# HG changeset patch
# User estrain
# Date 1773403014 0
# Node ID bca71d3aa1bfc43efb49af7c6cf15cf572024385
# Parent  353347ef23868eff339ca8e920af0a6cd308c69c
planemo upload commit 21086bad5baa43e0d616b6942ded72a70840495d

diff -r 353347ef2386 -r bca71d3aa1bf gtdbtk_classify_wf.xml
--- a/gtdbtk_classify_wf.xml	Thu Mar 12 20:16:30 2026 +0000
+++ b/gtdbtk_classify_wf.xml	Fri Mar 13 11:56:54 2026 +0000
@@ -2,7 +2,6 @@
     <description>by placement in GTDB reference tree</description>
         <requirements>
             <requirement type="package" version="2.5.2">gtdbtk</requirement>
-            
         </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #import re
diff -r 353347ef2386 -r bca71d3aa1bf test-data/gtdbtk_database_versioned.loc.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtdbtk_database_versioned.loc.test	Fri Mar 13 11:56:54 2026 +0000
@@ -0,0 +1,26 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use a directory of GTDB-Tk databases.  The gtdbtk_databases.loc
+# file has this format (longer white space characters are TAB characters):
+#
+# <unique_build_id> <display_name>   <version> <directory_path>
+#
+# So, for example, if you have the gtdbtk 202 stored in 
+# /depot/data2/galaxy/gtdbtk/202/, 
+# then the gtdbtk_databases.loc entry would look like this:
+#
+# release202    gtdbtk database release 202 /depot/data2/galaxy/gtdbtk/release202
+#
+# and your /depot/data2/galaxy/gtdbtk/release202 directory
+# would contain GTDB-Tk database files for release 202, sommething like this:
+#
+#drwxr-sr-x  3 gvk G-824019    4096 Apr 20  2021 fastani/
+#-rw-r--r--  1 gvk G-824019 4810764 Apr 22  2021 manifest.tsv
+#drwxr-sr-x  4 gvk G-824019    4096 Apr 21  2021 markers/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 masks/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 metadata/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 21  2021 mrca_red/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 msa/
+#drwxr-sr-x  4 gvk G-824019    4096 Apr 21  2021 pplacer/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 radii/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 taxonomy/
+gtdbtk214	GTDB-Tk database	214	${__HERE__}/gtdbtk214/
diff -r 353347ef2386 -r bca71d3aa1bf tool-data/gtdbtk_database_versioned.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gtdbtk_database_versioned.loc.sample	Fri Mar 13 11:56:54 2026 +0000
@@ -0,0 +1,25 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use a directory of GTDB-Tk databases.  The gtdbtk_databases.loc
+# file has this format (longer white space characters are TAB characters):
+#
+# <unique_build_id> <display_name>  <directory_path>
+#
+# So, for example, if you have the gtdbtk 202 stored in 
+# /depot/data2/galaxy/gtdbtk/202/, 
+# then the gtdbtk_databases.loc entry would look like this:
+#
+# release202    gtdbtk database release 202 /depot/data2/galaxy/gtdbtk/release202
+#
+# and your /depot/data2/galaxy/gtdbtk/release202 directory
+# would contain GTDB-Tk database files for release 202, sommething like this:
+#
+#drwxr-sr-x  3 gvk G-824019    4096 Apr 20  2021 fastani/
+#-rw-r--r--  1 gvk G-824019 4810764 Apr 22  2021 manifest.tsv
+#drwxr-sr-x  4 gvk G-824019    4096 Apr 21  2021 markers/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 masks/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 metadata/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 21  2021 mrca_red/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 msa/
+#drwxr-sr-x  4 gvk G-824019    4096 Apr 21  2021 pplacer/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 radii/
+#drwxr-sr-x  2 gvk G-824019    4096 Apr 20  2021 taxonomy/
diff -r 353347ef2386 -r bca71d3aa1bf tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Mar 13 11:56:54 2026 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of GTDB-Tk database versions 202 and higher -->
+    <table name="gtdbtk_database_versioned" comment_char="#">
+        <columns>value, name, version, path</columns>
+        <file path="test-data/gtdbtk_database_versioned.loc" />
+    </table>
+</tables>
\ No newline at end of file