changeset 1:fbe4eedec466 draft

Uploaded

--- a/diamand.xml	Sat Feb 07 05:23:48 2015 -0500
+++ b/diamand.xml	Sat Feb 07 05:32:30 2015 -0500
@@ -71,9 +71,8 @@
           </param>
           <when value="indexed">
             <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
-              <options from_data_table="diamond_indexes">
+              <options from_data_table="diamond_database">
                 <column name="value" index="0"/>
-                <column name="dbkey" index="1"/>
                 <column name="name" index="2"/>
                 <column name="db_path" index="3"/>
                 <filter type="sort_by" column="2"/>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/diamond_database.loc.sample	Sat Feb 07 05:32:30 2015 -0500
@@ -0,0 +1,10 @@
+#This is a sample file that enables the diamind to find the protein databases
+#You will need to create these data files and then create 
+#a diamond_database.loc file similar to this one (store it in this directory) 
+#that points to the directories in which those files are stored. 
+#The diamond_database_indices.loc file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <display_name>   <file_base_path>
+#
+#So, for example:
+#ncbi_nr	NCBI NR database (1-1-2015)	/data/db/diamond/1-1-2015/nr.dmnd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Sat Feb 07 05:32:30 2015 -0500
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Locations of indexes in the Bowtie mapper format -->
+    <table name="diamond_database" comment_char="#">
+        <columns>value, name, db_path</columns>
+        <file path="tool-data/diamond_database.loc" />
+    </table>
+</tables>