Mercurial > repos > iuc > checkm2_build_database

changeset 2:757826aa89c3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_checkm2 commit 043f6bb449b27287b413a937b21d918569cfdad7
author iuc
date Sun, 19 Jan 2025 18:47:59 +0000
parents ef5a5463bc3b
children 6fd780865107
files data_manager/checkm2_datamanager.xml data_manager_conf.xml test-data/checkm2.loc tool-data/checkm2.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 6 files changed, 7 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/checkm2_datamanager.xml	Tue Jan 14 21:33:10 2025 +0000
+++ b/data_manager/checkm2_datamanager.xml	Sun Jan 19 18:47:59 2025 +0000
@@ -27,6 +27,7 @@
     "checkm2":[
       {
         "path":"uniref100.KO.1.dmnd",
+        "dbkey":"@TOOL_VERSION@",
         "name":"CheckM2 diamond DB downloaded with version @TOOL_VERSION@",
         "version":"@TOOL_VERSION@",
         "value":"@TOOL_VERSION@"
--- a/data_manager_conf.xml	Tue Jan 14 21:33:10 2025 +0000
+++ b/data_manager_conf.xml	Sun Jan 19 18:47:59 2025 +0000
@@ -3,6 +3,7 @@
         <data_table name="checkm2">
             <output>
                 <column name="value"/>
+                <column name="dbkey"/>
                 <column name="name"/>
                 <column name="version"/>
                 <column name="path" output_ref="out_file">
--- a/test-data/checkm2.loc	Tue Jan 14 21:33:10 2025 +0000
+++ b/test-data/checkm2.loc	Sun Jan 19 18:47:59 2025 +0000
@@ -1,2 +1,2 @@
 
-1.0.2	CheckM2 diamond DB downloaded with version 1.0.2	1.0.2	/tmp/tmpf_hplx2a/galaxy-dev/tool-data/checkm2/1.0.2/uniref100.KO.1.dmnd
+1.0.2   1.0.2	CheckM2 diamond DB downloaded with version 1.0.2	1.0.2	/tmp/tmpf_hplx2a/galaxy-dev/tool-data/checkm2/1.0.2/uniref100.KO.1.dmnd
--- a/tool-data/checkm2.loc.sample	Tue Jan 14 21:33:10 2025 +0000
+++ b/tool-data/checkm2.loc.sample	Sun Jan 19 18:47:59 2025 +0000
@@ -10,9 +10,9 @@
 #The checkm2_db_versioned.loc file has this format (longer white space
 #characters are TAB characters):
 #
-#<unique_build_id>	<display_name>	<version>	<file_base_path>
+#<unique_build_id>  <dbkey>  <display_name>	<version>	<file_base_path>
 
 #The <version> column indicates the checkm2 version that generated the database
 
 #
-#diamond_db_1.0.2	Diamond database	1.0.2	/mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd
+#diamond_db_1.0.2   1.0.2	Diamond database	1.0.2	/mnt/galaxyIndices/Checkm2_database/uniref100.KO.1.dmnd
--- a/tool_data_table_conf.xml.sample	Tue Jan 14 21:33:10 2025 +0000
+++ b/tool_data_table_conf.xml.sample	Sun Jan 19 18:47:59 2025 +0000
@@ -1,6 +1,6 @@
 <tables>
     <table name="checkm2" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, version, path</columns>
+        <columns>value, dbkey, name, version, path</columns>
         <file path="tool-data/checkm2.loc" />
     </table>
 </tables>
\ No newline at end of file
--- a/tool_data_table_conf.xml.test	Tue Jan 14 21:33:10 2025 +0000
+++ b/tool_data_table_conf.xml.test	Sun Jan 19 18:47:59 2025 +0000
@@ -1,7 +1,7 @@
 <tables>
     <!-- Location of rnastar indexes for testing -->
     <table name="checkm2" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, version, path</columns>
+        <columns>value, dbkey, name, version, path</columns>
         <file path="${__HERE__}/test-data/checkm2.loc" />
     </table>
 </tables>
\ No newline at end of file