comparison survival/survival.xml @ 24:51181b91c57e draft

Uploaded

23:501cd6a5cd31

    <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' 
    </command>
<inputs>
        <param format="csv" type="data" name="input"  value="" label="survival data" help="
   e.g. survival table
   X obsT status X1    X2

    <param name="typeselect" 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="quantile" />
  <when value="kaplan-meier"/>
  <when value="fleming-harrington"/>
  <when value="fh2"/>
          </conditional>
    
     <conditional name="error">
      <param name="error" type="select" label="Type of error:">
        <option value="greenwood">greenwood</option>
        <option value="tsiatis">tsiatis</option>
      </param>
    </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>
    </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>
    </conditional>
    
    </inputs>
    <outputs>
        <data format="csv" name="fit" label="survfit.csv" />

24:51181b91c57e

    <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

    <param name="typeselect" 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"/>
  <when value="fleming-harrington"/>
  <when value="fh2"/>
          </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" />