# HG changeset patch
# User jjohnson
# Date 1572987222 18000
# Node ID 9d94fe7ce8b919d2ae6c1874347e0958f67e629a
# Parent  a74d61dbd15578b4f13b31ebad1a8d775eb12829
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit e711920c41c8862d7d8133f7b455cf475924e103

diff -r a74d61dbd155 -r 9d94fe7ce8b9 data_manager/data_manager_eggnog.py
--- a/data_manager/data_manager_eggnog.py	Mon Nov 04 16:38:44 2019 -0500
+++ b/data_manager/data_manager_eggnog.py	Tue Nov 05 15:53:42 2019 -0500
@@ -6,8 +6,9 @@
 import json
 import os.path
 import sqlite3
+import sys
 from sqlite3 import OperationalError
-import sys
+
 
 def _get_db_version(sqlitedb_path):
     version = '4.5'
@@ -18,40 +19,47 @@
         cur.execute(query)
         version = cur.fetchone()[0]
     except OperationalError as e:
-        print('Assuming eggnog version %s because %s   %s' % (version, sqlitedb_path, e), file=sys.stderr)
+        print('Assuming eggnog version %s because %s   %s' %
+              (version, sqlitedb_path, e), file=sys.stderr)
     return version
 
+
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument( '--config_file' )
-    parser.add_argument( '--install_path' )
-    parser.add_argument( '--dbs', default='')
+    parser.add_argument('--config_file')
+    parser.add_argument('--install_path')
+    parser.add_argument('--dbs', default='')
     args = parser.parse_args()
 
-    eggnog_db_path = os.path.join(args.install_path,'eggnog.db') 
+    eggnog_db_path = os.path.join(args.install_path, 'eggnog.db')
     if not os.path.exists(eggnog_db_path):
         print('Can not open: %s' % eggnog_db_path, file=sys.stderr)
         exit(1)
     db_version = _get_db_version(eggnog_db_path)
 
-    params = json.loads( open( args.config_file ).read() )
-    data_manager_dict = {}
-    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    # params = json.loads(open(args.config_file).read())
+    dm_dict = {}
+    dm_dict['data_tables'] = dm_dict.get('data_tables', {})
     data_table = 'eggnog_mapper_db'
-    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
-    data_table_entry = dict(value=db_version, name=db_version, path=eggnog_db_path)
-    data_manager_dict['data_tables'][data_table].append( data_table_entry )
+    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)
+    dm_dict['data_tables'][data_table].append(data_table_entry)
     data_table = 'eggnog_mapper_hmm_dbs'
-    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
+    dm_dict['data_tables'][data_table]\
+        = dm_dict['data_tables'].get(data_table, [])
     if args.dbs:
         dbs = [x.strip() for x in args.dbs.split(',')]
         for db in dbs:
             key = '%s_%s' % (db_version, db)
-            data_table_entry = dict(key=key, db_version=db_version, value=db, name=db, path=db)
-            data_manager_dict['data_tables'][data_table].append( data_table_entry )
+            data_table_entry = dict(key=key, db_version=db_version,
+                                    value=db, name=db, path=db)
+            dm_dict['data_tables'][data_table].append(data_table_entry)
 
     # save info to json file
-    open( args.config_file, 'wb' ).write( json.dumps( data_manager_dict ) )
+    open(args.config_file, 'wb').write(json.dumps(dm_dict))
+
 
 if __name__ == "__main__":
     main()
diff -r a74d61dbd155 -r 9d94fe7ce8b9 data_manager/data_manager_eggnog.xml
--- a/data_manager/data_manager_eggnog.xml	Mon Nov 04 16:38:44 2019 -0500
+++ b/data_manager/data_manager_eggnog.xml	Tue Nov 05 15:53:42 2019 -0500
@@ -1,7 +1,7 @@
-<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@" tool_type="manage_data">
+<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@.0" tool_type="manage_data">
     <description>Download a new database</description>
     <macros>
-        <token name="@VERSION@">4.5.1</token>
+        <token name="@VERSION@">1.0.3</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">eggnog-mapper</requirement>
@@ -12,17 +12,19 @@
 #set params = json.loads(open(str($out_file)).read())
 #set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
 #if $dbs:
-#set $eggnogdbs = ' '.join($dbs.split(','))
+#set $eggnogdbs = ' '.join(str($dbs).split(','))
 #else
 #set $eggnogdbs = 'none'
-#endif
+#end if
 #if $test == 'false'
-mkdir -p '${target_directory}' &&
+mkdir -p '${install_path}' &&
 download_eggnog_data.py 
   $diamond_database -y -q --data_dir $install_path $eggnogdbs
 ' '.join(dbs.split(',')) &&
+#else
+#set $install_path = '/Users/jj/gx/gh/jj/tools-galaxyp/tools/eggnog_mapper/test-data/cached_locally'
 #end if
-python '${__tool_directory__}/data_manager_eggnog.py --config_file $out_file --install_path $target_directory --dbs '$dbs'
+python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs'
     ]]></command>
     <inputs>
         <param name="test" type="hidden" value="false" />
@@ -158,6 +160,9 @@
     <help><![CDATA[
 This tool downloads eggnog data using download_eggnog_data.py 
 and populates the data tables: eggnog_mapper_db and eggnog_mapper_hmm_dbs.
+The data is located at: http://eggnogdb.embl.de/download/emapperdb-4.5.1/
+The optional eggNOG HMM databases: http://eggnogdb.embl.de/download/emapperdb-4.5.1/hmmdb_levels/ 
+can vary from 1G to 80G in size.
     ]]></help>
     <citations>
         <citation type="doi">10.1093/nar/gkv1248</citation>
diff -r a74d61dbd155 -r 9d94fe7ce8b9 data_manager_conf.xml
--- a/data_manager_conf.xml	Mon Nov 04 16:38:44 2019 -0500
+++ b/data_manager_conf.xml	Tue Nov 05 15:53:42 2019 -0500
@@ -7,9 +7,9 @@
         <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
         <column name="path" output_ref="out_file" >
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}</target>
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">eggnog_data/${value}</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/eggnog_data/${value}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>