# HG changeset patch
# User rhpvorderman
# Date 1532526580 14400
# Node ID bfc8a44fce7545f7984b4bcd850448a224869ae4
# Parent  b40737d199540e76be1140b4d01984c3c54381b2
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110

diff -r b40737d19954 -r bfc8a44fce75 data_manager/data_manager_select_index_by_path.xml
--- a/data_manager/data_manager_select_index_by_path.xml	Mon Jul 16 10:42:19 2018 -0400
+++ b/data_manager/data_manager_select_index_by_path.xml	Wed Jul 25 09:49:40 2018 -0400
@@ -7,7 +7,7 @@
     </requirements>
     <description>Link to indexes on the filesystem that have already been built</description>
     <command detect_errors="exit_code"><![CDATA[
-        python $__tool_directory__/path_name_value_key_manager.py
+        python3 $__tool_directory__/path_name_value_key_manager.py
         --value "${value}"
         --dbkey "${dbkey}"
         --name "${name}"
@@ -39,6 +39,8 @@
                 <option value='picard_indexes'>picard_indexes</option>
                 <option value='tophat2_indexes'>tophat2_indexes</option>
                 <option value="rnastar_index2">rnastar_index2</option>
+                <option value="kraken_databases">kraken_database</option>
+                <option value="centrifuge_indices">centrifuge_indices</option>
             </param>
             <when value="rnastar_index2">
                 <param name="with_gtf" type="select" value="" label="Index with embedded gtf?">
diff -r b40737d19954 -r bfc8a44fce75 data_manager/indexes.yml
--- a/data_manager/indexes.yml	Mon Jul 16 10:42:19 2018 -0400
+++ b/data_manager/indexes.yml	Wed Jul 25 09:49:40 2018 -0400
@@ -117,3 +117,15 @@
   name: tophat2 index
   extensions:
     - .bt2
+
+centrifuge_indices:
+  name: Centrifuge index
+  folder: []
+  prefix: false
+
+kraken_databases:
+  name: Kraken database
+  folder:
+    - database.idx
+    - database.kdb
+  prefix: false
\ No newline at end of file
diff -r b40737d19954 -r bfc8a44fce75 tool-data/centrifuge_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/centrifuge_indices.loc.sample	Wed Jul 25 09:49:40 2018 -0400
@@ -0,0 +1,17 @@
+# centrifuge_indices.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for GOTTCHA.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a bowtie_indices.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample), 
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has three text columns seperated by TABS.
+#
+# <unique_id>	<display_name>	<file_base_path>
+#
+#bacteria_v20150825	Bacteria	/depot/data2/galaxy/gottcha/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species
+#viruses_v20150825	Viruses	/depot/data2/galaxy/gottcha/GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species
+test	test	foo/bar/baz
diff -r b40737d19954 -r bfc8a44fce75 tool-data/kraken_databases.loc.sample
diff -r b40737d19954 -r bfc8a44fce75 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Jul 16 10:42:19 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Wed Jul 25 09:49:40 2018 -0400
@@ -52,4 +52,12 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/tophat2_indices.loc" />
     </table>
+    <table name="kraken_databases" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/kraken_databases.loc" />
+    </table>
+        <table name="centrifuge_indices" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/centrifuge_indices.loc" />
+    </table>
  </tables>