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1 <tool id="survival" name="survival" version="1.0.0">
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2 <description>core survival analysis</description>
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3 <requirements>
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4 <requirement type="package" version="2.40_1">r-survival</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive">
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7 Rscript '$__tool_directory__/survival.R' '$input' '$type' '$error' '$conf_type' '$conf_lower' '$fit' '$png'
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8 </command>
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9 <inputs>
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10 <param format="csv" type="data" name="input" value="" label="survival data" help="
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11 e.g. survival table
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12 X obsT status X1 X2
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13 17 1815 FALSE 2 HOXA1
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14 18 145 TRUE 1 HOXA1
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15 19 2506 FALSE 1 HOXA1
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16 20 1382 TRUE 1 HOXA1 ''"/>
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17
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18 <conditional name="type">
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19 <param format="text" name="type" type="select" label="Type of survival curve:">
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20 <option name="type" format="text" type="text" value="kaplan-meier">kaplan-meier</option>
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21 <option name="type" format="text" type="text" value="fleming-harrington">fleming-harrington</option>
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22 <option name="type" format="text" type="text" value="fh2">fleming-harrington</option>
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23 </param>
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24 </conditional>
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25
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26 <conditional name="error">
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27 <param name="error" type="select" label="Type of error:">
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28 <option name="error" format="text" type="text" value="greenwood">greenwood</option>
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29 <option name="error" format="text" type="text" value="tsiatis">tsiatis</option>
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30 </param>
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31 </conditional>
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32
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33 <conditional name="conf_type">
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34 <param name="conf_type" type="select" label="Type of conf_type:">
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35 <option name="conf_type" format="text" type="text" value="log">log</option>
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36 <option name="conf_type" format="text" type="text" value="log-log">log-log</option>
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37 <option name="conf_type" format="text" type="text" value="plain">plain</option>
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38 <option name="conf_type" format="text" type="text" value="none">none</option>
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39 </param>
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40 </conditional>
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41
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42 <conditional name="conf_lower">
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43 <param name="conf_lower" type="select" label="Type of conf_lower:">
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44 <option name="conf_lower" format="text" type="text" value="usual">usual</option>
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45 <option name="conf_lower" format="text" type="text" value="peto">fleming-harrington</option>
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46 <option name="conf_lower" format="text" type="text" value="modified">fleming-harrington</option>
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47 </param>
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48 </conditional>
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49
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50 </inputs>
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51 <outputs>
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52 <data format="csv" name="fit" label="survfit.csv" />
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53 <data format="png" name="png" label="survfit.png" />
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="test">
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58 <element name="test-data">
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59 <collection type="data">
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60 <element format="csv" name="input" label="test-data/input.csv"/>
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61 </collection>
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62 </element>
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63 </param>
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64 <output format="csv" name="fit" label="test-data/survfit.csv"/>
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65 <output fformat="png" name="png" label="test-data/survfit.png"/>
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66 </test>
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67 </tests>
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68 <help>
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69 **Computes an estimate of a survival curve for censored data using either the Kaplan-Meier or the Fleming-Harrington method or computes the predicted survivor function for a Cox proportional hazards model.**
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70 </help>
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71 <citations>
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72 <citation>https://CRAN.R-project.org/package=survival</citation>
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73 </citations>
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74 </tool>
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