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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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25
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18 <conditional name="type">
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19 <param name="type" type="select" label="Type of survival curve:">
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21
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20 <option value="kaplan-meier">kaplan-meier</option>
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21 <option value="fleming-harrington">fleming-harrington</option>
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22 <option value="fh2">fh2</option>
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23 </param>
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22
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24 <when value="kaplan-meier"/>
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25 <when value="fleming-harrington"/>
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26 <when value="fh2"/>
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21
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27 </conditional>
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28
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29 <conditional name="error">
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30 <param name="error" type="select" label="Type of error:">
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31 <option value="greenwood">greenwood</option>
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32 <option value="tsiatis">tsiatis</option>
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33 </param>
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34 <when value="greenwood" />
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35 <when value="tsiatis"/>
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36 </conditional>
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37
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38 <conditional name="conf_type">
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39 <param name="conf_type" type="select" label="Type of conf.type:">
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40 <option value="log">log</option>
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41 <option value="log-log">log-log</option>
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42 <option value="plain">plain</option>
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43 <option value="none">none</option>
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44 </param>
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45 <when value="log" />
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46 <when value="log-log"/>
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47 <when value="plain" />
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48 <when value="none"/>
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49 </conditional>
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50
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51 <conditional name="conf_lower">
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52 <param name="conf_lower" type="select" label="Type of conf.lower:">
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53 <option value="usual">usual</option>
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54 <option value="peto">peto</option>
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55 <option value="modified">modified</option>
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56 </param>
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57 <when value="usual" />
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58 <when value="peto" />
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59 <when value="modified" />
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60 </conditional>
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61
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62 </inputs>
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63 <outputs>
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64 <data format="csv" name="fit" label="survfit.csv" />
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65 <data format="png" name="png" label="survfit.png" />
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="test">
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70 <element name="test-data">
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71 <collection type="data">
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72 <element format="csv" name="input" label="test-data/input.csv"/>
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73 </collection>
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74 </element>
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75 </param>
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76 <output format="csv" name="fit" label="test-data/survfit.csv"/>
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77 <output fformat="png" name="png" label="test-data/survfit.png"/>
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78 </test>
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79 </tests>
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80 <help>
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81 **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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82 </help>
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83 <citations>
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84 <citation>https://CRAN.R-project.org/package=survival</citation>
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85 </citations>
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86 </tool>
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