From 10266414252fc8a001ecc6ae8843bffd5e660f2e Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Wed, 8 Jun 2011 13:25:45 -0400
Subject: [PATCH] Don't provde the output filename to the upload tool if it's
 outside Galaxy's files_path, since this means we're only linking data and the
 output paths are not used (and may contain non-shell-safe characters).  Fixes
 issue #533.

---
 tools/data_source/upload.xml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml
index 138d97f4ee4..52baca23d50 100644
--- a/tools/data_source/upload.xml
+++ b/tools/data_source/upload.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 
-<tool name="Upload File" id="upload1" version="1.1.2">
+<tool name="Upload File" id="upload1" version="1.1.3">
   <description>
     from your computer  
   </description>
@@ -11,7 +11,12 @@
     #while $varExists('output%i' % $outnum):
         #set $output = $getVar('output%i' % $outnum)
         #set $outnum += 1
-        ${output.dataset.dataset.id}:${output.files_path}:${output}
+        #set $file_name = $output.file_name
+        ## FIXME: This is not future-proof for other uses of external_filename (other than for use by the library upload's "link data" feature)
+        #if $output.dataset.dataset.external_filename:
+            #set $file_name = "None"
+        #end if
+        ${output.dataset.dataset.id}:${output.files_path}:${file_name}
     #end while
   </command>
   <inputs nginx_upload="true">