# HG changeset patch
# User iuc
# Date 1506415561 14400
# Node ID b340f0750aa55f0ad62d6ed745db3b6286584422
# Parent  9bcfe0aabf5d2b3664383c8c11897bc9d0aef6aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447

diff -r 9bcfe0aabf5d -r b340f0750aa5 macros.xml
--- a/macros.xml	Sat Jul 01 17:45:57 2017 -0400
+++ b/macros.xml	Tue Sep 26 04:46:01 2017 -0400
@@ -27,9 +27,9 @@
             <when value="cached">
                 <param name="input_chain" type="select" label="Lift Over To">
                     <options from_file="liftOver.loc">
-                        <column name="name" index="1"/>
-                        <column name="value" index="2"/>
-                        <column name="dbkey" index="0"/>
+                        <column name="dbkey" index="0"/><!-- species/build 'from' -->
+                        <column name="name" index="1"/><!-- species/build 'to' -->
+                        <column name="value" index="2"/><!-- path of chain file -->
                         <filter type="data_meta" ref="input" key="dbkey" column="0"/>
                     </options>
                 </param>
diff -r 9bcfe0aabf5d -r b340f0750aa5 tool-data/liftOver.loc.sample
--- a/tool-data/liftOver.loc.sample	Sat Jul 01 17:45:57 2017 -0400
+++ b/tool-data/liftOver.loc.sample	Tue Sep 26 04:46:01 2017 -0400
@@ -8,6 +8,9 @@
 #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
 #then the liftOver.loc entry would look like this:
 #
+#<FromSpecies>  <ToSpecies> <PathToChainFile>
+#<dbkey>        <name>      <value>
+#
 #anoCar1	galGal3		/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
 #
 #and your /depot/data2/galaxy/anoCar1/liftOver directory would 
diff -r 9bcfe0aabf5d -r b340f0750aa5 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Sep 26 04:46:01 2017 -0400
@@ -0,0 +1,12 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of all liftOver files -->
+    <table name="liftOver" comment_char="#">
+         <columns>dbkey, name, value</columns>
+        <file path="tool-data/liftOver.loc" />
+    </table>
+</tables>