Added tool version directories for hyphy tools, also added galaxy/tools/util directory to house utility code used acroos multiple tools.

tool_conf.xml.main

@@ -127,9 +127,9 @@
 	-->
   </section>
  <section name="Evolution: HyPhy" id="hyphy">
-    <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
-    <tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
-    <tool file="hyphy/hyphy_dnds_wrapper.xml" />
+    <tool file="hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.xml" />
+    <tool file="hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.xml" />
+    <tool file="hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.xml" />
  </section>
  <!--
  These are deprecated

tool_conf.xml.sample

@@ -130,9 +130,9 @@
 	<tool file="regVariation/getIndels_3way.xml" />
   </section>
  <section name="Evolution: HyPhy" id="hyphy">
-    <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
-    <tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
-    <tool file="hyphy/hyphy_dnds_wrapper.xml" />
+    <tool file="hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.xml" />
+    <tool file="hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.xml" />
+    <tool file="hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.xml" />
  </section>
  <!--
  These are deprecated

tools/hyphy/hyphy_branch_lengths_wrapper1/1.0.0/hyphy_branch_lengths_wrapper.py

@@ -1,7 +1,7 @@
 #Dan Blankenberg
 #takes commandline tree def and input multiple fasta alignment file and runs the branch length ananlysis
 import os, sys
-import hyphy_util
+from galaxy.tools.util import hyphy_util
 
 #Retrieve hard coded hyphy path, this will need to be the same across the cluster
 HYPHY_PATH = hyphy_util.HYPHY_PATH

tools/hyphy/hyphy_dnds_wrapper1/1.0.0/hyphy_dnds_wrapper.py

@@ -1,7 +1,7 @@
 #Guru
 #takes fasta alignments, a distance metric and builds neighbor joining trees
 import os, sys
-import hyphy_util
+from galaxy.tools.util import hyphy_util
 
 #Retrieve hard coded hyphy path, this will need to be the same across the cluster
 HYPHY_PATH = hyphy_util.HYPHY_PATH

tools/hyphy/hyphy_nj_tree_wrapper1/1.0.0/hyphy_nj_tree_wrapper.py

@@ -1,7 +1,7 @@
 #Dan Blankenberg
 #takes fasta alignments, a distance metric and builds neighbor joining trees
 import os, sys
-import hyphy_util
+from galaxy.tools.util import hyphy_util
 
 #Retrieve hard coded hyphy path, this will need to be the same across the cluster
 HYPHY_PATH = hyphy_util.HYPHY_PATH