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author insilico-bob
date Tue, 27 Nov 2018 14:20:40 -0500
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<?xml version='1.1' encoding='utf-8'?>
<tool id="Matrix_Transformations" name="Matrix Transformations" version="2.2">
  <description> by Rows, Columns, All by method</description>
 <command interpreter="python">Matrix_Transformations.py '$p_input' '$extra.choice' '$extra.axes' '$extra.scalevalue' '$extra.offsetvalue' '$output_file'</command>

 <inputs>
    <conditional name="extra">
 	  <param name="choice" type="select" label="Choose Normalization Method">
 		<option value="mean_center_normalization">Mean Centered Normalization</option>
 		<option value="median_center_normalization">Median Centered Normalization</option>
 		<option value="ln_normalization">Log2 Normalization w offset</option>
 		<option value="log_normalization">Log10 Normalization w offset</option>
 		<option value="z_score_normalization">Z-Score Normalization</option>
		<option value="transpose">Matrix Transpose</option>
 		<option value="add_offset">Add Offset Value</option>
 		<option value="scale">Scale by Multiple</option>
 		<option value="divide_by_sum">Divide by Sum</option>
	  </param>
 	    <when value="add_offset">
			<param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Add value to each Matrix element."/>
	 		<param name="scalevalue" type="text" size="10" hidden="true"   value="1.0"/>
	 		<param name="axes" type="text" size="10" hidden="true"  value="neither"/>
	    </when>
	    <when value="scale">
			<param name="scalevalue" type="text" size="10" value="1.0" label="Matrix Value scaling" help="multiply value with each Matrix element."/>
	 		<param name="offsetvalue" type="text" size="10" hidden="true"   value="0"/>
	 		<param name="axes" type="text" size="10" hidden="true"  value="neither"/>
	    </when>
	    <when value="ln_normalization">
			<param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Calculate log2 for each Matrix element then add offset."/>
	 		<param name="scalevalue" type="text" size="10" hidden="true"   value="1.0"/>
 			<param name="axes" type="select" label="Choose Axis">
 				<option value="Row">Row</option>
 				<option value="Column">Column</option>
 			</param>
	    </when>
	    <when value="log_normalization">
			<param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Calculate log10 for each Matrix element then add offset."/>
	 		<param name="scalevalue" type="text" size="10" hidden="true"   value="1.0"/>
 			<param name="axes" type="select" label="Choose Axis">
 				<option value="Row">Row</option>
 				<option value="Column">Column</option>
 			</param>
	    </when>	
 		<when value="z_score_normalization">
	 		<param name="offsetvalue" type="text" size="10" hidden="true"   value="0"/>
	 		<param name="scalevalue" type="text" size="10" hidden="true"   value="1.0"/>
 			<param name="axes" type="select" label="Choose Axis">
 				<option value="Row">Row</option>
 				<option value="Column">Column</option>
 			</param>
	    </when> 		
 		<when value="mean_center_normalization">
	 		<param name="offsetvalue" type="text" size="10" hidden="true"   value="0"/>
	 		<param name="scalevalue" type="text" size="10" hidden="true"   value="1.0"/>
 			<param name="axes" type="select" label="Choose Axis">
 				<option value="Row">Row</option>
 				<option value="Column">Column</option>
 			</param>
	    </when>
 		<when value="median_center_normalization">
	 		<param name="offsetvalue" type="text" size="10" hidden="true"   value="0"/>
	 		<param name="scalevalue" type="text" size="10" hidden="true"   value="1.0"/>
 			<param name="axes" type="select" label="Choose Axis">
 				<option value="Row">Row</option>
 				<option value="Column">Column</option>
 			</param>
	    </when>
		<when value="transpose">
	 		<param name="offsetvalue" type="text" size="10" hidden="true"   value="0"/>
	 		<param name="scalevalue" type="text" size="10" hidden="true"   value="1.0"/>
	 		<param name="axes" type="text" size="10" hidden="true"  value="neither"/>
	    </when>
 		<when value="divide_by_sum">
	 		<param name="offsetvalue" type="text" size="10" hidden="true"   value="0"/>
	 		<param name="scalevalue" type="text" size="10" hidden="true"   value="1.0"/>
 			<param name="axes" type="select" label="Choose Axis">
 				<option value="Row">Row</option>
 				<option value="Column">Column</option>
 			</param>
	    </when>
    </conditional>

 	<param name="p_input" type="data" format="tabular" label="Input Matrix"> </param>

<!--  need scipy!!!!
		<option value="rank">Rank Normalization</option>
		<when value="rank">
	 		<param name="offsetvalue" type="text" size="10" hidden="true"   value="0"/>
	 		<param name="scalevalue" type="text" size="10" hidden="true"   value="1.0"/>
	    </when>
 	
 	<param name="axes" type="select" label="Choose Axis">
 		<option value="Row">Row</option>
 		<option value="Column">Column</option>
 	</param>
--> 	
 </inputs>



 <outputs>
 	<data name="output_file" format="tabular" />
 </outputs>
 
 </tool>