjustment Method for Columns" >
+    		<option value="none" selected="true">No Adjustment</option>
+    		<option value="mad">Median Absolute Deviation</option>
+    		<option value="sd">Standard Deviation</option>
+    	</param>
+    	
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="Normalized Matrix"/>
+    </outputs>
+<help>
+.. class:: infomark
+     
+**Normalize Matrix - Tool to normalize a matrix**
+
+----
+
+**Parameters**
+
+- **Center Rows** Centering Method for Rows
+
+         * No Centering
+	 * Mean
+	 * Median
+
+- **Center Rows** Centering Method for Columns
+
+         * No Centering
+	 * Mean
+	 * Median
+
+- **Variance Adjustment for Rows** Variance Adjustment Method for Rows
+
+         * No Adjustment
+	 * Median Absolute Deviation
+	 * Standard Deviation
+
+- **Variance Adjustment for Rows** Variance Adjustment Method for Columns
+
+         * No Adjustment
+	 * Median Absolute Deviation
+	 * Standard Deviation
+
+</help>
+</tool>