diff data_manager/data_manager_eggnog.xml @ 3:9d94fe7ce8b9 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit e711920c41c8862d7d8133f7b455cf475924e103

--- 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>