Mercurial > repos > testtool > survival
comparison survival/survival.xml @ 3:e31c47bf46a4 draft
Uploaded
author | testtool |
---|---|
date | Mon, 02 Oct 2017 07:54:12 -0400 |
parents | 6cc0c5eb71b2 |
children | 4aad7b654682 |
comparison
equal
deleted
inserted
replaced
2:ce6df2bd21cd | 3:e31c47bf46a4 |
---|---|
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' '$fit' '$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="e.g. ''"/> | 10 <param format="csv" type="data" name="input" value="" label="survival data" help=" |
11 e.g. survival table | |
12 X obsT status X1 X2 | |
13 17 1815 FALSE 2 HOXA1 | |
14 18 145 TRUE 1 HOXA1 | |
15 19 2506 FALSE 1 HOXA1 | |
16 20 1382 TRUE 1 HOXA1 ''"/> | |
17 | |
18 <conditional name="select_type1"> | |
19 <param name="input_type_selector1" type="select" label="Type of survival curve:"> | |
20 <option value="kaplan-meier">kaplan-meier</option> | |
21 <option value="fleming-harrington">fleming-harrington</option> | |
22 <option value="fh2">fleming-harrington</option> | |
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> | |
33 </conditional> | |
34 | |
35 <conditional name="select_type2"> | |
36 <param name="input_type_selector2" type="select" label="Type of error:"> | |
37 <option value="greenwood">greenwood</option> | |
38 <option value="tsiatis">tsiatis</option> | |
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> | |
46 </conditional> | |
47 | |
48 <conditional name="select_type3"> | |
49 <param name="input_type_selector3" type="select" label="Type of conf.type:"> | |
50 <option value="log">log</option> | |
51 <option value="log-log">log-log</option> | |
52 <option value="plain">plain</option> | |
53 <option value="none">none</option> | |
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> | |
67 </conditional> | |
68 | |
69 <conditional name="select_type4"> | |
70 <param name="input_type_selector4" type="select" label="Type of conf.lower:"> | |
71 <option value="usual">usual</option> | |
72 <option value="peto">fleming-harrington</option> | |
73 <option value="modified">fleming-harrington</option> | |
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> | |
84 </conditional> | |
85 | |
11 </inputs> | 86 </inputs> |
12 <outputs> | 87 <outputs> |
13 <data format="csv" name="fit" label="survfit.csv" /> | 88 <data format="csv" name="fit" label="survfit.csv" /> |
14 <data format="png" name="png" label="survfit.png" /> | 89 <data format="png" name="png" label="survfit.png" /> |
15 </outputs> | 90 </outputs> |
25 <output format="csv" name="fit" label="test-data/survfit.csv"/> | 100 <output format="csv" name="fit" label="test-data/survfit.csv"/> |
26 <output fformat="png" name="png" label="test-data/survfit.png"/> | 101 <output fformat="png" name="png" label="test-data/survfit.png"/> |
27 </test> | 102 </test> |
28 </tests> | 103 </tests> |
29 <help> | 104 <help> |
30 **Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier** | 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.** |
31 </help> | 106 </help> |
32 <citations> | 107 <citations> |
33 <citation>https://CRAN.R-project.org/package=survival</citation> | 108 <citation>https://CRAN.R-project.org/package=survival</citation> |
34 </citations> | 109 </citations> |
35 </tool> | 110 </tool> |