Mercurial > repos > testtool > survival
view survival/survival.xml @ 26:7ed63f8104a5 draft
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author | testtool |
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date | Mon, 02 Oct 2017 10:22:28 -0400 |
parents | a0ae4293a398 |
children | 5fc179380f8c |
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<tool id="survival" name="survival" version="1.0.0"> <description>core survival analysis</description> <requirements> <requirement type="package" version="2.40_1">r-survival</requirement> </requirements> <command detect_errors="aggressive"> Rscript '$__tool_directory__/survival.R' '$input' '$type' '$error' '$conf_type' '$conf_lower' '$fit' '$png' </command> <inputs> <param format="csv" type="data" name="input" value="" label="survival data" help=" e.g. survival table X obsT status X1 X2 17 1815 FALSE 2 HOXA1 18 145 TRUE 1 HOXA1 19 2506 FALSE 1 HOXA1 20 1382 TRUE 1 HOXA1 ''"/> <conditional name="typeselection"> <param name="typeselection" type="select" label="Type of survival curve:"> <option value="kaplan-meier">kaplan-meier</option> <option value="fleming-harrington">fleming-harrington</option> <option value="fh2">fh2</option> </param> <when value="kaplan-meier"> <param name = "type" value = "kaplan-meier"/> <when/> <when value="fleming-harrington"> <param name = "type" value="fleming-harrington"/> <when/> <when value="fh2"> <param name = "type" value="fh2"/> <when/> </conditional> <conditional name="error"> <param name="error" type="select" label="Type of error:"> <option value="greenwood">greenwood</option> <option value="tsiatis">tsiatis</option> </param> <when value="greenwood" /> <when value="tsiatis"/> </conditional> <conditional name="conf_type"> <param name="conf_type" type="select" label="Type of conf.type:"> <option value="log">log</option> <option value="log-log">log-log</option> <option value="plain">plain</option> <option value="none">none</option> </param> <when value="log" /> <when value="log-log"/> <when value="plain" /> <when value="none"/> </conditional> <conditional name="conf_lower"> <param name="conf_lower" type="select" label="Type of conf.lower:"> <option value="usual">usual</option> <option value="peto">peto</option> <option value="modified">modified</option> </param> <when value="usual" /> <when value="peto" /> <when value="modified" /> </conditional> </inputs> <outputs> <data format="csv" name="fit" label="survfit.csv" /> <data format="png" name="png" label="survfit.png" /> </outputs> <tests> <test> <param name="test"> <element name="test-data"> <collection type="data"> <element format="csv" name="input" label="test-data/input.csv"/> </collection> </element> </param> <output format="csv" name="fit" label="test-data/survfit.csv"/> <output fformat="png" name="png" label="test-data/survfit.png"/> </test> </tests> <help> **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.** </help> <citations> <citation>https://CRAN.R-project.org/package=survival</citation> </citations> </tool>