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1 <tool id="select_consensus_k" name="Select Consensus Clustering K" force_history_refresh="True">
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2 <command interpreter="python">select.k.from.consensus.cluster.py
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3 -r ${cc_results}
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4 -c ${change_min}
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5 -m $metric_cond.metric
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6 -h $report
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7 -p ${report.files_path}
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8 #if str($metric_cond.metric) == 'survival':
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9 -s $metric_cond.survival
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10 -e $metric_cond.mode
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11 #end if
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12 -o ${cluster_class}
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13 </command>
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14 <inputs>
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15 <param name="cc_results" type="data" format="rdata" label="Consensus Clustering Results File" help="Specify the result from a consensus clustering run (see help below)"/>
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16 <conditional name="metric_cond">
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17 <param name="metric" type="select" label="Change Metric" help="Specify the choice of 'change' metric to use">
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18 <option value="difference">Difference</option>
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19 <option value="silhouette">silhouette</option>
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20 <option value="survival">survival</option>
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21 </param>
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22 <when value="survival">
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23 <param name="survival" type="data" label="Clinical Data" optional="true" help="Specify Clinical data to use"/>
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24 <param name="mode" type="select" label="Survival Report Mode" help="Mode to use when performing Log-Rank tests">
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25 <option value="all">All</option>
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26 <option value="one">One</option>
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27 <option value="both">Both</option>
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28 </param>
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29 </when>
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30 </conditional>
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31 <param name="change_min" type="float" label="Minimum relative change (AUC; pivot point for search)" value="0.1" help="Specify threshold to determine the minimum relative change"/>
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32
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33 </inputs>
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34 <outputs>
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35 <data format="rdata" name="cluster_class" label="Select K from Consensus Clustering Report (RData)"/>
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36 <data format="html" name="report" label="Select K from Consensus Clustering Report (HTML)"/>
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37 </outputs>
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38 <help>
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39 .. class:: infomark
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40
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41 **Select an choice of K from consensus clustering result**
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42
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43 ----
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44
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45 **Parameters**
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46
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47 - **Consensus Clustering Results File** Specify the result from a consensus clustering run (**MUST BE THE RDATA** outuput)
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48
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49 - **Change Metric** Specify the choice of 'change' metric to use. Choice of:
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50
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51 * Difference (relative difference in AUC between different choices of K)
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52 * Silhouette (Max average silhouette width - search anchored by 'Change Min')
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53 * Survival (Min p-value from Log-rank tests - search anchored by 'Change Min') **NOTE: WE DISCOURAGE USING THIS METRIC.**
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54
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55 - **Change Min** Threshold to determine the minimum relative change that's used to decide the choice of K
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56
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57
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58 - **IF 'SURVIVAL' IS THE CHANGE METRIC, the following become available:**
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59
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60 - **Clinical Data** Specify Clinical data to use for performing the Log-Rank tests if 'Survival' is the metric
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61 * **(MUST SPECIFY A PROPERLY FORMATTED CLINICAL DATA FILE** - See the "Format Raw TCGA sample IDs")
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62
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63 - **Clinical Report Mode** Mode to use when performing Log-Rank tests. Choice of:
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64
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65 * All - All clusters versus each other
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66 * One - One cluster versus a meta-cluster composed of the others. Search performed exhaustively.
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67 * Both - Perform both all-v-all and and one-v-others test; select the choice of K that gives the best
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68
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69 </help>
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70 </tool>
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