# HG changeset patch
# User galaxyp
# Date 1643118578 0
# Node ID 3d12bbd5c0bac3d571cff9a495b31112eea81e8f
# Parent  46d2e3ed9530c9a00aeea8a60136e50e404d00bf
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"

diff -r 46d2e3ed9530 -r 3d12bbd5c0ba data_manager/data_manager_eggnog.py
--- a/data_manager/data_manager_eggnog.py	Fri Feb 19 18:52:23 2021 +0000
+++ b/data_manager/data_manager_eggnog.py	Tue Jan 25 13:49:38 2022 +0000
@@ -42,13 +42,21 @@
     data_table = 'eggnog_mapper_db_versioned'
     dm_dict['data_tables'][data_table]\
         = dm_dict['data_tables'].get(data_table, [])
-    # Versionning is super confusing:
+    # DB versionning was super confusing for eggnog-mapper 2.0.x:
     # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
-    # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0)
-    # db v4.5 are not compatible with eggnog-mapper 2.0
+    # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0)
+    # (db v4.5 are not compatible with eggnog-mapper 2.0)
+    # Starting with eggnog-mapper 2.1.* db versioning looks better: 2.1.0 requires db v5.0.2
     version = "2.0"
     if "4.5" in db_version:
+        # special case: eggnog-mapper 1.x
         version = "1.0"
+    elif db_version.startswith('2.'):
+        # special case: eggnog-mapper 2.0.x
+        version = "2.0"
+    else:
+        # normal case or eggno-mapper >= 2.1
+        version = db_version
     data_table_entry = dict(value=db_version, name=db_version,
                             path=args.install_path, version=version)
     dm_dict['data_tables'][data_table].append(data_table_entry)
diff -r 46d2e3ed9530 -r 3d12bbd5c0ba data_manager/data_manager_eggnog.xml
--- a/data_manager/data_manager_eggnog.xml	Fri Feb 19 18:52:23 2021 +0000
+++ b/data_manager/data_manager_eggnog.xml	Tue Jan 25 13:49:38 2022 +0000
@@ -25,7 +25,7 @@
     <help><![CDATA[
 This tool downloads eggnog data using download_eggnog_data.py
 and populates the data tables: eggnog_mapper_db_versioned.
-The data is located at: http://eggnog5.embl.de/download/emapperdb-5.0.0/
+The data is located at: http://eggnog5.embl.de/download/emapperdb-5.0.2/
 can vary from 1G to 80G in size.
 
 The data will be downloaded to the specified directory.
diff -r 46d2e3ed9530 -r 3d12bbd5c0ba data_manager/eggnog_macros.xml
--- a/data_manager/eggnog_macros.xml	Fri Feb 19 18:52:23 2021 +0000
+++ b/data_manager/eggnog_macros.xml	Tue Jan 25 13:49:38 2022 +0000
@@ -1,14 +1,15 @@
 <?xml version="1.0"?>
 <macros>
-   <token name="@VERSION@">2.0.1</token>
-   <token name="@EGGNOG_DB_VERSION@">2.0</token>
+   <token name="@VERSION@">2.1.6</token>
+   <token name="@EGGNOG_DB_VERSION@">5.0.2</token>
     <!--
-    # Versionning is super confusing:
+    # DB versionning was super confusing for eggnog-mapper 2.0.x:
     # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
-    # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0)
-    # db v4.5 are not compatible with eggnog-mapper 2.0
+    # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0)
+    # (db v4.5 are not compatible with eggnog-mapper 2.0)
+    # Starting with eggnog-mapper 2.1.* db versioning looks better: 2.1.0 requires db v5.0.2
     -->
-   <token name="@IDX_VERSION@">2.0</token>
+   <token name="@IDX_VERSION@">5.0.2</token>
    <xml name="citations">
         <citations>
             <citation type="doi">10.1093/nar/gkv1248</citation>
@@ -26,6 +27,8 @@
     <xml name="data_manager_params">
         <param name="test" type="hidden" value="false" />
         <param name="diamond_database" type="boolean" truevalue="" falsevalue="-D" checked="true" label="Install the diamond database" help="Takes ~9Gb, you most probably want it."/>
+        <param name="mmseqs_database" type="boolean" truevalue="-M" falsevalue="" checked="true" label="Install the MMseqs2 database" help="Required for mmseqs seed ortholog search mode. Takes ~11Gb, you most probably want it."/>
+        <param name="pfam_database" type="boolean" truevalue="-P" falsevalue="" checked="true" label="Install the Pfam database" help="Rquired for de novo annotation or realignment. Takes ~3Gb, you most probably want it."/>
     </xml>
     <xml name="data_manager_outputs">
         <outputs>
@@ -40,7 +43,7 @@
 #end if
 mkdir -p '${install_path}' &&
 download_eggnog_data.py
-  $diamond_database -y -q
+  $diamond_database $mmseqs_database $pfam_database -y -q
 #if $test == 'true'
   -s
 #end if
diff -r 46d2e3ed9530 -r 3d12bbd5c0ba test-data/cached_locally/eggnog.db
Binary file test-data/cached_locally/eggnog.db has changed
diff -r 46d2e3ed9530 -r 3d12bbd5c0ba test-data/cached_locally/eggnog.taxa.db
Binary file test-data/cached_locally/eggnog.taxa.db has changed
diff -r 46d2e3ed9530 -r 3d12bbd5c0ba test-data/cached_locally/eggnog_mapper_db_versioned.loc
--- a/test-data/cached_locally/eggnog_mapper_db_versioned.loc	Fri Feb 19 18:52:23 2021 +0000
+++ b/test-data/cached_locally/eggnog_mapper_db_versioned.loc	Tue Jan 25 13:49:38 2022 +0000
@@ -1,2 +1,2 @@
 #value	name	path	version
-2.0	eggNOG_2.0	${__HERE__}	2.0
+5.0.2	eggNOG_5.0.2	${__HERE__}	5.0.2
diff -r 46d2e3ed9530 -r 3d12bbd5c0ba tool-data/eggnog_mapper_db_versioned.loc.sample
--- a/tool-data/eggnog_mapper_db_versioned.loc.sample	Fri Feb 19 18:52:23 2021 +0000
+++ b/tool-data/eggnog_mapper_db_versioned.loc.sample	Tue Jan 25 13:49:38 2022 +0000
@@ -3,9 +3,9 @@
 #
 # eggnog-mapper requires the following files to be installed in the data directory:
 #  https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz
-#  http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz
+#  http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.db.gz
 # A complete diamond database is available from:
-#  http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog_proteins.dmnd.gz
+#  http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz
 #
 # The python script download_eggnog_data.py,
 # included with eggnog_mapper, can be used to download the files to the correct directory