# HG changeset patch
# User melissacline
# Date 1411532334 25200
# Node ID 7f03b062f3300c45cf98d28928467f20b4f10b55
# Parent  ff0cdac9636e4043e137b92a896c5a2d80bb1a4a
Cleaned up the user interface a bit

diff -r ff0cdac9636e -r 7f03b062f330 xena_import.py
--- a/xena_import.py	Mon Sep 15 12:05:28 2014 -0700
+++ b/xena_import.py	Tue Sep 23 21:18:54 2014 -0700
@@ -43,7 +43,12 @@
     fp.close()
 
     # Finally, copy the genomic data into the Xena directory
-    shutil.copy(args.genomicDataPathname, xenaFileDir)
+    try:
+        shutil.copy(args.genomicDataPathname, xenaFileDir)
+    except:
+        print "Unexpected error", sys.exc_info()[0]
+    else:
+        print "Data copied successfully to Xena"
 
 if __name__ == "__main__":
     main()
diff -r ff0cdac9636e -r 7f03b062f330 xena_import.xml
--- a/xena_import.xml	Mon Sep 15 12:05:28 2014 -0700
+++ b/xena_import.xml	Tue Sep 23 21:18:54 2014 -0700
@@ -4,13 +4,20 @@
     <requirement type="package" version="1.0">installXena</requirement>
   </requirements>
   <command interpreter="python">
-    xena_import.py ${xenaInputData} ${cohort} ${metadataType} 
+    xena_import.py ${xenaInputData} ${cohort} ${metadataType} > ${outfile}
   </command>
   <inputs>
     <param format="data" type="data" name="xenaInputData" label="Data to import to Xena" optional="false"/>
     <param format="str" type="text" name="cohort" label="Cohort" optional="false"/>
-    <param format="str" type="text" name="metadataType" label="Data Type (e.g. clinicalMatrix)" optional="false"/>
+    <param format="str" type="select" name="metadataType" label="File Format">
+      <option value="genomicMatrix">Rows(Identifiers) by Columns (Samples)</option>
+      <option value="clinicalMatrix">Rows(Samples) by Columns (Identifiers)</option>
+      <option value="mutationVector">Mutation Data</option>
+    </param>
   </inputs>
+  <outputs>
+    <data foramt="txt" name="outfile"/>
+  </outputs>
   <help>
     To Appear
   </help>