diff survival/survival.xml @ 3:e31c47bf46a4 draft

Uploaded

--- a/survival/survival.xml	Fri Sep 29 18:41:35 2017 -0400
+++ b/survival/survival.xml	Mon Oct 02 07:54:12 2017 -0400
@@ -4,10 +4,85 @@
         <requirement type="package" version="2.40_1">r-survival</requirement>
     </requirements>
     <command detect_errors="aggressive">
-        Rscript '$__tool_directory__/survival.R' '$input'  '$fit'  '$png'
+        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. ''"/>
+        <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">
+        <param name="type" type="text" value="kaplan-meier" label="kaplan-meier" />
+      </when>
+      <when value="fleming-harrington">
+        <param name="type" type="text" value="fleming-harrington" label="fleming-harrington" />
+      </when>
+      <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>
+      <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="log">
+        <param name="type" type="text" value="log" label="log" />
+      </when>
+      <when value="log-log">
+        <param name="type" type="text" value="log-log" label="log-log" />
+      </when>
+      <when value="plain">
+        <param name="type" type="text" value="plain" label="plain" />
+      </when>
+       <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">
+        <param name="type" type="text" value="usual" label="usual" />
+      </when>
+      <when value="peto">
+        <param name="type" type="text" value="peto" label="peto" />
+      </when>
+      <when value="modified">
+        <param name="type" type="text" value="modified" label="modified" />
+      </when>
+    </conditional>
+    
     </inputs>
     <outputs>
         <data format="csv" name="fit" label="survfit.csv" />
@@ -27,7 +102,7 @@
         </test>
     </tests>
   <help>
-**Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier**
+**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>