# HG changeset patch
# User jjohnson
# Date 1573067205 18000
# Node ID ea9772670fb5a1113af65c25def32490d062928a
# Parent  9d94fe7ce8b919d2ae6c1874347e0958f67e629a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit ab8f3af4dd052475db01f8120df0f9da6e8fff29

diff -r 9d94fe7ce8b9 -r ea9772670fb5 data_manager/data_manager_eggnog.py
--- a/data_manager/data_manager_eggnog.py	Tue Nov 05 15:53:42 2019 -0500
+++ b/data_manager/data_manager_eggnog.py	Wed Nov 06 14:06:45 2019 -0500
@@ -44,7 +44,7 @@
     dm_dict['data_tables'][data_table]\
         = dm_dict['data_tables'].get(data_table, [])
     data_table_entry = dict(value=db_version, name=db_version,
-                            path=eggnog_db_path)
+                            path=args.install_path)
     dm_dict['data_tables'][data_table].append(data_table_entry)
     data_table = 'eggnog_mapper_hmm_dbs'
     dm_dict['data_tables'][data_table]\
diff -r 9d94fe7ce8b9 -r ea9772670fb5 data_manager/data_manager_eggnog.xml
--- a/data_manager/data_manager_eggnog.xml	Tue Nov 05 15:53:42 2019 -0500
+++ b/data_manager/data_manager_eggnog.xml	Wed Nov 06 14:06:45 2019 -0500
@@ -16,14 +16,19 @@
 #else
 #set $eggnogdbs = 'none'
 #end if
-#if $test == 'false'
+#if $test == 'true'
+#import os.path
+#set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally')
+echo $install_path >> /Users/jj/gxt/gxt/eggnog_install_path &&
+#end if
 mkdir -p '${install_path}' &&
 download_eggnog_data.py 
-  $diamond_database -y -q --data_dir $install_path $eggnogdbs
-' '.join(dbs.split(',')) &&
-#else
-#set $install_path = '/Users/jj/gx/gh/jj/tools-galaxyp/tools/eggnog_mapper/test-data/cached_locally'
+  $diamond_database -y -q 
+#if $test == 'true'
+  -s
 #end if
+  --data_dir '$install_path' 
+  $eggnogdbs &&
 python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs'
     ]]></command>
     <inputs>
@@ -150,6 +155,7 @@
         <test>
             <param name="test" value="true"/>
             <param name="diamond_database" value="false"/>
+            <param name="dbs" value="thaNOG"/>
             <output name="out_file">
                 <assert_contents>
                     <has_text text="eggnog_mapper_db" />