view cluster.tools/fix.and.merge.TCGA.sample.IDs.xml @ 2:b442996b66ae draft

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<tool id="fix_and_merge_TCGA_samples_IDs" name="Fix and Merge TCGA sample IDs" force_history_refresh="True">
    <command interpreter="python">fix.and.merge.TCGA.sample.IDs.py
-d $dataset -n ${num_components} ${remove_normals}
-o ${output}

</command>
    <inputs>
    	<param name="dataset" type="data" format='tabular' label="Matrix with Full TCGA Aliquot Barcodes"/>
	<param name="num_components" type="integer" label="Number of barcode components to use (min number is 3)" value="3" />
	<param name="remove_normals" type="boolean" label="Remove Normals from Matrix? (check to exclude)" truevalue="-r" falsevalue="" checked="True" />
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="Matrix with TCGA Patient Barcodes (filtered and merged)"/>
    </outputs>
<help>
.. class:: infomark
     
**Update and Merge TCGA Sample IDs** - This will limit the TCGA sample IDs to the specified numnber of elements (min is 3).  If necessary, samples will be merged (by averaging)

**OUTPUT:**  A new matrix using sample (columns) that use the specified number of components

----

**Parameters**

- **Matrix with TCGA barcode sample IDs (e.g. TCGA-AE-####-01-)** Specify a data matrix with TCGA barcodes

- **Number of barcode components to use** Specify the number of barcode components to use in new matrix that is produced **(min number is 3)**

- **Remove Normals from Matrix?** - Remove any normals from the matrix (if necessary)

</help>
</tool>