# HG changeset patch
# User peter-waltman
# Date 1362185648 18000
# Node ID 3d3a8595b981daac91ba2ec2df9c48382da9c6e5
# Parent  cbc3ecce98eef3964649280141f2c59962013fb7
Uploaded

diff -r cbc3ecce98ee -r 3d3a8595b981 cluster.tools/normalize.matrix.by.other.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/normalize.matrix.by.other.xml	Fri Mar 01 19:54:08 2013 -0500
@@ -0,0 +1,78 @@
+<tool id="normalize_matrix_by_other" name="Normalize Matrix By Other Matrix" force_history_refresh="True">
+    <command interpreter="python">normalize.matrix.by.other.py
+-d ${dataset}
+-D ${dataset2}
+-c ${ctr_method} 
+
+#if str($ctr_method) == "median":
+-o ${output_median}
+#end if
+
+#if str($ctr_method) == "mean":
+-o ${output_mean}
+#end if
+
+-r ${return_normalizer_matrix}
+
+#if str($return_normalizer_matrix) == 'yes':
+-O ${output_normal}
+#end if
+</command>
+    <inputs>
+      <param name="dataset" type="data" format='tabular' label="Target Data (Matrix to be normalized)" help="Matrix to be normalized (e.g. disease)"/>
+      <param name="dataset2" type="data" format='tabular' label="Reference Data (Matrix that will be used to normalize other)" help="Matrix to be normalizer (e.g. normals)"/>
+      <param name="ctr_method" type="select" label="Centering Metric for Genes" help="Specify Metric to Use for Center Rows (Genes)" >
+	<option value="median" selected="true">Median</option>
+	<option value="mean">Mean</option>
+      </param>
+      <param name="return_normalizer_matrix"  type='select'  display="radio" label="?" help="Specify whether or not to return a a normalized version of the Reference matrix">
+	<option value="yes" selected='true' >Yes</option>
+	<option value="no">No</option>
+      </param>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="output_median" label="Median Normalized Matrix (by Reference Set)">
+	<filter>(ctr_method)=="median"</filter>
+      </data>
+      <data format="tabular" name="output_mean" label="Mean Normalized Matrix (by Reference Set)">
+	<filter>(ctr_method)=="mean"</filter>
+      </data>
+      <data format="tabular" name="output_normal" label="Normalized Reference Matrix">
+	<filter>(return_normal_matrix)=="yes"</filter>
+      </data>
+    </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>