# HG changeset patch
# User iuc
# Date 1731942598 0
# Node ID 0c255951902a4bfe43eb460ea38e01aecf16df4f
# Parent  641ac96ab63a67ae23371073c7979ba45d1ac317
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_groot_database_downloader commit 15ce75a21f8a3b314b0a8a420fc5b4fffe846171

diff -r 641ac96ab63a -r 0c255951902a data_manager/data_manager_groot_database_downloader.xml
--- a/data_manager/data_manager_groot_database_downloader.xml	Thu Oct 17 14:20:17 2024 +0000
+++ b/data_manager/data_manager_groot_database_downloader.xml	Mon Nov 18 15:09:58 2024 +0000
@@ -2,7 +2,7 @@
     <description> Download pre-clustered ARG database that are ready to be indexed</description>
     <macros>
         <token name="@TOOL_VERSION@">1.1.2</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@PROFILE@">22.05</token>
     </macros>
     <requirements>
@@ -12,7 +12,9 @@
     </requirements>
     <command><![CDATA[
         if [ -f '/usr/local/ssl/cacert.pem' ] ; then export SSL_CERT_FILE='/usr/local/ssl/cacert.pem' ; fi &&
+        mkdir -p '$out_file.extra_files_path' &&
         groot get -d '$database' --identity '$identity' &&
+        mv ${database}.${identity} '$out_file.extra_files_path' &&
         cp '$dmjson' '$out_file'
     ]]></command>
     <configfiles>
@@ -24,7 +26,7 @@
       {
         "value": "$database.$identity-@TOOL_VERSION@-#echo date.today().strftime('%d%m%Y')#",
         "name": "$database ($identity percent identity)",
-        "path": "/$database.$identity",
+        "path": "$database.$identity",
         "version": "@TOOL_VERSION@"
       }
     ]
@@ -57,7 +59,7 @@
                     <has_text text='"version": "1.1.2"'/>
                     <has_text_matching expression='"value": "arg-annot.90-1.1.2-[0-9]{8}"'/>
                     <has_text text='"name": "arg-annot (90 percent identity)"'/>
-                    <has_text text='"path": "/arg-annot.90"'/>
+                    <has_text text='"path": "arg-annot.90"'/>
                 </assert_contents>
             </output>
         </test>
diff -r 641ac96ab63a -r 0c255951902a data_manager_conf.xml
--- a/data_manager_conf.xml	Thu Oct 17 14:20:17 2024 +0000
+++ b/data_manager_conf.xml	Mon Nov 18 15:09:58 2024 +0000
@@ -8,9 +8,9 @@
                 <column name="path" output_ref="out_file">
                     <move type="directory">
                         <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">groot_database/data/${value}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">groot_database/${path}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/groot_database/data/${value}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/groot_database/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
                 <column name="version"/> <!-- columns that are going to be specified by the Data Manager Tool -->
diff -r 641ac96ab63a -r 0c255951902a test-data/groot_database.loc
--- a/test-data/groot_database.loc	Thu Oct 17 14:20:17 2024 +0000
+++ b/test-data/groot_database.loc	Mon Nov 18 15:09:58 2024 +0000
@@ -1,2 +1,1 @@
-arg-annot.90-16102024	arg-annot (90 percent identity)	/tmp/tmpjmmj2x3o/galaxy-dev/tool-data/groot_database/data/arg-annot.90-16102024	1.1.2
-arg-annot.90-1.1.2-16102024	arg-annot (90 percent identity)	/tmp/tmpqdkgcsoq/galaxy-dev/tool-data/groot_database/data/arg-annot.90-1.1.2-16102024	1.1.2
+arg-annot.90-1.1.2-18112024	arg-annot (90 percent identity)	/tmp/tmprimr087u/galaxy-dev/tool-data/groot_database/arg-annot.90	1.1.2