From 752c889dfa7db2d62379288eada28cbae86be4c0 Mon Sep 17 00:00:00 2001
From: Richard Burhans <burhans@bx.psu.edu>
Date: Mon, 20 Sep 2010 15:32:20 -0400
Subject: [PATCH] Reworked tool config for CTD tool due to potential bug in
 galaxy command line generation

---
 tools/human_genome_variation/ctd.xml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tools/human_genome_variation/ctd.xml b/tools/human_genome_variation/ctd.xml
index 28651312674..21b9ab93d03 100644
--- a/tools/human_genome_variation/ctd.xml
+++ b/tools/human_genome_variation/ctd.xml
@@ -2,13 +2,15 @@
   <description>analysis of chemicals, diseases, or genes</description>
 
   <command interpreter="perl">
+    ctd.pl $input $numerical_column $inType.inputType
     #if $inType.inputType == "disease"
-      ctd.pl $input $numerical_column $inType.inputType $inType.report ANY $out_file1
+      $inType.report ANY
     #else if $inType.reportType.report == "cgixns"
-      ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report $inType.reportType.actType $out_file1
+      $inType.reportType.report $inType.reportType.actType
     #else
-      ctd.pl $input $numerical_column $inType.inputType $inType.reportType.report ANY $out_file1
+      $inType.reportType.report ANY
     #end if
+    $out_file1
   </command>
 
   <inputs>