# HG changeset patch
# User david-hoover
# Date 1349388330 14400
# Node ID 0cd513d5ad7224c121d4753a7bbcc41b98407dbf
# Parent  6b847627403f9cc3ab8dec6d945ceee484b14db1
Uploaded

diff -r 6b847627403f -r 0cd513d5ad72 convertvcf4toannovar/convertvcf4toannovar.py
--- a/convertvcf4toannovar/convertvcf4toannovar.py	Thu Oct 04 17:56:51 2012 -0400
+++ b/convertvcf4toannovar/convertvcf4toannovar.py	Thu Oct 04 18:05:30 2012 -0400
@@ -1,6 +1,6 @@
 # convertvcf4toannovar.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
 # to make a new Galaxy tool called convertvcf4toannovar
-# User hooverdm@helix.nih.gov at 04/10/2012 17:56:26
+# User hooverdm@helix.nih.gov at 04/10/2012 18:05:10
 # rgToolFactory.py
 # see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
 # 
diff -r 6b847627403f -r 0cd513d5ad72 convertvcf4toannovar/convertvcf4toannovar.xml
--- a/convertvcf4toannovar/convertvcf4toannovar.xml	Thu Oct 04 17:56:51 2012 -0400
+++ b/convertvcf4toannovar/convertvcf4toannovar.xml	Thu Oct 04 18:05:30 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="convertvcf4toannovar" name="convertvcf4toannovar" version="0.03">
+<tool id="convertvcf4toannovar" name="convertvcf4toannovar" version="0.04">
             <description>Convert VCF4 file to ANNOVAR input format</description>
             <command interpreter="python">
             convertvcf4toannovar.py --script_path "$runMe" --interpreter "sh" 
@@ -15,13 +15,7 @@
             </outputs>
             <configfiles>
             <configfile name="runMe">
-            #!/bin/bash
-
-
-export PATH=/usr/local/annovar:$PATH
-
-
-convert2annovar.pl $1 --format vcf4 > $2 2> /dev/null
+            convert2annovar.pl $1 --format vcf4 > $2 2> /dev/null
             </configfile>
             </configfiles>
             <tests><test>
@@ -38,8 +32,8 @@
 
 **Script**
 Pressing execute will run the following code over your input file and generate some outputs in your history::
- #!/bin/bash   export PATH=/usr/local/annovar:$PATH   convert2annovar.pl $1 --format vcf4 > $2 2> /dev/null
-**Attribution** This Galaxy tool was created by hooverdm@helix.nih.gov at 04/10/2012 17:56:26
+ convert2annovar.pl $1 --format vcf4 > $2 2> /dev/null
+**Attribution** This Galaxy tool was created by hooverdm@helix.nih.gov at 04/10/2012 18:05:10
 using the Galaxy Tool Factory.
 See https://bitbucket.org/fubar/galaxytoolfactory for details of that project
             </help>