Update funannotate

data_managers/data_manager_funannotate/.shed.yml

@@ -6,5 +6,6 @@ long_description: |
   annotation tool and updates the funannotate data table.
 name: data_manager_funannotate
 owner: iuc
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate
+homepage_url: https://github.com/galaxyproject/tools-iuc/
 type: unrestricted

data_managers/data_manager_funannotate/data_manager/funannotate.xml

@@ -1,23 +1,47 @@
-<tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.3" tool_type="manage_data" profile="20.01">
+<tool id="data_manager_funannotate" name="Funannotate data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
+    <macros>
+        <token name="@TOOL_VERSION@">1.8.15</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="1.8.9">funannotate</requirement>
-        <requirement type="package" version="2.26.0">requests</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
     </requirements>
     <version_command>funannotate check --show-versions</version_command>
     <command detect_errors="exit_code"><![CDATA[
-#if $wget:
-    ## Asked for wget, we assume there's a certificate problem on (at least) one
-    ## of the many requested servers, force disable of all checks
-    echo "check_certificate = off" > \$HOME/.wgetrc &&
-#end if
+        #if $wget:
+            ## Asked for wget, we assume there's a certificate problem on (at least) one
+            ## of the many requested servers, force disable of all checks
+            echo "check_certificate = off" > \$HOME/.wgetrc &&
+        #end if
 
-python -u '$__tool_directory__/funannotate.py'
-$partial_data
-$wget
-\$(date +'%Y-%m-%d-%H%M%S')
-'funannotate'
-'${output_file}'
+        funannotate setup
+            -d '$output_file.extra_files_path'
+        #if $partial_data
+            -i merops -b eukaryota
+        #else
+            -b all
+        #end if
+            $wget
+        &&
+        cp '$dmjson' '$output_file'
     ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+#from datetime import datetime
+#set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S")
+    {
+      "data_tables":{
+        "funannotate":[
+          {
+            "value":"$version_id",
+            "description":"Funannotate database $version_id",
+            "format_version":"1.0",
+            "path":"$output_file.extra_files_path"
+          }
+        ]
+      }
+    }]]></configfile>
+    </configfiles>
     <inputs>
         <param name="partial_data" type="hidden" value="" help="Used for testing"/>
         <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
@@ -31,7 +55,7 @@ $wget
             <output name="output_file">
                 <assert_contents>
                     <has_text text="Funannotate database "/>
-                    <has_text text='"format_version": "1.0"'/>
+                    <has_text text='"format_version":"1.0"'/>
                 </assert_contents>
             </output>
         </test>
@@ -41,7 +65,7 @@ $wget
             <output name="output_file">
                 <assert_contents>
                     <has_text text="Funannotate database "/>
-                    <has_text text='"format_version": "1.0"'/>
+                    <has_text text='"format_version":"1.0"'/>
                 </assert_contents>
             </output>
         </test>

data_managers/data_manager_funannotate/test-data/funannotate.loc

@@ -7,3 +7,10 @@
 # for example
 # 2021-07-20-120000	Funannotate database 2021-07-20-120000	1.0	/tmp/database/funannotate/2021-07-20-120000
 # 2021-05-27-120000	Funannotate database 2021-05-27-120000	3.0	/tmp/database/funannotate/2021-05-27-120000
+2025-02-17-000000	Funannotate database 2025-02-17-000000		/tmp/tmpm1ezjinx/galaxy-dev/tool-data/funannotate/2025-02-17-000000
+2025-02-17-210445	Funannotate database 2025-02-17-210445		/tmp/tmpg0tuguj6/galaxy-dev/tool-data/funannotate/2025-02-17-210445
+2025-02-17-210504	Funannotate database 2025-02-17-210504		/tmp/tmpg0tuguj6/galaxy-dev/tool-data/funannotate/2025-02-17-210504
+2025-02-17-210714	Funannotate database 2025-02-17-210714	1.0	/tmp/tmpdtjxf3c7/galaxy-dev/tool-data/funannotate/2025-02-17-210714
+2025-02-17-210732	Funannotate database 2025-02-17-210732	1.0	/tmp/tmpdtjxf3c7/galaxy-dev/tool-data/funannotate/2025-02-17-210732
+2025-02-17-211010	Funannotate database 2025-02-17-211010	1.0	/tmp/tmp07fm9fgh/galaxy-dev/tool-data/funannotate/2025-02-17-211010
+2025-02-17-211028	Funannotate database 2025-02-17-211028	1.0	/tmp/tmp07fm9fgh/galaxy-dev/tool-data/funannotate/2025-02-17-211028

data_managers/data_manager_funannotate_options/.shed.yml

@@ -0,0 +1,11 @@
+categories:
+- Data Managers
+description: Install funannotate databases for funannotate tool
+long_description: |
+  This data managers fetches data from various databases for the funannotate
+  annotation tool and updates the funannotate data table.
+name: data_manager_funannotate
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate
+homepage_url: https://github.com/galaxyproject/tools-iuc/
+type: unrestricted