Mercurial > repos > md-anderson-bioinformatics > matrix_manipulation
diff Matrix_Transformations.xml @ 1:f1bcd79cd923 draft default tip
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author | insilico-bob |
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date | Tue, 27 Nov 2018 14:20:40 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Matrix_Transformations.xml Tue Nov 27 14:20:40 2018 -0500 @@ -0,0 +1,106 @@ +<?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> \ No newline at end of file