|
0
|
1 <tool id="extract_cons_cluster_from_result" name="Extract Clustering from ConsensusCluster Results (choice of K)" force_history_refresh="True">
|
|
|
2 <command interpreter="python">extract.cons.cluster.from.result.py
|
|
|
3 -r ${results_file}
|
|
|
4 -k ${k_select}
|
|
|
5
|
|
|
6 #if str($out_format.format) == 'rdata':
|
|
|
7 -d ${output_rdata}
|
|
|
8 #end if
|
|
|
9 #if str($out_format.format) == 'tabular':
|
|
|
10 -o ${output_tab}
|
|
|
11 #end if
|
|
|
12
|
|
|
13 </command>
|
|
|
14 <inputs>
|
|
|
15 <param name="results_file" type="data" format="rdata" label="Consensus Clustering Results File" help="Specify the result from a consensus clustering run (RData format)"/>
|
|
|
16 <param name="k_select" type="integer" label="Choice of K" value="4" help="Specify the choice of K to extract from the clustering result"/>
|
|
|
17 <conditional name="out_format" >
|
|
|
18 <param name="format" type="select" label="Select Output Format" help="Specify the output format (RData file or tab-delimited" >
|
|
|
19 <option value="rdata" selected='true' >RData</option>
|
|
|
20 <option value="tabular">Tab-delimited</option>
|
|
|
21 </param>
|
|
|
22 </conditional>
|
|
|
23 </inputs>
|
|
|
24 <outputs>
|
|
|
25 <data format="rdata" name="output_rdata" label="CCPlus cluster RData file" >
|
|
|
26 <filter>(out_format['format']=="rdata")</filter>
|
|
|
27 </data>
|
|
|
28 <data format="tabular" name="output_tab" label="Tabbed File" >
|
|
|
29 <filter>(out_format['format']=="tabular")</filter>
|
|
|
30 </data>
|
|
|
31 </outputs>
|
|
|
32 <help>
|
|
|
33
|
|
|
34 .. class:: infomark
|
|
|
35
|
|
|
36 **Retrieves a class assignment for a user-specified choice of K, from a specified Consensus Clustering result**
|
|
|
37
|
|
|
38 **Parameters**
|
|
|
39 - **Consensus Clustering Results File** Specify the result from a consensus clustering run (**MUST BE THE RData** outuput)
|
|
|
40
|
|
|
41 - **Choice of K** Specify the choice of K to extract from the clustering result
|
|
|
42
|
|
|
43 - **Select Output Format** Specify the output format (Choice of):
|
|
|
44 * RData file
|
|
|
45 * Tab-delimited
|
|
|
46 </help>
|
|
|
47 </tool>
|
