diff data_manager/data_manager_metaphlan_download.xml @ 6:d8dc037e3c13 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 3c1a0c4a94f78437c6df74b5348826e33e734a05

--- a/data_manager/data_manager_metaphlan_download.xml	Fri Jun 14 21:14:55 2024 +0000
+++ b/data_manager/data_manager_metaphlan_download.xml	Mon Jul 29 07:13:31 2024 +0000
@@ -12,10 +12,32 @@
         <exit_code range="1:" level="fatal" description="Error"/>
     </stdio>
     <command><![CDATA[
-python '$__tool_directory__/data_manager_metaphlan_download.py'
-    --index '$index'
-    --json '$out_file'
+        metaphlan --install --index '$index' --bowtie2db '$out_file.extra_files_path/$index' &&
+        cp '$dmjson' '$out_file'
     ]]></command>
+     <configfiles>
+        <configfile name="dmjson"><![CDATA[
+#from datetime import date
+{
+  "data_tables":{
+    "genomad":[
+      {
+        "dbkey": "$index",
+        "value": "${index}-#echo date.today().strftime('%d%m%Y')#",
+        "name": "MetaPhlAn clade-specific marker genes ($index)",
+        "path": "$out_file.extra_files_path/$index",
+        "db_version": #slurp
+#if "SGB" in str($index)
+"SGB"#slurp
+#else
+"legacy"#slurp
+#end if
+      }
+    ]
+  }
+}]]>
+        </configfile>
+    </configfiles>
     <inputs>
         <param name="index" type="select" label="Version">
             <option value="mpa_vOct22_CHOCOPhlAnSGB_202403" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202403</option>
@@ -34,8 +56,11 @@
             <param name="index" value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/>
             <output name="out_file">
                 <assert_contents>
-                    <has_text text="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/>
-                    <has_text text="MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"/>
+                    <has_text text='"db_version": "SGB"'/>
+                    <has_text text='"dbkey": "mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"'/>
+                    <has_text_matching expression='"value": "mpa_vJan21_TOY_CHOCOPhlAnSGB_202103-[0-9]{8}"'/>
+                    <has_text text='"name": "MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"'/>
+                    <has_text_matching expression='.*"path": ".*/mpa_vJan21_TOY_CHOCOPhlAnSGB_202103".*'/>
                 </assert_contents>
             </output>
         </test>