# HG changeset patch
# User testtool
# Date 1506723087 14400
# Node ID 6cc0c5eb71b2db969136392b42cbce807502d1bd

Uploaded

diff -r 000000000000 -r 6cc0c5eb71b2 survival/._.DS_Store
Binary file survival/._.DS_Store has changed
diff -r 000000000000 -r 6cc0c5eb71b2 survival/._survival.xml
Binary file survival/._survival.xml has changed
diff -r 000000000000 -r 6cc0c5eb71b2 survival/survival.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/survival/survival.R	Fri Sep 29 18:11:27 2017 -0400
@@ -0,0 +1,18 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+input =args[1]
+fit = args[2]
+png = args[3]
+
+#fit a Kaplan-Meier and plot it
+input<-("test-data/input.csv")
+fit <- survfit(Surv(obsT, status) ~ X1, type="kaplan-meier", conf.type="log", data=read.csv(input))
+
+res <- summary(fit,times=c(1,2,3))
+save.df <- as.data.frame(res[c("strata", "time", "n.risk", "n.event", "surv", "std.err", "lower", "upper")])
+write.csv(save.df, file = "survfit.csv")
+
+png("fit.png")
+plot(fit)
+dev.off()
+
diff -r 000000000000 -r 6cc0c5eb71b2 survival/survival.xml
--- /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>
diff -r 000000000000 -r 6cc0c5eb71b2 survival/test-data/._.DS_Store
Binary file survival/test-data/._.DS_Store has changed
diff -r 000000000000 -r 6cc0c5eb71b2 survival/test-data/fit.png
Binary file survival/test-data/fit.png has changed
diff -r 000000000000 -r 6cc0c5eb71b2 survival/test-data/input.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/survival/test-data/input.csv	Fri Sep 29 18:11:27 2017 -0400
@@ -0,0 +1,16 @@
+"","obsT","status","X1","X2"
+"17",1815,FALSE,"2","HOXA1"
+"18",145,TRUE,"1","HOXA1"
+"19",2506,FALSE,"1","HOXA1"
+"20",1382,TRUE,"1","HOXA1"
+"21",2561,FALSE,"2","HOXA1"
+"22",740,TRUE,"1","HOXA1"
+"23",322,TRUE,"1","HOXA1"
+"24",8,TRUE,"1","HOXA1"
+"25",235,TRUE,"2","HOXA1"
+"26",1430,FALSE,"1","HOXA1"
+"27",22,TRUE,"1","HOXA1"
+"28",214,TRUE,"1","HOXA1"
+"30",277,TRUE,"1","HOXA1"
+"31",1740,FALSE,"1","HOXA1"
+"32",478,TRUE,"1","HOXA1"
diff -r 000000000000 -r 6cc0c5eb71b2 survival/test-data/survfit.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/survival/test-data/survfit.csv	Fri Sep 29 18:11:27 2017 -0400
@@ -0,0 +1,7 @@
+"","strata","time","n.risk","n.event","surv","std.err","lower","upper"
+"1","X1=1",1,12,0,1,0,1,1
+"2","X1=1",2,12,0,1,0,1,1
+"3","X1=1",3,12,0,1,0,1,1
+"4","X1=2",1,3,0,1,0,1,1
+"5","X1=2",2,3,0,1,0,1,1
+"6","X1=2",3,3,0,1,0,1,1