comparison survival/survival.xml @ 16:53dff79c833b draft

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author testtool
date Mon, 02 Oct 2017 08:23:18 -0400
parents bc54ac99e130
children 2d38d5edc913
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15:37a59e6c6c02 16:53dff79c833b
2 <description>core survival analysis</description> 2 <description>core survival analysis</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.40_1">r-survival</requirement> 4 <requirement type="package" version="2.40_1">r-survival</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"> 6 <command detect_errors="aggressive">
7 Rscript '$__tool_directory__/survival.R' '$input' '$type' '$error' '$conf_type' '$conf_lower' '$fit' '$png' 7 Rscript '$__tool_directory__/survival.R' '$input' '$type' '$error' '$conf.type' '$conf.lower' '$fit' '$png'
8 </command> 8 </command>
9 <inputs> 9 <inputs>
10 <param format="csv" type="data" name="input" value="" label="survival data" help=" 10 <param format="csv" type="data" name="input" value="" label="survival data" help="
11 e.g. survival table 11 e.g. survival table
12 X obsT status X1 X2 12 X obsT status X1 X2
13 17 1815 FALSE 2 HOXA1 13 17 1815 FALSE 2 HOXA1
14 18 145 TRUE 1 HOXA1 14 18 145 TRUE 1 HOXA1
15 19 2506 FALSE 1 HOXA1 15 19 2506 FALSE 1 HOXA1
16 20 1382 TRUE 1 HOXA1 ''"/> 16 20 1382 TRUE 1 HOXA1 ''"/>
17 17
18 <conditional name="type"> 18 <conditional name="select_type1">
19 <param name="type" type="select" label="Type of survival curve:"> 19 <param name="input_type_selector1" type="select" label="Type of survival curve:">
20 <option value="kaplan-meier">kaplan-meier</option> 20 <option value="kaplan-meier">kaplan-meier</option>
21 <option value="fleming-harrington">fleming-harrington</option> 21 <option value="fleming-harrington">fleming-harrington</option>
22 <option value="fh2">fh2</option> 22 <option value="fh2">fleming-harrington</option>
23 </param> 23 </param>
24 <when value="kaplan-meier">
25 <param name="type" type="text" value="kaplan-meier" label="kaplan-meier" />
26 </when>
27 <when value="fleming-harrington">
28 <param name="type" type="text" value="fleming-harrington" label="fleming-harrington" />
29 </when>
30 <when value="fh2">
31 <param name="type" type="text" value="fh2" label="fh2" />
32 </when>
24 </conditional> 33 </conditional>
25 34
26 <conditional name="error"> 35 <conditional name="select_type2">
27 <param name="error" type="select" label="Type of error:"> 36 <param name="input_type_selector2" type="select" label="Type of error:">
28 <option value="greenwood">greenwood</option> 37 <option value="greenwood">greenwood</option>
29 <option value="tsiatis">tsiatis</option> 38 <option value="tsiatis">tsiatis</option>
30 </param> 39 </param>
40 <when value="greenwood">
41 <param name="type" type="text" value="greenwood" label="greenwood" />
42 </when>
43 <when value="tsiatis">
44 <param name="type" type="text" value="tsiatis" label="tsiatis" />
45 </when>
31 </conditional> 46 </conditional>
32 47
33 <conditional name="conf_type"> 48 <conditional name="select_type3">
34 <param name="conf_type" type="select" label="Type of conf_type:"> 49 <param name="input_type_selector3" type="select" label="Type of conf.type:">
35 <option value="log">log</option> 50 <option value="log">log</option>
36 <option value="log-log">log-log</option> 51 <option value="log-log">log-log</option>
37 <option value="plain">plain</option> 52 <option value="plain">plain</option>
38 <option value="none">none</option> 53 <option value="none">none</option>
39 </param> 54 </param>
55 <when value="log">
56 <param name="type" type="text" value="log" label="log" />
57 </when>
58 <when value="log-log">
59 <param name="type" type="text" value="log-log" label="log-log" />
60 </when>
61 <when value="plain">
62 <param name="type" type="text" value="plain" label="plain" />
63 </when>
64 <when value="none">
65 <param name="type" type="text" value="none" label="none" />
66 </when>
40 </conditional> 67 </conditional>
41 68
42 <conditional name="conf_lower"> 69 <conditional name="select_type4">
43 <param name="conf_lower" type="select" label="Type of conf_lower:"> 70 <param name="input_type_selector4" type="select" label="Type of conf.lower:">
44 <option value="usual">usual</option> 71 <option value="usual">usual</option>
45 <option value="peto">peto</option> 72 <option value="peto">fleming-harrington</option>
46 <option value="modified">modified</option> 73 <option value="modified">fleming-harrington</option>
47 </param> 74 </param>
75 <when value="usual">
76 <param name="type" type="text" value="usual" label="usual" />
77 </when>
78 <when value="peto">
79 <param name="type" type="text" value="peto" label="peto" />
80 </when>
81 <when value="modified">
82 <param name="type" type="text" value="modified" label="modified" />
83 </when>
48 </conditional> 84 </conditional>
49 85
50 </inputs> 86 </inputs>
51 <outputs> 87 <outputs>
52 <data format="csv" name="fit" label="survfit.csv" /> 88 <data format="csv" name="fit" label="survfit.csv" />