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changeset 15:37a59e6c6c02 draft

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Deleted selected files
author testtool
date Mon, 02 Oct 2017 08:23:11 -0400
parents 35ab97d72ea7
children 53dff79c833b
files survival.xml
diffstat 1 files changed, 0 insertions(+), 110 deletions(-) [+]
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line diff
--- a/survival.xml	Mon Oct 02 08:23:07 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,110 +0,0 @@
-<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="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" />
-        <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>