# HG changeset patch
# User yating-l
# Date 1493914949 14400
# Node ID 95f5152ffac482978fdf9003d0b2c9b8fa1aa78b
# Parent  45bcb36d6cfe717d120ba7dca44db204e8700611
planemo upload

diff -r 45bcb36d6cfe -r 95f5152ffac4 data_manager_conf.xml
--- a/data_manager_conf.xml	Thu May 04 12:12:12 2017 -0400
+++ b/data_manager_conf.xml	Thu May 04 12:22:29 2017 -0400
@@ -8,9 +8,10 @@
                     <column name="path" output_ref="out_file">
                         <move type="directory">
                             <source>${path}</source>
-                            <target base="${GALAXY_DATA_MANAGER_DATA_PATH">${value}</target>
+                            <target base="${GALAXY_DATA_MANAGER_DATA_PATH">${value}/${path}</target>
                         </move>
-                        <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}</value_translation>
+                        <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/${path}</value_translation>
+                        <value_translation type="function">abspath</value_translation>
                     </column>
                 </output>
             </data_table>
diff -r 45bcb36d6cfe -r 95f5152ffac4 tool-data/glimmer_hmm.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/glimmer_hmm.loc.sample	Thu May 04 12:22:29 2017 -0400
@@ -0,0 +1,16 @@
+#This file lists the locations of all the trained_dir files
+#under the "trained_dir" directory (a directory that contains a directory
+#for each organism used by glimmer_hmm).
+#This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_id>	<display_name>	<file_path>
+#
+#glimmer_hmm.loc could look something like this:
+#
+#human  Human   /path/to/trained_dir/human
+#celegans   Celegan /path/to/trained_dir/Celegans
+#arabidopsis    Arabidopsis /path/to/trained_dir/arabidopsis
+#rice   Rice    /path/to/trained_dir/rice
+#zebrafish  Zebrafish   /path/to/trained_dir/zebrafish
+#