data table tweaks

remove dbkey column rename tables
galaxyproject · Nov 15, 2024 · 1942fb2 · 1942fb2
1 parent 857f362
commit 1942fb2
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Showing 6 changed files with 14 additions and 15 deletions.
diff --git a/tools/checkm2/checkm2.xml b/tools/checkm2/checkm2.xml
@@ -1,9 +1,9 @@
-<tool id="checkm2" name="checkm2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="checkm2" name="checkm2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
     <description>Rapid assessment of genome bin quality using machine learning</description>
     <macros>
         <token name="@TOOL_VERSION@">1.0.2</token>
-        <token name="@VERSION_SUFFIX@">1</token>
-        <token name="@IDX_DATA_TABLE@">checkm2_db_versioned</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@IDX_DATA_TABLE@">checkm2</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">checkm2</xref>

diff --git a/tools/checkm2/test-data/checkm2.loc b/tools/checkm2/test-data/checkm2.loc
@@ -0,0 +1,3 @@
+##Checkm2 versioned indexes
+#build_id	display_name	path	version
+001	test_db	${__HERE__}/Checkm2_database/uniref100.KO.1.dmnd	1.0.2
diff --git a/tools/checkm2/test-data/checkm2_db_versioned.loc b/tools/checkm2/test-data/checkm2_db_versioned.loc
diff --git a/...tool-data/checkm2_db_versioned.loc.sample → tools/checkm2/tool-data/checkm2.loc.sample b/...tool-data/checkm2_db_versioned.loc.sample → tools/checkm2/tool-data/checkm2.loc.sample
@@ -10,9 +10,9 @@
 #The checkm2_db_versioned.loc file has this format (longer white space
 #characters are TAB characters):
 #
-#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>	<version>
+#<unique_build_id>	<display_name>	<file_base_path>	<version>
 
 #The <version> column indicates the checkm2 version that generated the database
 
 #
-#diamond_db_1.0.2   diamond_db    Diamond databas   /mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd 1.0.2
+#diamond_db_1.0.2	Diamond database	/mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd	1.0.2
diff --git a/tools/checkm2/tool_data_table_conf.xml.sample b/tools/checkm2/tool_data_table_conf.xml.sample
@@ -1,6 +1,6 @@
 <tables>
-    <table name="checkm2_db_versioned" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path, version</columns>
-        <file path="tool-data/checkm2_db_versioned.loc" />
+    <table name="checkm2" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, path, version</columns>
+        <file path="tool-data/checkm2.loc" />
     </table>
 </tables>
diff --git a/tools/checkm2/tool_data_table_conf.xml.test b/tools/checkm2/tool_data_table_conf.xml.test
@@ -1,7 +1,6 @@
 <tables>
-    <!-- Location of rnastar indexes for testing -->
-    <table name="checkm2_db_versioned" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, name, path, version</columns>
-        <file path="${__HERE__}/test-data/checkm2_db_versioned.loc" />
+    <table name="checkm2" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, path, version</columns>
+        <file path="${__HERE__}/test-data/checkm2.loc" />
     </table>
 </tables>