diff survival/survival.xml @ 0:6cc0c5eb71b2 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/survival/survival.xml	Fri Sep 29 18:11:27 2017 -0400
@@ -0,0 +1,35 @@
+<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'  '$fit'  '$png'
+    </command>
+<inputs>
+        <param format="csv" type="data" name="input"  value="" label="survival data" help="e.g. ''"/>
+    </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>
+**Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier**
+</help>
+<citations>
+ <citation>https://CRAN.R-project.org/package=survival</citation>
+</citations>
+</tool>