# HG changeset patch
# User bcrain-completegenomics
# Date 1339091208 14400
# Node ID 551fce709627e973942721e80e7d49f4691dc587
# Parent  a48451470c73b716cd214063740a6a93e553759a
Uploaded

diff -r a48451470c73 -r 551fce709627 cgatools_suite/.DS_Store
Binary file cgatools_suite/.DS_Store has changed
diff -r a48451470c73 -r 551fce709627 cgatools_suite/._datatypes_conf.xml
Binary file cgatools_suite/._datatypes_conf.xml has changed
diff -r a48451470c73 -r 551fce709627 cgatools_suite/._tool_config.xml
Binary file cgatools_suite/._tool_config.xml has changed
diff -r a48451470c73 -r 551fce709627 cgatools_suite/._tool_config.xml.sample.xml
Binary file cgatools_suite/._tool_config.xml.sample.xml has changed
diff -r a48451470c73 -r 551fce709627 cgatools_suite/._tool_data_table_conf.xml
Binary file cgatools_suite/._tool_data_table_conf.xml has changed
diff -r a48451470c73 -r 551fce709627 cgatools_suite/._tool_data_table_conf.xml.sample.xml
Binary file cgatools_suite/._tool_data_table_conf.xml.sample.xml has changed
diff -r a48451470c73 -r 551fce709627 cgatools_suite/datatypes_conf.xml
--- a/cgatools_suite/datatypes_conf.xml	Wed Jun 06 18:24:37 2012 -0400
+++ b/cgatools_suite/datatypes_conf.xml	Thu Jun 07 13:46:48 2012 -0400
@@ -9,9 +9,9 @@
       Add the following section to datatypes_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
     -->
     <!-- Start Complete Genomics Datatypes -->
-    <datatype extension="cg_var" type="galaxy.datatypes.completegenomics:CG_Var" display_in_upload="true" />
-    <datatype extension="cg_mastervar" type="galaxy.datatypes.completegenomics:CG_MasterVar" display_in_upload="true" />
-    <datatype extension="cg_gene" type="galaxy.datatypes.completegenomics:CG_Gene" display_in_upload="true" />
+    <datatype extension="cg_var" type="galaxy.datatypes.tabular:CG_Var" display_in_upload="true" />
+    <datatype extension="cg_mastervar" type="galaxy.datatypes.tabular:CG_MasterVar" display_in_upload="true" />
+    <datatype extension="cg_gene" type="galaxy.datatypes.tabular:CG_Gene" display_in_upload="true" />
     <!-- End Complete Genomics Datatypes -->
   </registration>
   <sniffers>
diff -r a48451470c73 -r 551fce709627 cgatools_suite/tool_config.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cgatools_suite/tool_config.xml	Thu Jun 07 13:46:48 2012 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<toolbox>
+    <!-- 
+      Add the following section to tool_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
+    -->
+  <section name="Complete Genomics" id="cgi">
+    <label text="cgatools" id="cgi_cgatools" />
+    <tool file="cgatools/listvariants.xml" />
+    <tool file="cgatools/testvariants.xml" />
+    <tool file="cgatools/listtestvariants.xml" />
+    <tool file="cgatools/join.xml" />
+    <tool file="cgatools/calldiff.xml" />
+    <tool file="cgatools/snpdiff.xml" />
+    <tool file="cgatools/junctiondiff.xml" />
+    <tool file="cgatools/varfilter.xml" />
+    <label text="Perl scripts" id="cgi_perl" />
+    <tool file="cgi_scripts/List_Unique_Variants.xml" />
+    <tool file="cgi_scripts/Calculate_TestVariants_Variant_Frequencies.xml" />
+  </section>
+</toolbox>
\ No newline at end of file
diff -r a48451470c73 -r 551fce709627 cgatools_suite/tool_config.xml.sample.xml
--- a/cgatools_suite/tool_config.xml.sample.xml	Wed Jun 06 18:24:37 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-<?xml version="1.0"?>
-<toolbox>
-    <!-- 
-      Add the following section to tool_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
-    -->
-  <section name="Complete Genomics" id="cgi">
-    <label text="cgatools" id="cgi_cgatools" />
-    <tool file="cgatools/listvariants.xml" />
-    <tool file="cgatools/testvariants.xml" />
-    <tool file="cgatools/listtestvariants.xml" />
-    <tool file="cgatools/join.xml" />
-    <tool file="cgatools/calldiff.xml" />
-    <tool file="cgatools/snpdiff.xml" />
-    <tool file="cgatools/junctiondiff.xml" />
-    <tool file="cgatools/varfilter.xml" />
-    <label text="Perl scripts" id="cgi_perl" />
-    <tool file="cgi_scripts/List_Unique_Variants.xml" />
-    <tool file="cgi_scripts/Calculate_TestVariants_Variant_Frequencies.xml" />
-  </section>
-</toolbox>
\ No newline at end of file
diff -r a48451470c73 -r 551fce709627 cgatools_suite/tool_data_table_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cgatools_suite/tool_data_table_conf.xml	Thu Jun 07 13:46:48 2012 -0400
@@ -0,0 +1,12 @@
+<tables>
+    <!-- 
+         Add the following section to tool_data_table_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
+    -->
+    <!-- Start Location of cgatools crr files -->
+    <table name="cg_crr_files" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/cg_crr_files.loc" />
+    </table>
+    <!-- End Location of cgatools crr files -->
+</tables>
+
diff -r a48451470c73 -r 551fce709627 cgatools_suite/tool_data_table_conf.xml.sample.xml
--- a/cgatools_suite/tool_data_table_conf.xml.sample.xml	Wed Jun 06 18:24:37 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<tables>
-    <!-- 
-         Add the following section to tool_data_table_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
-    -->
-    <!-- Start Location of cgatools crr files -->
-    <table name="cg_crr_files" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/cg_crr_files.loc" />
-    </table>
-    <!-- End Location of cgatools crr files -->
-</tables>
-