Merge pull request #6337 from paulzierep/update-gtdb-tk

Update gtdb-tk
galaxyproject · Sep 25, 2024 · 0f5d58e · 0f5d58e
2 parents d2d7bf4 + 2f8cb60
commit 0f5d58e
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 5 deletions.
diff --git a/tools/gtdbtk/gtdbtk_classify_wf.xml b/tools/gtdbtk/gtdbtk_classify_wf.xml
@@ -37,9 +37,9 @@ $advanced.force
     ]]></command>
     <inputs>
         <param name="input" type="data" format="fasta,fasta.gz" multiple="true" label="Fasta (Genome) files"/>
-        <param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk required GTDB version R207_v2. Please contact your service administrator if this version is not available to select.">
+        <param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk requires GTDB version 207 or 214. Please contact your service administrator if this version is not available to select.">
             <options from_data_table="gtdbtk_database_versioned">
-                <filter type="regexp" column="3" value="^2(07|14)$"/>
+                <filter type="regexp" column="version" value="^2(07|14)$"/>
                 <validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
             </options>
         </param>

diff --git a/tools/gtdbtk/macros.xml b/tools/gtdbtk/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.3.2</token>
-    <token name="@VERSION_SUFFIX@">4</token>
+    <token name="@VERSION_SUFFIX@">5</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
         <requirements>

diff --git a/...k/test-data/gtdbtk_database_versioned.loc → ...t-data/gtdbtk_database_versioned.loc.test b/...k/test-data/gtdbtk_database_versioned.loc → ...t-data/gtdbtk_database_versioned.loc.test
@@ -23,4 +23,4 @@
 #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 v214	${__HERE__}/gtdbtk214/
+gtdbtk214	GTDB-Tk database	214	${__HERE__}/gtdbtk214/
diff --git a/tools/gtdbtk/tool_data_table_conf.xml.test b/tools/gtdbtk/tool_data_table_conf.xml.test
@@ -1,7 +1,8 @@
+<?xml version="1.0"?>
 <tables>
     <!-- Locations of GTDB-Tk database versions 202 and higher -->
     <table name="gtdbtk_database_versioned" comment_char="#">
         <columns>value, name, version, path</columns>
-        <file path="tool-data/gtdbtk_database_versioned.loc" />
+        <file path="${__HERE__}/test-data/gtdbtk_database_versioned.loc.test" />
     </table>
 </tables>