Mercurial > repos > testtool > survival
comparison survival/survival.xml @ 16:53dff79c833b draft
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author | testtool |
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date | Mon, 02 Oct 2017 08:23:18 -0400 |
parents | bc54ac99e130 |
children | 2d38d5edc913 |
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15:37a59e6c6c02 | 16:53dff79c833b |
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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" /> |