From f762bd37805fe4c20d9bbcc336d26edbcf6b2d57 Mon Sep 17 00:00:00 2001
From: Richard Burhans <burhans@bx.psu.edu>
Date: Wed, 21 Sep 2011 16:50:18 -0400
Subject: [PATCH] aaChanges tool: Added an option to keep the columns from the
 SNP dataset

---
 tools/evolution/codingSnps.xml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/evolution/codingSnps.xml b/tools/evolution/codingSnps.xml
index c9c8ccdf4ac..59ac49e721a 100644
--- a/tools/evolution/codingSnps.xml
+++ b/tools/evolution/codingSnps.xml
@@ -2,7 +2,7 @@
   <description>amino-acid changes caused by a set of SNPs</description>
 
   <command interpreter="perl">
-    codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 > $out_file1
+    codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep > $out_file1
   </command>
 
   <inputs>
@@ -13,6 +13,10 @@
     <param format="interval" name="input2" type="data" label="Gene dataset">
       <validator type="dataset_metadata_in_file" filename="codingSnps.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are not currently available for the specified build." split="\t" />
     </param>
+    <param name="keep" type="select" label="Keep columns from SNP dataset">
+      <option value="0" selected="true">No</option>
+      <option value="1">Yes</option>
+    </param>
   </inputs>
 
   <outputs>