view cluster.tools/cutree.xml @ 0:0decf3fd54bc draft

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<tool id="cutree" name="Re-Run Cutree on Previous Hierarchical Clustering Result" force_history_refresh="True">
    <command interpreter="python">cutree.py
-d $dataset 
-k ${numk} 
-o ${rdata_output}

</command>
    <inputs>
    	<param name="dataset" type="data" format='rdata' label="Cluster Result" help="Specify the cluster result to analayze (MUST BE IN rdata format; see help below)"/>
    	<param name="numk" type="integer" label="Number of Clusters" value="5" help="Specify the number of clusters to use"/>
    </inputs>
    <outputs>
        <data format="rdata" name="rdata_output" label="Cutree from Hierarchical Clustering Result (RData)"/>
    </outputs>
<help>
- **Cluster Result** - Specify the cluster result to analayze (MUST BE IN rdata format), and must contain the same objects that are produced by the 'Partition Clustering,' 'Hierarchical Clustering (HAC),' or 'Consensus Clustering' tools.  Specifically, it must contain the following objects

         * A 'treecl.res' or 'partcl.res' object - corresponding to whether the cluster results is from a partition or tree clustering method
         * A 'data' object that contains the data that was passed into the clustering method.  NOTE, it is better for this to be the actual data passed in, rather than the data prior to the pre-processing that was performed prior to the actual clustering.

- **Number of Clusters** Specify the number of clusters to use

</help>
</tool>