view cluster.tools/extract.cons.cluster.from.result.xml @ 9:a3c03541fe6f draft default tip

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<tool id="extract_cons_cluster_from_result" name="Extract Clustering from ConsensusCluster Results (choice of K)" force_history_refresh="True">
    <command interpreter="python">extract.cons.cluster.from.result.py
-r ${results_file}
-k ${k_select}

#if str($out_format.format) == 'rdata':
-d ${output_rdata}
#end if
#if str($out_format.format) == 'tabular':
-o ${output_tab}
#end if

</command>
    <inputs>
    	<param name="results_file" type="data" format="rdata" label="Consensus Clustering Results File" help="Specify the result from a consensus clustering run (RData format)"/>
    	<param name="k_select" type="integer" label="Choice of K" value="4" help="Specify the choice of K to extract from the clustering result"/>
	<conditional name="out_format" >
	  <param name="format" type="select" label="Select Output Format" help="Specify the output format (RData file or tab-delimited" >
	    <option value="rdata" selected='true' >RData</option>
	    <option value="tabular">Tab-delimited</option>
	  </param>
	</conditional>
    </inputs>
    <outputs>
        <data format="rdata" name="output_rdata" label="CCPlus cluster RData file" >
	  <filter>(out_format['format']=="rdata")</filter>
	</data>
        <data format="tabular" name="output_tab" label="Tabbed File" >
	  <filter>(out_format['format']=="tabular")</filter>
	</data>
    </outputs>
<help>

.. class:: infomark
     
**Retrieves a class assignment for a user-specified choice of K, from a specified Consensus Clustering result**

**Parameters**
 - **Consensus Clustering Results File** Specify the result from a consensus clustering run (**MUST BE THE RData** outuput)

 - **Choice of K** Specify the choice of K to extract from the clustering result

 - **Select Output Format**  Specify the output format (Choice of):
         * RData file 
         * Tab-delimited
</help>
</tool>