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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="select_type1">
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19 <param name="input_type_selector1" type="select" label="Type of survival curve:">
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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">fleming-harrington</option>
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23 </param>
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24 <when value="kaplan-meier">
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25 <param name="type" type="text" value="kaplan-meier" label="kaplan-meier" />
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26 </when>
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27 <when value="fleming-harrington">
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28 <param name="type" type="text" value="fleming-harrington" label="fleming-harrington" />
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29 </when>
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30 <when value="fh2">
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31 <param name="type" type="text" value="fh2" label="fh2" />
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32 </when>
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33 </conditional>
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34
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35 <conditional name="select_type2">
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36 <param name="input_type_selector2" type="select" label="Type of error:">
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37 <option value="greenwood">greenwood</option>
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38 <option value="tsiatis">tsiatis</option>
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39 </param>
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40 <when value="greenwood">
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41 <param name="type" type="text" value="greenwood" label="greenwood" />
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42 </when>
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43 <when value="tsiatis">
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44 <param name="type" type="text" value="tsiatis" label="tsiatis" />
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45 </when>
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46 </conditional>
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47
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48 <conditional name="select_type3">
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49 <param name="input_type_selector3" type="select" label="Type of conf.type:">
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50 <option value="log">log</option>
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51 <option value="log-log">log-log</option>
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52 <option value="plain">plain</option>
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53 <option value="none">none</option>
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54 </param>
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55 <when value="log">
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56 <param name="type" type="text" value="log" label="log" />
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57 </when>
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58 <when value="log-log">
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59 <param name="type" type="text" value="log-log" label="log-log" />
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60 </when>
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61 <when value="plain">
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62 <param name="type" type="text" value="plain" label="plain" />
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63 </when>
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64 <when value="none">
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65 <param name="type" type="text" value="none" label="none" />
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66 </when>
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67 </conditional>
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68
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69 <conditional name="select_type4">
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70 <param name="input_type_selector4" type="select" label="Type of conf.lower:">
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71 <option value="usual">usual</option>
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72 <option value="peto">fleming-harrington</option>
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73 <option value="modified">fleming-harrington</option>
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74 </param>
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75 <when value="usual">
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76 <param name="type" type="text" value="usual" label="usual" />
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77 </when>
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78 <when value="peto">
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79 <param name="type" type="text" value="peto" label="peto" />
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80 </when>
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81 <when value="modified">
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82 <param name="type" type="text" value="modified" label="modified" />
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83 </when>
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84 </conditional>
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85
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86 </inputs>
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87 <outputs>
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88 <data format="csv" name="fit" label="survfit.csv" />
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89 <data format="png" name="png" label="survfit.png" />
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="test">
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94 <element name="test-data">
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95 <collection type="data">
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96 <element format="csv" name="input" label="test-data/input.csv"/>
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97 </collection>
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98 </element>
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99 </param>
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100 <output format="csv" name="fit" label="test-data/survfit.csv"/>
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101 <output fformat="png" name="png" label="test-data/survfit.png"/>
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102 </test>
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103 </tests>
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104 <help>
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105 **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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106 </help>
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107 <citations>
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108 <citation>https://CRAN.R-project.org/package=survival</citation>
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109 </citations>
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110 </tool>
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