comparison survival/survival.xml @ 17:2d38d5edc913 draft

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16:53dff79c833b

    <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="select_type1">
      <param name="input_type_selector1" type="select" label="Type of survival curve:">
        <option value="kaplan-meier">kaplan-meier</option>
        <option value="fleming-harrington">fleming-harrington</option>
        <option value="fh2">fleming-harrington</option>
      </param>
      <when value="kaplan-meier">

      <when value="fh2">
        <param name="type" type="text" value="fh2" label="fh2" />
      </when>
    </conditional>
    
    <conditional name="select_type2">
      <param name="input_type_selector2" type="select" label="Type of error:">
        <option value="greenwood">greenwood</option>
        <option value="tsiatis">tsiatis</option>
      </param>
      <when value="greenwood">
        <param name="type" type="text" value="greenwood" label="greenwood" />

      <when value="tsiatis">
        <param name="type" type="text" value="tsiatis" label="tsiatis" />
      </when>
    </conditional>
       
          <conditional name="select_type3">
      <param name="input_type_selector3" 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="none">
        <param name="type" type="text" value="none" label="none" />
      </when>
    </conditional>
    
        <conditional name="select_type4">
      <param name="input_type_selector4" type="select" label="Type of conf.lower:">
        <option value="usual">usual</option>
        <option value="peto">fleming-harrington</option>
        <option value="modified">fleming-harrington</option>
      </param>
      <when value="usual">

17:2d38d5edc913

    <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="type">
      <param name="type" type="select" label="Type of survival curve:">
        <option value="kaplan-meier">kaplan-meier</option>
        <option value="fleming-harrington">fleming-harrington</option>
        <option value="fh2">fleming-harrington</option>
      </param>
      <when value="kaplan-meier">

      <when value="fh2">
        <param name="type" type="text" value="fh2" label="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">
        <param name="type" type="text" value="greenwood" label="greenwood" />

      <when value="tsiatis">
        <param name="type" type="text" value="tsiatis" label="tsiatis" />
      </when>
    </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="none">
        <param name="type" type="text" value="none" label="none" />
      </when>
    </conditional>
    
        <conditional name="conf_lower">
      <param name="conf_lower" type="select" label="Type of conf_lower:">
        <option value="usual">usual</option>
        <option value="peto">fleming-harrington</option>
        <option value="modified">fleming-harrington</option>
      </param>
      <when value="usual">