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1 <tool id="gen_survival_curve" name="Generate Kaplan-Meiers Plot for Cluster Result" force_history_refresh="True">
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2 <command interpreter="python">gen.survival.curves.py
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3 -C ${cluster_cls}
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4 -S ${survial_data}
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5 -M ${mode}
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6 -T "${title}"
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7 -I ${image_format_cond.image_format}
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8 #if str($image_format_cond.image_format) == 'png':
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9 -O $report_png
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10 #end if
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11 #if str($image_format_cond.image_format) == 'pdf':
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12 -O $report_pdf
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13 #end if
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14 </command>
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15 <inputs>
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16 <param name="cluster_cls" type="data" format="rdata" label="Clustering Classification" help="Specify the clustering classification (must be RData file, see help)"/>
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17 <param name="survial_data" type="data" format="tabular" label="Clinical Data" help="Specify the clinical data to use for the Kaplan-Meiers Plot (see help)"/>
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18 <param name="mode" type="select" display='radio' label="Report Mode" help="Specify the mode to use when performing Log-Rank tests">
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19 <option value="all" selected='true' >All</option>
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20 <option value="one">One</option>
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21 <option value="both">Both</option>
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22 </param>
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23 <conditional name="image_format_cond">
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24 <param name="image_format" type="select" display='radio' label="Image format" help="">
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25 <option value="pdf">PDF</option>
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26 <option value="png" selected='true' >PNG (html wrapper)</option>
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27 </param>
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28 </conditional>
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29
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30 <param name="title" type="text" label="Title" value="Report" help="Specify title to use in Kaplan-Meiers Plot"/>
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31 </inputs>
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32 <outputs>
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33 <data format="png" name="report_png" label="Kaplan-Meier Survival Plot (PNG)">
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34 <filter>(image_format_cond['image_format']=="png")</filter>
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35 </data>
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36 <data format="pdf" name="report_pdf" label="Kaplan-Meier Survival Plot (PDF)">
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37 <filter>(image_format_cond['image_format']=="pdf")</filter>
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38 </data>
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39 </outputs>
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40 <help>
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41 .. class:: infomark
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42
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43 **Generate a Kaplan-Meiers Plot for a given cluster result**
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44
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45 ----
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46
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47 **Parameters**
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48
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49 - **Clustering Classification** Specify the clustering classification (RData file format - use the 'Convert tab-delimited Cluster Assignments to RData" tool to convert assignments in tab-delimited format).
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50
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51 - **Clinical Data** Clinical data to use for the Kaplan-Meiers Plot (must be formated - See the "Format Raw TCGA sample IDs")
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52
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53 - **Report Mode** Mode to use when performing Log-Rank tests **(MUST SPECIFY A PROPERLY FORMATTED CLINICAL DATA FILE)** . Choice of:
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54
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55 * All - All clusters versus each other
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56 * One - One cluster versus a meta-cluster composed of the others. Search performed exhaustively.
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57 * 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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58
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59 - **Title** - Title to use for Kaplan-Meiers Plot
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60
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61 </help>
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62 </tool>
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