view cluster.tools/remove.tcga.normals.xml @ 9:a3c03541fe6f draft default tip

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<tool id="remove_tcga_normal_samples" name="Remove TGCA Normal Samples" force_history_refresh="True">
    <command interpreter="python">remove.tcga.normals.py
-d $dataset
-o ${output_tumor}
-r ${return_normal_matrix}
#if str($return_normal_matrix) == 'yes':
-O ${output_normal}
#end if
    </command>
    <inputs>
      <param name="dataset" type="data" format='tabular' label="Matrix containing TCGA Normal Samples"/>
      <param name="return_normal_matrix"  type='select'  display="radio" label="Return Normals in Separate File?" help="Specify whether or not to return a file containing the normals">
	<option value="yes" selected='true' >Yes</option>
	<option value="no">No</option>
      </param>
    </inputs>
    <outputs>
      <data format="tabular" name="output_tumor" label="Tumor Sample Matrix"/>
      <data format="tabular" name="output_normal" label="Normal Sample Matrix">
	<filter>(return_normal_matrix)=="yes"</filter>
      </data>
    </outputs>
<help>
.. class:: infomark
     
**Remove Normal Samples** - Tool to remove the normal samples from a matrix **(ASSUMES samples are in the columns of matrix)**

**OUTPUT:**  A new matrix without normal samples

----

**INPUT**

- **Matrix that contains normal samples** Input matrix that potentially contains normal samples 


</help>
</tool>