view cluster.tools/normalize.matrix.by.other.xml @ 9:a3c03541fe6f draft default tip

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<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>