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

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<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>